From 27359751ac013359e3f9ef359637f5889ce75752 Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 14:22:12 +0100 Subject: [PATCH 01/19] chore: ignore upload scripts --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index c48fa80..294b7c7 100644 --- a/.gitignore +++ b/.gitignore @@ -30,4 +30,6 @@ __pycache__/ Sandbox.ipynb test.ipynb -*.zarr \ No newline at end of file +*.zarr + +upload* \ No newline at end of file From 58565b8ac08158c2ec117bc973854ae31956c3da Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 15:10:16 +0100 Subject: [PATCH 02/19] feat: add wrapper to store cached artifacts --- .../integrations/lamindb_wrappers.py | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 src/spatialdata_db/integrations/lamindb_wrappers.py diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py new file mode 100644 index 0000000..7f1c1df --- /dev/null +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -0,0 +1,45 @@ +import warnings +import shutil +from pathlib import Path +from typing import Optional, Union +import lamindb as ln + +LAMIN_TRACK_WARNING = "! run input wasn't tracked, call `ln.track()` and re-run" + +def store_artifact(artifact: ln.Artifact, path: Union[str, Path] = Path("."), name: Optional[str] = None) -> str: + """ + Store a cached artifact in a specified directory, rename it if needed, and suppress lamin's warning if the notebook is not tracked. + + Parameters: + - artifact (lamindb.Artifact): The artifact object from lamindb. + - path (Union[str, Path]): Directory where the cached artifact should be stored (default: "."). + - name (Optional[str]): If provided, renames the cached artifact to this name (default: None). + + Returns: + - str: The absolute path to the stored artifact. + + Raises: + - FileNotFoundError: If the artifact cannot be found after caching. + - PermissionError: If moving the artifact fails due to insufficient permissions. + - RuntimeError: If caching fails for any reason. + """ + target_dir = Path(path).resolve() + target_dir.mkdir(parents=True, exist_ok=True) + + try: + warnings.filterwarnings("ignore", message=LAMIN_TRACK_WARNING) + cached_path = Path(artifact.cache()).resolve() + except Exception as e: + raise RuntimeError(f"Failed to cache artifact: {e}") + + final_path = target_dir / (name if name else cached_path.name) + + if cached_path != final_path: + try: + shutil.move(str(cached_path), str(final_path)) + except PermissionError as e: + raise PermissionError(f"Failed to move artifact due to insufficient permissions: {e}") from e + except OSError as e: + raise OSError(f"Failed to move artifact due to an OS error: {e}") from e + + return str(final_path) From 00d328aba9026ed9c9c0de11267f13fad2589626 Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 16:48:39 +0100 Subject: [PATCH 03/19] fix: catch filenotfound error --- src/spatialdata_db/integrations/lamindb_wrappers.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py index 7f1c1df..c16b3f1 100644 --- a/src/spatialdata_db/integrations/lamindb_wrappers.py +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -39,6 +39,8 @@ def store_artifact(artifact: ln.Artifact, path: Union[str, Path] = Path("."), na shutil.move(str(cached_path), str(final_path)) except PermissionError as e: raise PermissionError(f"Failed to move artifact due to insufficient permissions: {e}") from e + except FileNotFoundError as e: + raise FileNotFoundError(f"Failed to find cached artifact: {e}") from e except OSError as e: raise OSError(f"Failed to move artifact due to an OS error: {e}") from e From df3d22f900ded1d41bc6128aa13301160af67fda Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 17:05:27 +0100 Subject: [PATCH 04/19] fix: throw error when object already exists --- .../integrations/lamindb_wrappers.py | 30 ++++++++++++------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py index c16b3f1..03198ca 100644 --- a/src/spatialdata_db/integrations/lamindb_wrappers.py +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -1,39 +1,47 @@ -import warnings import shutil +import warnings from pathlib import Path -from typing import Optional, Union + import lamindb as ln LAMIN_TRACK_WARNING = "! run input wasn't tracked, call `ln.track()` and re-run" -def store_artifact(artifact: ln.Artifact, path: Union[str, Path] = Path("."), name: Optional[str] = None) -> str: + +def store_artifact( + artifact: ln.Artifact, path: str | Path = Path("."), name: str | None = None, overwrite: bool = False +) -> str: """ Store a cached artifact in a specified directory, rename it if needed, and suppress lamin's warning if the notebook is not tracked. - Parameters: + Parameters + ---------- - artifact (lamindb.Artifact): The artifact object from lamindb. - path (Union[str, Path]): Directory where the cached artifact should be stored (default: "."). - name (Optional[str]): If provided, renames the cached artifact to this name (default: None). + - overwrite (bool): If True, overwrites an existing file. Defaults to False. - Returns: + Returns + ------- - str: The absolute path to the stored artifact. - Raises: + Raises + ------ - FileNotFoundError: If the artifact cannot be found after caching. - PermissionError: If moving the artifact fails due to insufficient permissions. - RuntimeError: If caching fails for any reason. + - FileExistsError: If the target file already exists and overwrite=False. """ target_dir = Path(path).resolve() target_dir.mkdir(parents=True, exist_ok=True) - try: - warnings.filterwarnings("ignore", message=LAMIN_TRACK_WARNING) - cached_path = Path(artifact.cache()).resolve() - except Exception as e: - raise RuntimeError(f"Failed to cache artifact: {e}") + warnings.filterwarnings("ignore", message=LAMIN_TRACK_WARNING) + cached_path = Path(artifact.cache()).resolve() final_path = target_dir / (name if name else cached_path.name) + if final_path.exists() and not overwrite: + raise FileExistsError(f"Target file already exists: {final_path}. Use overwrite=True to replace it.") + if cached_path != final_path: try: shutil.move(str(cached_path), str(final_path)) From 4738bf17d599344af952ad3f9cbd34f72f2876dc Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 17:05:40 +0100 Subject: [PATCH 05/19] fix: import store_artifact --- src/spatialdata_db/integrations/__init__.py | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 src/spatialdata_db/integrations/__init__.py diff --git a/src/spatialdata_db/integrations/__init__.py b/src/spatialdata_db/integrations/__init__.py new file mode 100644 index 0000000..7f82c5e --- /dev/null +++ b/src/spatialdata_db/integrations/__init__.py @@ -0,0 +1,3 @@ +from .lamindb_wrappers import store_artifact + +__all__ = ["store_artifact"] From e20d1d31cf5e5f8f343d2422f5592fb9dff287a1 Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 17:05:59 +0100 Subject: [PATCH 06/19] test: function store_artifact --- tests/integrations/test_lamin_wrappers.py | 113 ++++++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 tests/integrations/test_lamin_wrappers.py diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py new file mode 100644 index 0000000..d9d84fa --- /dev/null +++ b/tests/integrations/test_lamin_wrappers.py @@ -0,0 +1,113 @@ +import os +import shutil +from pathlib import Path +from unittest.mock import MagicMock + +import lamindb as ln +import pytest + +from spatialdata_db.integrations import store_artifact + +DEFAULT_FILE_NAME = "test_data.zarr" + + +@pytest.fixture(scope="function") +def fake_artifact(tmp_path): + artifact = MagicMock(spec=ln.Artifact) # Mock with ln.Artifact attributes + zarr_path = tmp_path / DEFAULT_FILE_NAME + zarr_path.mkdir() + + artifact.cache = MagicMock(return_value=str(zarr_path)) # Explicitly add the `cache` method + return artifact + + +def test_store_artifact_custom_path(fake_artifact, tmp_path): + """Test storing artifact in a provided directory.""" + artifact = fake_artifact + target_path = tmp_path / "custom_dir" + target_path.mkdir() + + result_path = store_artifact(artifact, path=target_path) + + assert Path(result_path).exists() + assert Path(result_path).parent == target_path + + +def test_store_artifact_rename(fake_artifact, tmp_path): + """Test storing artifact with a custom name.""" + artifact = fake_artifact + target_path = tmp_path / "custom_dir" + target_path.mkdir() + + new_name = "renamed_data.zarr" + result_path = store_artifact(artifact, path=target_path, name=new_name) + + assert Path(result_path).exists() + assert Path(result_path).name == new_name + assert Path(result_path).parent == target_path + + +def test_store_artifact_file_not_found(tmp_path): + """Test that FileNotFoundError is raised if artifact.cache() points to a non-existent file.""" + artifact = MagicMock(spec=ln.Artifact) + zarr_path = tmp_path / "missing.zarr" + + # Explicitly add the `cache` method + artifact.cache = MagicMock(return_value=str(zarr_path)) + + target_path = tmp_path / "custom_dir" + with pytest.raises(FileNotFoundError): + store_artifact(artifact, path=target_path) + + +def test_store_artifact_permission_error(fake_artifact, tmp_path): + """Test that PermissionError is raised if the target directory is not writable.""" + artifact = fake_artifact + locked_dir = tmp_path / "locked" + locked_dir.mkdir() + os.chmod(locked_dir, 0o400) # Read-only directory + + with pytest.raises(PermissionError): + store_artifact(artifact, path=locked_dir) + + os.chmod(locked_dir, 0o700) # Restore permissions + + +def test_store_artifact_os_error(fake_artifact, monkeypatch, tmp_path): + """Test that OSError is raised if a simulated system error occurs.""" + artifact = fake_artifact + + def mock_move(*args, **kwargs): + raise OSError("Mocked OS error") + + monkeypatch.setattr(shutil, "move", mock_move) + + target_path = tmp_path / "custom_dir" + with pytest.raises(OSError, match="Mocked OS error"): + store_artifact(artifact, path=target_path) + + +def test_store_artifact_overwrite_false(fake_artifact, tmp_path): + """Test that FileExistsError is raised if overwrite=False and file exists.""" + artifact = fake_artifact + target_path = tmp_path / "existing_dir" + target_path.mkdir() + existing_file = target_path / DEFAULT_FILE_NAME + existing_file.mkdir() + + with pytest.raises(FileExistsError): + store_artifact(artifact, path=target_path, overwrite=False) + + +def test_store_artifact_overwrite_true(fake_artifact, tmp_path): + """Test that artifact is stored correctly when overwrite=True.""" + artifact = fake_artifact + target_path = tmp_path / "existing_dir" + target_path.mkdir() + existing_file = target_path / DEFAULT_FILE_NAME + existing_file.mkdir() + + result_path = store_artifact(artifact, path=target_path, overwrite=True) + + assert Path(result_path).exists() + assert Path(result_path).name == DEFAULT_FILE_NAME From babf1475ceef25cd38547248d01aaae30321faf5 Mon Sep 17 00:00:00 2001 From: zimea Date: Thu, 13 Feb 2025 17:10:44 +0100 Subject: [PATCH 07/19] refactor: rename to store_dataset to better reflect functionality --- src/spatialdata_db/integrations/__init__.py | 4 ++-- .../integrations/lamindb_wrappers.py | 2 +- tests/integrations/test_lamin_wrappers.py | 16 ++++++++-------- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/spatialdata_db/integrations/__init__.py b/src/spatialdata_db/integrations/__init__.py index 7f82c5e..8833c05 100644 --- a/src/spatialdata_db/integrations/__init__.py +++ b/src/spatialdata_db/integrations/__init__.py @@ -1,3 +1,3 @@ -from .lamindb_wrappers import store_artifact +from .lamindb_wrappers import store_dataset -__all__ = ["store_artifact"] +__all__ = ["store_dataset"] diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py index 03198ca..2843fa9 100644 --- a/src/spatialdata_db/integrations/lamindb_wrappers.py +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -7,7 +7,7 @@ LAMIN_TRACK_WARNING = "! run input wasn't tracked, call `ln.track()` and re-run" -def store_artifact( +def store_dataset( artifact: ln.Artifact, path: str | Path = Path("."), name: str | None = None, overwrite: bool = False ) -> str: """ diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py index d9d84fa..30cdcd7 100644 --- a/tests/integrations/test_lamin_wrappers.py +++ b/tests/integrations/test_lamin_wrappers.py @@ -6,7 +6,7 @@ import lamindb as ln import pytest -from spatialdata_db.integrations import store_artifact +from spatialdata_db.integrations import store_dataset DEFAULT_FILE_NAME = "test_data.zarr" @@ -27,7 +27,7 @@ def test_store_artifact_custom_path(fake_artifact, tmp_path): target_path = tmp_path / "custom_dir" target_path.mkdir() - result_path = store_artifact(artifact, path=target_path) + result_path = store_dataset(artifact, path=target_path) assert Path(result_path).exists() assert Path(result_path).parent == target_path @@ -40,7 +40,7 @@ def test_store_artifact_rename(fake_artifact, tmp_path): target_path.mkdir() new_name = "renamed_data.zarr" - result_path = store_artifact(artifact, path=target_path, name=new_name) + result_path = store_dataset(artifact, path=target_path, name=new_name) assert Path(result_path).exists() assert Path(result_path).name == new_name @@ -57,7 +57,7 @@ def test_store_artifact_file_not_found(tmp_path): target_path = tmp_path / "custom_dir" with pytest.raises(FileNotFoundError): - store_artifact(artifact, path=target_path) + store_dataset(artifact, path=target_path) def test_store_artifact_permission_error(fake_artifact, tmp_path): @@ -68,7 +68,7 @@ def test_store_artifact_permission_error(fake_artifact, tmp_path): os.chmod(locked_dir, 0o400) # Read-only directory with pytest.raises(PermissionError): - store_artifact(artifact, path=locked_dir) + store_dataset(artifact, path=locked_dir) os.chmod(locked_dir, 0o700) # Restore permissions @@ -84,7 +84,7 @@ def mock_move(*args, **kwargs): target_path = tmp_path / "custom_dir" with pytest.raises(OSError, match="Mocked OS error"): - store_artifact(artifact, path=target_path) + store_dataset(artifact, path=target_path) def test_store_artifact_overwrite_false(fake_artifact, tmp_path): @@ -96,7 +96,7 @@ def test_store_artifact_overwrite_false(fake_artifact, tmp_path): existing_file.mkdir() with pytest.raises(FileExistsError): - store_artifact(artifact, path=target_path, overwrite=False) + store_dataset(artifact, path=target_path, overwrite=False) def test_store_artifact_overwrite_true(fake_artifact, tmp_path): @@ -107,7 +107,7 @@ def test_store_artifact_overwrite_true(fake_artifact, tmp_path): existing_file = target_path / DEFAULT_FILE_NAME existing_file.mkdir() - result_path = store_artifact(artifact, path=target_path, overwrite=True) + result_path = store_dataset(artifact, path=target_path, overwrite=True) assert Path(result_path).exists() assert Path(result_path).name == DEFAULT_FILE_NAME From 3e28b4cc73f7cfc9805731fc32ad07bace23c5e0 Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 10:25:29 +0100 Subject: [PATCH 08/19] fix: delete non-working suppression of Lamin warning --- src/spatialdata_db/integrations/lamindb_wrappers.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py index 2843fa9..4357050 100644 --- a/src/spatialdata_db/integrations/lamindb_wrappers.py +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -1,17 +1,14 @@ import shutil -import warnings from pathlib import Path import lamindb as ln -LAMIN_TRACK_WARNING = "! run input wasn't tracked, call `ln.track()` and re-run" - def store_dataset( artifact: ln.Artifact, path: str | Path = Path("."), name: str | None = None, overwrite: bool = False ) -> str: """ - Store a cached artifact in a specified directory, rename it if needed, and suppress lamin's warning if the notebook is not tracked. + Store a cached artifact in a specified directory, rename it if needed. Parameters ---------- @@ -34,8 +31,8 @@ def store_dataset( target_dir = Path(path).resolve() target_dir.mkdir(parents=True, exist_ok=True) - warnings.filterwarnings("ignore", message=LAMIN_TRACK_WARNING) - cached_path = Path(artifact.cache()).resolve() + cached_path = artifact.cache() + cached_path = Path(cached_path).resolve() final_path = target_dir / (name if name else cached_path.name) From b948fe4dfdd6b80320ce4f31b049dba63a0aa4e7 Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 10:39:37 +0100 Subject: [PATCH 09/19] docs: add short notebook for the store_dataset function --- .../download_dataset_from_lamin.ipynb | 1201 +++++++++++++++++ 1 file changed, 1201 insertions(+) create mode 100644 docs/notebooks/download_dataset_from_lamin.ipynb diff --git a/docs/notebooks/download_dataset_from_lamin.ipynb b/docs/notebooks/download_dataset_from_lamin.ipynb new file mode 100644 index 0000000..ef663f4 --- /dev/null +++ b/docs/notebooks/download_dataset_from_lamin.ipynb @@ -0,0 +1,1201 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[92m→\u001b[0m connected lamindb: scverse/spatialdata-db\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/lustre/groups/ml01/workspace/lea.zimmermann/software/miniconda3/envs/sddb_test/lib/python3.11/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n", + " warnings.warn(\n" + ] + } + ], + "source": [ + "import lamindb as ln\n", + "import shutil\n", + "import spatialdata as sd\n", + "from spatialdata_db.integrations import store_dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Get a list of available datasets:" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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id
301J3fKc0m6IfFKqGT10000NoneView Visium SpatialData Example in Vitessce.vitessce.jsonNoneNone1842_ogAN9X4lJ-dYDkdL3SEYwNaNNonemd5TrueFalse12NoneNoneTrue257.02025-02-03 13:28:06.909252+00:008None1
300dBWsSTHSEVoYm7t70000vitessce_examples/visium.sdata.zarrVisium SpatialData Example.zarrdatasetNone14731802454r3hK7svWsNx1TIWdRyRsw9167.0Nonemd5-dTrueTrue12NoneNoneTrueNaN2025-02-03 13:11:16.519472+00:008None1
298wlgPi3jjfVoYUWjA0000None10X, Visium, Mouse, healthy, brain, 2023.zarrNonespatialdata116459181Ss6q2vgfyG3ARYWp0SUmsg443.0Nonemd5-dTrueTrue12NoneNoneTrue252.02025-01-21 14:17:50.268625+00:008None1
292bENTLCi4bBxkFdk30000None10X, anndata, Human, healthy, lymph node.anndata.zarrdatasetAnnData1990027410f1ev_U6XEzhfdyka2aSVA2038.0Nonemd5-dTrueTrue12NoneNoneTrue230.02025-01-20 16:49:45.453742+00:008None1
257Gdt4nEPT3QTzdmXc0000None10X, Visium, Human, healthy, lymph node.ome.zarrdatasetNone13404384mTHeMyuDsPVFBsfON2SZMQ265.0Nonemd5-dTrueTrue12NoneNoneTrue230.02024-12-19 09:56:39.264348+00:008None1
293jsq1NJbwJfXL1EtX0000NoneView Human Lymph Node Example in Vitessce.vitessce.jsonNoneNone3005qHci84d3Z-fLw8ML_3S0lgNaNNonemd5TrueFalse12NoneNoneTrue250.02025-01-20 16:51:28.656230+00:008None1
290u7ShvF2TOpFCKKOT0000None10X, Visium, Human, unknown, spinal_cord, 2020.zarrNonespatialdata27522152jW3Cq3su6K5FgMgaaz9DvA263.0Nonemd5-dTrueTrue12NoneNoneTrueNaN2025-01-19 21:54:04.931463+00:008None1
2884gLfyEWea7fJpXyQ0000None10X, Visium, Mouse, unknown, brain, 2020.zarrNonespatialdata54817412yocuS6gw1aoX2zwDNZsebg327.0Nonemd5-dTrueTrue12NoneNoneTrue243.02025-01-19 21:51:51.708790+00:008None1
284AqRfNjb1YHyMDZt00000None10X, Visium, Mouse, healthy, brain, 2022.zarrNonespatialdata54817400NTOnZzCUoYiXjypzHEud7g327.0Nonemd5-dTrueTrue12NoneNoneTrue239.02025-01-19 21:45:48.348520+00:008None1
278h298F4wLSpYnMo2C0000None10X, Visium, Human, unknown, brain_cerebellum,....zarrNonespatialdata28680862I3p1SB4RL5YR8EcLcsZsNQ227.0Nonemd5-dTrueTrue12NoneNoneTrue248.02025-01-19 21:34:25.397573+00:008None1
276o4CvH5ipm5g1Psyy0000None10X, Visium, Human, healthy, prostate, 2021.zarrNonespatialdata34069617Mjt1UQFsL-sd_eEXGnJWjQ259.0Nonemd5-dTrueTrue12NoneNoneTrue247.02025-01-19 21:32:33.064038+00:008None1
274PmbrQBYxBxayyhls0000None10X, Visium, Human, unknown, heart, 2020.zarrNonespatialdata41793228tNEMxpH6G5uoTY3CxRRMGw263.0Nonemd5-dTrueTrue12NoneNoneTrue245.02025-01-19 21:30:51.916798+00:008None1
272wg5zQhHX5cQ9UG4N0000None10X, Visium, Mouse, unknown, brain, 2020.zarrNonespatialdata57953090raOCaxJLh_weCxY7z4mu3w327.0Nonemd5-dTrueTrue12NoneNoneTrue244.02025-01-19 21:29:00.556320+00:008None1
271KgUohDusDLA4S6WW0000None10X, Visium, Mouse, unknown, brain, 2020.zarrNonespatialdata38143587Xdl3V5khe8508IjaJQhm8g327.0Nonemd5-dTrueTrue12NoneNoneTrue241.02025-01-19 21:26:41.761595+00:008None1
2708Xdm6p3J8FPOxok00000None10X, Visium, Mouse, unknown, brain, 2020.zarrNonespatialdata381435871SFkEeE1UvvswCpuCstDPw327.0Nonemd5-dTrueTrue12NoneNoneTrue241.02025-01-19 21:25:28.550886+00:008None1
269McoRBaiIuHp0Q8RQ0000None10X, Visium, Mouse, healthy, brain, 2022.zarrNonespatialdata54841203PlYRrY4VI-frNKHES5gvqw327.0Nonemd5-dTrueTrue12NoneNoneTrue240.02025-01-19 21:23:37.660374+00:008None1
268SYTEY2CR0OfTdq4N0000None10X, Visium, Mouse, unknown, brain, 2019.zarrNonespatialdata56180342pgkbcq_Rhf24MfhY-1zc1Q327.0Nonemd5-dTrueTrue12NoneNoneTrueNaN2025-01-19 21:19:25.551402+00:008None1
2668XBBsxnNHuWCOeOb0000None10X, Visium, Human, large intestine colorectal....zarrNonespatialdata52401277TUrS6Myy91ExOsSws_zQ2A323.0Nonemd5-dTrueTrue12NoneNoneTrue237.02025-01-19 16:42:31.115433+00:008None1
265LumVWsITkcZQteL70000NoneVisium vitessce demo.vitessce.jsonNoneNone2047SdxuKSaTOOT23HkA2jlLdgNaNNonemd5TrueFalse12NoneNoneTrue235.02025-01-16 19:17:02.333550+00:008None1
2630BDn4bWTAMtQmOXS0000NoneView Human Lymph Node Example in Vitessce.vitessce.jsonNoneNone3005-PchR8TOA4y0lj6IjmayiANaNNonemd5TrueFalse12NoneNoneTrue231.02025-01-08 13:31:22.631439+00:008None1
2561X1HPFLZIq5Qlwra0000NoneAnnData object for Human lymph node, 10X Genomics.anndata.zarrdatasetAnnData199002959YolRLEIAX6AE9IGLRSOjGA2038.0Nonemd5-dTrueTrue12NoneNoneTrue230.02024-12-19 09:55:30.210836+00:008None1
262I38PyB0QZJLwi3Io0000NoneView Human Lymph Node Example in Vitessce.vitessce.jsonNoneNone29876QGkKjYdn3QMkGBLOAip0wNaNNonemd5TrueFalse12NoneNoneTrue229.02024-12-19 10:12:16.511765+00:008None1
239Co2Bwl9TymNlnv9c0000None10X, Visium, Human, breast cancer, breast, 2022.zarrNonespatialdata53442529Z05oc7m9alFGiMo1l33DOQ311.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 15:04:08.589580+00:008None1
2308mjX2vs8KhTS3Y4c0000None10X, Visium, Human, prostate cancer, prostate,....zarrNonespatialdata60838635TNg5OjUQowqBR_B0komdBQ326.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 11:05:27.316266+00:008None1
228J6HsBBMXCJ8amco80000None10X, Xenium, Human, cancer, intestine_colon, 2023.zarrNonespatialdata5129800776AyFqQ-0ipr-sgDzUuEErmg786.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 10:59:12.338173+00:008None1
227AcJ31iZl6KgZR7BO0000None10X, Xenium, Human, healthy, heart, 2024.zarrNonespatialdata1483994224f7BgRVX9kNxvnSpm4BrOMA368.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 10:56:05.258469+00:008None1
226fVvF7TCAlJfKsWgo0000None10X, Xenium, Human, glioblastoma, brain, 2024.zarrNonespatialdata25439820101Y7XqV167fo0hN6xNsRQSWw2426.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 10:48:23.337843+00:008None1
2245UbbJ6cR0WzaBDHB0000None10X, Xenium, Human, acute lymphoid leukemia, b....zarrNonespatialdata2490544230JBdHTZJUvNltQNjFB8UdcQ598.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 10:27:24.088735+00:008None1
222ubllg1iYQBaiDJfW0000None10X, VisiumHD, Mouse, Healthy, Brain, 2024.zarrNonespatialdata1099865189r3sSzfkOliLFFfhDzmP9hw2215.0Nonemd5-dTrueTrue12NoneNoneTrue197.02024-12-16 10:07:09.710482+00:008None1
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\n", + "222 10X, VisiumHD, Mouse, Healthy, Brain, 2024 .zarr \n", + "\n", + " kind otype size hash n_files \\\n", + "id \n", + "301 None None 1842 _ogAN9X4lJ-dYDkdL3SEYw NaN \n", + "300 dataset None 1473180245 4r3hK7svWsNx1TIWdRyRsw 9167.0 \n", + "298 None spatialdata 116459181 Ss6q2vgfyG3ARYWp0SUmsg 443.0 \n", + "292 dataset AnnData 199002741 0f1ev_U6XEzhfdyka2aSVA 2038.0 \n", + "257 dataset None 13404384 mTHeMyuDsPVFBsfON2SZMQ 265.0 \n", + "293 None None 3005 qHci84d3Z-fLw8ML_3S0lg NaN \n", + "290 None spatialdata 27522152 jW3Cq3su6K5FgMgaaz9DvA 263.0 \n", + "288 None spatialdata 54817412 yocuS6gw1aoX2zwDNZsebg 327.0 \n", + "284 None spatialdata 54817400 NTOnZzCUoYiXjypzHEud7g 327.0 \n", + "278 None spatialdata 28680862 I3p1SB4RL5YR8EcLcsZsNQ 227.0 \n", + "276 None spatialdata 34069617 Mjt1UQFsL-sd_eEXGnJWjQ 259.0 \n", + "274 None spatialdata 41793228 tNEMxpH6G5uoTY3CxRRMGw 263.0 \n", + "272 None spatialdata 57953090 raOCaxJLh_weCxY7z4mu3w 327.0 \n", + "271 None spatialdata 38143587 Xdl3V5khe8508IjaJQhm8g 327.0 \n", + "270 None spatialdata 38143587 1SFkEeE1UvvswCpuCstDPw 327.0 \n", + "269 None spatialdata 54841203 PlYRrY4VI-frNKHES5gvqw 327.0 \n", + "268 None spatialdata 56180342 pgkbcq_Rhf24MfhY-1zc1Q 327.0 \n", + "266 None spatialdata 52401277 TUrS6Myy91ExOsSws_zQ2A 323.0 \n", + "265 None None 2047 SdxuKSaTOOT23HkA2jlLdg NaN \n", + "263 None None 3005 -PchR8TOA4y0lj6IjmayiA NaN \n", + "256 dataset AnnData 199002959 YolRLEIAX6AE9IGLRSOjGA 2038.0 \n", + "262 None None 2987 6QGkKjYdn3QMkGBLOAip0w NaN \n", + "239 None spatialdata 53442529 Z05oc7m9alFGiMo1l33DOQ 311.0 \n", + "230 None spatialdata 60838635 TNg5OjUQowqBR_B0komdBQ 326.0 \n", + "228 None spatialdata 5129800776 AyFqQ-0ipr-sgDzUuEErmg 786.0 \n", + "227 None spatialdata 1483994224 f7BgRVX9kNxvnSpm4BrOMA 368.0 \n", + "226 None spatialdata 25439820101 Y7XqV167fo0hN6xNsRQSWw 2426.0 \n", + "224 None spatialdata 2490544230 JBdHTZJUvNltQNjFB8UdcQ 598.0 \n", + "222 None spatialdata 1099865189 r3sSzfkOliLFFfhDzmP9hw 2215.0 \n", + "\n", + " n_observations _hash_type _key_is_virtual _overwrite_versions space_id \\\n", + "id \n", + "301 None md5 True False 1 \n", + "300 None md5-d True True 1 \n", + "298 None md5-d True True 1 \n", + "292 None md5-d True True 1 \n", + "257 None md5-d True True 1 \n", + "293 None md5 True False 1 \n", + "290 None md5-d True True 1 \n", + "288 None md5-d True True 1 \n", + "284 None md5-d True True 1 \n", + "278 None md5-d True True 1 \n", + "276 None md5-d True True 1 \n", + "274 None md5-d True True 1 \n", + "272 None md5-d True True 1 \n", + "271 None md5-d True True 1 \n", + "270 None md5-d True True 1 \n", + "269 None md5-d True True 1 \n", + "268 None md5-d True True 1 \n", + "266 None md5-d True True 1 \n", + "265 None md5 True False 1 \n", + "263 None md5 True False 1 \n", + "256 None md5-d True True 1 \n", + "262 None md5 True False 1 \n", + "239 None md5-d True True 1 \n", + "230 None md5-d True True 1 \n", + "228 None md5-d True True 1 \n", + "227 None md5-d True True 1 \n", + "226 None md5-d True True 1 \n", + "224 None md5-d True True 1 \n", + "222 None md5-d True True 1 \n", + "\n", + " storage_id schema_id version is_latest run_id \\\n", + "id \n", + "301 2 None None True 257.0 \n", + "300 2 None None True NaN \n", + "298 2 None None True 252.0 \n", + "292 2 None None True 230.0 \n", + "257 2 None None True 230.0 \n", + "293 2 None None True 250.0 \n", + "290 2 None None True NaN \n", + "288 2 None None True 243.0 \n", + "284 2 None None True 239.0 \n", + "278 2 None None True 248.0 \n", + "276 2 None None True 247.0 \n", + "274 2 None None True 245.0 \n", + "272 2 None None True 244.0 \n", + "271 2 None None True 241.0 \n", + "270 2 None None True 241.0 \n", + "269 2 None None True 240.0 \n", + "268 2 None None True NaN \n", + "266 2 None None True 237.0 \n", + "265 2 None None True 235.0 \n", + "263 2 None None True 231.0 \n", + "256 2 None None True 230.0 \n", + "262 2 None None True 229.0 \n", + "239 2 None None True 197.0 \n", + "230 2 None None True 197.0 \n", + "228 2 None None True 197.0 \n", + "227 2 None None True 197.0 \n", + "226 2 None None True 197.0 \n", + "224 2 None None True 197.0 \n", + "222 2 None None True 197.0 \n", + "\n", + " created_at created_by_id _aux _branch_code \n", + "id \n", + "301 2025-02-03 13:28:06.909252+00:00 8 None 1 \n", + "300 2025-02-03 13:11:16.519472+00:00 8 None 1 \n", + "298 2025-01-21 14:17:50.268625+00:00 8 None 1 \n", + "292 2025-01-20 16:49:45.453742+00:00 8 None 1 \n", + "257 2024-12-19 09:56:39.264348+00:00 8 None 1 \n", + "293 2025-01-20 16:51:28.656230+00:00 8 None 1 \n", + "290 2025-01-19 21:54:04.931463+00:00 8 None 1 \n", + "288 2025-01-19 21:51:51.708790+00:00 8 None 1 \n", + "284 2025-01-19 21:45:48.348520+00:00 8 None 1 \n", + "278 2025-01-19 21:34:25.397573+00:00 8 None 1 \n", + "276 2025-01-19 21:32:33.064038+00:00 8 None 1 \n", + "274 2025-01-19 21:30:51.916798+00:00 8 None 1 \n", + "272 2025-01-19 21:29:00.556320+00:00 8 None 1 \n", + "271 2025-01-19 21:26:41.761595+00:00 8 None 1 \n", + "270 2025-01-19 21:25:28.550886+00:00 8 None 1 \n", + "269 2025-01-19 21:23:37.660374+00:00 8 None 1 \n", + "268 2025-01-19 21:19:25.551402+00:00 8 None 1 \n", + "266 2025-01-19 16:42:31.115433+00:00 8 None 1 \n", + "265 2025-01-16 19:17:02.333550+00:00 8 None 1 \n", + "263 2025-01-08 13:31:22.631439+00:00 8 None 1 \n", + "256 2024-12-19 09:55:30.210836+00:00 8 None 1 \n", + "262 2024-12-19 10:12:16.511765+00:00 8 None 1 \n", + "239 2024-12-16 15:04:08.589580+00:00 8 None 1 \n", + "230 2024-12-16 11:05:27.316266+00:00 8 None 1 \n", + "228 2024-12-16 10:59:12.338173+00:00 8 None 1 \n", + "227 2024-12-16 10:56:05.258469+00:00 8 None 1 \n", + "226 2024-12-16 10:48:23.337843+00:00 8 None 1 \n", + "224 2024-12-16 10:27:24.088735+00:00 8 None 1 \n", + "222 2024-12-16 10:07:09.710482+00:00 8 None 1 " + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ln.Artifact.df()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Select an example uid - e.g. `wlgPi3jjfVoYUWjA0000` and retrieve the artifact:" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "artifact = ln.Artifact.get('wlgPi3jjfVoYUWjA0000')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "`store_dataset` will download the data associated to the artifact. Default path is `.` and the default name is the artifact uid. A different path and name can be used via the parameters `path` and `name`." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[93m!\u001b[0m run input wasn't tracked, call `ln.track()` and re-run\n" + ] + } + ], + "source": [ + "path = store_dataset(artifact=artifact)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/lustre/groups/ml01/workspace/lea.zimmermann/software/miniconda3/envs/sddb_test/lib/python3.11/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only'\n", + " compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs)\n" + ] + } + ], + "source": [ + "sdata = sd.read_zarr(path)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "SpatialData object, with associated Zarr store: /ictstr01/home/icb/lea.zimmermann/projects/spatialdata-db/spatialdata-db/docs/notebooks/wlgPi3jjfVoYUWjA.zarr\n", + "├── Images\n", + "│ ├── 'CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_full_image': DataTree[cyx] (3, 1578, 2000), (3, 789, 1000), (3, 394, 500), (3, 197, 250), (3, 98, 125)\n", + "│ ├── 'CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_hires_image': DataArray[cyx] (3, 1578, 2000)\n", + "│ └── 'CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_lowres_image': DataArray[cyx] (3, 474, 600)\n", + "├── Shapes\n", + "│ └── 'CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain': GeoDataFrame shape: (6965, 2) (2D shapes)\n", + "└── Tables\n", + " └── 'table': AnnData (6965, 19465)\n", + "with coordinate systems:\n", + " ▸ 'downscaled_hires', with elements:\n", + " CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_hires_image (Images), CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain (Shapes)\n", + " ▸ 'downscaled_lowres', with elements:\n", + " CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_lowres_image (Images), CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain (Shapes)\n", + " ▸ 'global', with elements:\n", + " CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_full_image (Images), CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain (Shapes)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sdata" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "shutil.rmtree(path)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "sddb_test", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.11" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} From 146542e9586aa68debba5515993cf6d1cc308719 Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 12:27:15 +0100 Subject: [PATCH 10/19] fix: init test lamin instance for github actions --- tests/integrations/test_lamin_wrappers.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py index 30cdcd7..38264cd 100644 --- a/tests/integrations/test_lamin_wrappers.py +++ b/tests/integrations/test_lamin_wrappers.py @@ -10,6 +10,10 @@ DEFAULT_FILE_NAME = "test_data.zarr" +# Only initialize a test instance in GitHub Actions +if os.getenv("GITHUB_ACTIONS") == "true": + ln.setup.init(storage="./test_lamindb") + @pytest.fixture(scope="function") def fake_artifact(tmp_path): From 56ae2d582fecce2edcf926fbf08174c437c22305 Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 12:28:53 +0100 Subject: [PATCH 11/19] chore: update required numba version to 0.61.0 --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 78bcb44..1786cfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ authors = [ { name = "Lea Zimmermann" }, { name = "Lukas Heumos" }, ] -requires-python = ">=3.10, <3.13" +requires-python = ">=3.10,<3.13" classifiers = [ "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: 3.10", @@ -27,11 +27,12 @@ classifiers = [ ] dependencies = [ "lamindb[aws,bionty,jupyter]>=1.0.4", + "numba>=0.61", + "session-info2", "spatialdata", "spatialdata-io", "spatialdata-plot", "vitessce", - "session-info2" ] optional-dependencies.dev = [ "pre-commit", From c7f5412a51714be217e1b38f3a77e5862ff90395 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 17 Feb 2025 12:45:47 +0000 Subject: [PATCH 12/19] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .gitignore | 2 +- .readthedocs.yaml | 26 +- CHANGELOG.md | 2 +- README.md | 10 +- .../1000j_to_zarr.py | 11 +- .../1001e_to_zarr.py | 11 +- .../10040_to_zarr.py | 9 +- .../10053_to_zarr.py | 11 +- .../10056_to_zarr.py | 11 +- .../1005m_to_zarr.py | 11 +- .../100my_to_zarr.py | 11 +- .../100w1_to_zarr.py | 11 +- .../100wk_to_zarr.py | 11 +- .../1012t_to_zarr.py | 11 +- .../1015d_to_zarr.py | 2 +- .../101cw_to_zarr.py | 11 +- .../101in_to_zarr.py | 11 +- .../101s6_to_zarr.py | 11 +- .../101t3_to_zarr.py | 9 +- .../101tu_to_zarr.py | 9 +- .../101x5_to_zarr.py | 9 +- .../1020c_to_zarr.py | 11 +- .../1020d_to_zarr.py | 9 +- .../10224_to_zarr.py | 11 +- .../1025z_to_zarr.py | 11 +- .../102cy_to_zarr.py | 9 +- .../102hp_to_zarr.py | 11 +- .../1031a_to_zarr.py | 11 +- .../1033x_to_zarr.py | 11 +- .../1039v_to_zarr.py | 11 +- .../103da_to_zarr.py | 2 +- .../103mc_to_zarr.py | 11 +- .../103mf_to_zarr.py | 9 +- .../103sf_to_zarr.py | 11 +- .../103sm_to_zarr.py | 11 +- .../103te_to_zarr.py | 11 +- .../103uy_to_zarr.py | 11 +- .../104cz_to_zarr.py | 9 +- .../104dm_to_zarr.py | 11 +- .../104dy_to_zarr.py | 9 +- .../104ee_to_zarr.py | 11 +- .../104pe_to_zarr.py | 11 +- .../105h4_to_zarr.py | 2 +- .../105jc_to_zarr.py | 11 +- .../105k3_to_zarr.py | 11 +- .../105ka_to_zarr.py | 11 +- .../105tt_to_zarr.py | 11 +- .../105vj_to_zarr.py | 11 +- .../105yf_to_zarr.py | 11 +- .../1063i_to_zarr.py | 9 +- .../1065r_to_zarr.py | 11 +- .../10676_to_zarr.py | 11 +- .../106ip_to_zarr.py | 11 +- .../106ru_to_zarr.py | 11 +- .../106s5_to_zarr.py | 11 +- .../106v2_to_zarr.py | 11 +- .../106ws_to_zarr.py | 9 +- .../106xa_to_zarr.py | 9 +- .../1074f_to_zarr.py | 9 +- .../107rk_to_zarr.py | 11 +- .../107rw_to_zarr.py | 11 +- .../107sr_to_zarr.py | 9 +- .../107yk_to_zarr.py | 9 +- .../107z9_to_zarr.py | 2 +- .../10817_to_zarr.py | 11 +- .../10834_to_zarr.py | 11 +- .../108d3_to_zarr.py | 9 +- .../108dr_to_zarr.py | 9 +- .../108h0_to_zarr.py | 9 +- .../108r9_to_zarr.py | 11 +- .../108rf_to_zarr.py | 11 +- .../108ty_to_zarr.py | 11 +- .../108x2_to_zarr.py | 2 +- .../1090h_to_zarr.py | 11 +- .../1091x_to_zarr.py | 9 +- .../1094t_to_zarr.py | 11 +- .../1097y_to_zarr.py | 11 +- .../109k1_to_zarr.py | 9 +- .../109pp_to_zarr.py | 11 +- .../109zw_to_zarr.py | 9 +- .../10a6w_to_zarr.py | 11 +- .../10a7t_to_zarr.py | 2 +- .../10ae2_to_zarr.py | 9 +- .../10ah4_to_zarr.py | 9 +- .../10ake_to_zarr.py | 11 +- .../10amj_to_zarr.py | 11 +- .../10ant_to_zarr.py | 11 +- .../10arp_to_zarr.py | 9 +- .../10c6u_to_zarr.py | 9 +- .../10caf_to_zarr.py | 11 +- .../10ci4_to_zarr.py | 11 +- .../10ckr_to_zarr.py | 11 +- .../10d9e_to_zarr.py | 11 +- .../10dcv_to_zarr.py | 9 +- .../10drc_to_zarr.py | 11 +- .../10dvd_to_zarr.py | 2 +- .../10e4w_to_zarr.py | 11 +- .../10e4x_to_zarr.py | 11 +- .../10e5i_to_zarr.py | 11 +- .../10e9s_to_zarr.py | 11 +- .../10ekd_to_zarr.py | 11 +- .../10etk_to_zarr.py | 11 +- .../10evh_to_zarr.py | 11 +- .../10f2z_to_zarr.py | 11 +- .../10fc7_to_zarr.py | 11 +- .../10fmm_to_zarr.py | 11 +- .../10fn9_to_zarr.py | 11 +- .../10fna_to_zarr.py | 11 +- .../10fpp_to_zarr.py | 9 +- .../10fri_to_zarr.py | 9 +- .../10fty_to_zarr.py | 11 +- .../10fyx_to_zarr.py | 9 +- .../10h3h_to_zarr.py | 2 +- .../10ha9_to_zarr.py | 11 +- .../10hay_to_zarr.py | 11 +- .../10hhx_to_zarr.py | 9 +- .../10hm6_to_zarr.py | 11 +- .../10hmw_to_zarr.py | 11 +- .../10huw_to_zarr.py | 11 +- .../10hxz_to_zarr.py | 11 +- .../10i70_to_zarr.py | 9 +- .../10i8s_to_zarr.py | 11 +- .../10ieh_to_zarr.py | 11 +- .../10if2_to_zarr.py | 11 +- .../10iky_to_zarr.py | 11 +- .../10ipu_to_zarr.py | 2 +- .../10j0z_to_zarr.py | 11 +- .../10jcz_to_zarr.py | 11 +- .../10jdw_to_zarr.py | 2 +- .../10jfe_to_zarr.py | 11 +- .../10jff_to_zarr.py | 11 +- .../10jft_to_zarr.py | 11 +- .../10jr4_to_zarr.py | 11 +- .../10jss_to_zarr.py | 11 +- .../10k3x_to_zarr.py | 9 +- .../10k5p_to_zarr.py | 11 +- .../10kia_to_zarr.py | 11 +- .../10kmy_to_zarr.py | 11 +- .../10ktp_make_vitessce.py | 26 +- .../10ktp_to_lamin.py | 1 + .../10ktp_to_zarr.py | 13 +- .../10kxi_to_zarr.py | 2 +- .../10kyn_to_zarr.py | 11 +- .../10kyp_to_zarr.py | 9 +- .../10kz2_to_zarr.py | 11 +- .../10kz7_to_zarr.py | 11 +- .../10m16_to_zarr.py | 11 +- .../10m49_to_zarr.py | 11 +- .../10mda_to_zarr.py | 11 +- .../10mx9_to_zarr.py | 11 +- .../10n1k_to_zarr.py | 9 +- .../10nc2_to_zarr.py | 2 +- .../10ndj_to_zarr.py | 11 +- .../10ndm_to_zarr.py | 9 +- .../10nfy_to_zarr.py | 11 +- .../10nsr_to_zarr.py | 9 +- .../10nzm_to_zarr.py | 2 +- .../10p19_to_zarr.py | 11 +- .../10p4f_to_zarr.py | 11 +- .../10p5f_to_zarr.py | 11 +- .../10pa3_to_zarr.py | 9 +- .../10pf0_to_zarr.py | 9 +- .../10ps4_to_zarr.py | 11 +- .../10pui_to_zarr.py | 9 +- .../10rm3_to_zarr.py | 11 +- .../10rx2_to_zarr.py | 11 +- .../10rxw_to_zarr.py | 11 +- .../10s7d_to_zarr.py | 2 +- .../10s8t_to_zarr.py | 11 +- .../10sja_to_zarr.py | 9 +- .../10sn3_to_zarr.py | 11 +- .../10sph_to_zarr.py | 11 +- .../10t8c_to_zarr.py | 11 +- .../10tei_to_zarr.py | 11 +- .../10thd_to_zarr.py | 11 +- .../10tsy_to_zarr.py | 9 +- .../10ttt_to_zarr.py | 11 +- .../10tyd_to_zarr.py | 11 +- .../10tzs_to_zarr.py | 11 +- .../10u63_to_zarr.py | 9 +- .../10u6u_to_zarr.py | 11 +- .../10u89_to_zarr.py | 9 +- .../10uac_to_zarr.py | 9 +- .../10uf7_to_zarr.py | 11 +- .../10uik_to_zarr.py | 11 +- .../10uxy_to_zarr.py | 9 +- .../10v4k_to_zarr.py | 11 +- .../10v61_to_zarr.py | 11 +- .../10vcj_to_zarr.py | 11 +- .../10vek_to_zarr.py | 2 +- .../10vj2_to_zarr.py | 11 +- .../10vtf_to_zarr.py | 11 +- .../10vyh_to_zarr.py | 11 +- .../10w2u_to_zarr.py | 2 +- .../10w6u_to_zarr.py | 11 +- .../10w90_to_zarr.py | 2 +- .../10wcj_to_zarr.py | 11 +- .../10wfn_to_zarr.py | 11 +- .../10wkh_to_zarr.py | 11 +- .../10wmu_to_zarr.py | 9 +- .../10wsf_to_zarr.py | 11 +- .../10wth_to_zarr.py | 11 +- .../10wv1_to_zarr.py | 11 +- .../10x88_to_zarr.py | 9 +- .../10xa2_to_zarr.py | 9 +- .../10xay_to_zarr.py | 9 +- .../10xtf_to_zarr.py | 11 +- .../10y80_to_zarr.py | 9 +- .../10yhc_to_zarr.py | 11 +- .../10yhv_to_zarr.py | 11 +- .../10z77_to_zarr.py | 11 +- .../10z91_to_zarr.py | 11 +- .../10zad_to_zarr.py | 11 +- .../10zj1_to_zarr.py | 9 +- .../10zm9_to_zarr.py | 9 +- .../10zvc_to_zarr.py | 11 +- .../10zwi_to_zarr.py | 9 +- .../10zyf_to_zarr.py | 11 +- .../cij6u_to_zarr.py | 15 +- .../eex9l_to_zarr.py | 9 +- .../eib0d_to_zarr.py | 9 +- .../gei4o_to_zarr.py | 9 +- .../ich1o_to_zarr.py | 9 +- .../ka3ja_to_zarr.py | 9 +- .../kie2u_to_zarr.py | 9 +- .../lu6ph_to_zarr.py | 9 +- .../ohgh2_to_zarr.py | 9 +- .../pee2u_to_zarr.py | 9 +- .../shoh6_to_zarr.py | 9 +- .../sie0e_to_zarr.py | 9 +- .../soo4t_to_zarr.py | 9 +- .../ush6c_to_zarr.py | 9 +- .../va9qu_to_zarr.py | 9 +- .../vak6a_to_zarr.py | 9 +- .../weer2_to_zarr.py | 9 +- docs/_static/css/custom.css | 2 +- docs/contributing.md | 18 +- docs/extensions/typed_returns.py | 2 +- .../download_dataset_from_lamin.ipynb | 2 +- scripts/add_metadata_from_csv.ipynb | 25 +- scripts/cleanup.ipynb | 1 + scripts/convert_to_sdata.ipynb | 43 ++-- scripts/create_uids.ipynb | 16 +- scripts/download_10X_data.ipynb | 57 ++--- scripts/download_10X_data.py | 61 ++--- scripts/parse_10X_ST_table.ipynb | 71 +++--- scripts/query_artifacts.ipynb | 4 +- scripts/rename_on_lustre.ipynb | 65 +++-- scripts/spatial_data_curator.ipynb | 225 +++++++++++++----- scripts/update_uid_master.py | 7 +- scripts/upload_1000j_visium.ipynb | 42 ++-- scripts/validator_demo.ipynb | 4 +- src/spatialdata_db/__init__.py | 5 +- src/spatialdata_db/parsing.py | 1 + 254 files changed, 1627 insertions(+), 1325 deletions(-) diff --git a/.gitignore b/.gitignore index 294b7c7..12dffb0 100644 --- a/.gitignore +++ b/.gitignore @@ -32,4 +32,4 @@ Sandbox.ipynb test.ipynb *.zarr -upload* \ No newline at end of file +upload* diff --git a/.readthedocs.yaml b/.readthedocs.yaml index fdf859d..a132982 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,18 +1,18 @@ version: 2 build: - os: ubuntu-24.04 - tools: - python: "3.12" - commands: - - asdf plugin add uv - - asdf install uv latest - - asdf global uv latest - - uv venv - - uv pip install .[doc] - - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html + os: ubuntu-24.04 + tools: + python: "3.12" + commands: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv venv + - uv pip install .[doc] + - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: - configuration: docs/conf.py - fail_on_warning: false + configuration: docs/conf.py + fail_on_warning: false submodules: - include: all + include: all diff --git a/CHANGELOG.md b/CHANGELOG.md index e7b7808..c185628 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][]. ### Added -- Basic tool, preprocessing and plotting functions +- Basic tool, preprocessing and plotting functions diff --git a/README.md b/README.md index a31db82..af4942f 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ Currently focusing on the following datasets for diversity in testing: - `jqmx8`: VisiumHD, Mouse, Intestine ## Setup vitessce + Currently, the `SpatialDataWrapper` is not yet merged and released. Therefore, we have to install it via ```bash @@ -19,10 +20,11 @@ pip install git+https://github.com/vitessce/vitessce-python.git@ig/spatial_data from Ilan's PR: https://github.com/vitessce/vitessce-python/pull/333 ## UID logic + - Absolute ID will be a 5 char string of lowercase letters and digits -> 60466176 IDs - Leaving out the letters [l, b, o, g, q] due to their similarity to [1, 6, 0, 9, 9] -> 28629151 IDs - Reserve ID spaces for technology providers - - 10 _ _ _ -> 29791 IDs for 10X Genomics - - vg _ _ _ -> 29791 IDs for Vizgen - - ns _ _ _ -> 29791 IDs for Nanostring - - xx _ _ _ -> 29791 IDs for miscellaneous, such as publication + - 10 \_ \_ \_ -> 29791 IDs for 10X Genomics + - vg \_ \_ \_ -> 29791 IDs for Vizgen + - ns \_ \_ \_ -> 29791 IDs for Nanostring + - xx \_ \_ \_ -> 29791 IDs for miscellaneous, such as publication diff --git a/data/1000j__10X__Visium__Human__large_intestine__20220328__v1.3.0/1000j_to_zarr.py b/data/1000j__10X__Visium__Human__large_intestine__20220328__v1.3.0/1000j_to_zarr.py index 00cc9ec..e1e52e7 100644 --- a/data/1000j__10X__Visium__Human__large_intestine__20220328__v1.3.0/1000j_to_zarr.py +++ b/data/1000j__10X__Visium__Human__large_intestine__20220328__v1.3.0/1000j_to_zarr.py @@ -1,10 +1,11 @@ uid = "1000j_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Intestinal_Cancer", counts_file=str(path_read / "Visium_FFPE_Human_Intestinal_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1001e__10X__Visium__Mouse__embryo__20230608__v2.1.0/1001e_to_zarr.py b/data/1001e__10X__Visium__Mouse__embryo__20230608__v2.1.0/1001e_to_zarr.py index a31dd39..a73d73d 100644 --- a/data/1001e__10X__Visium__Mouse__embryo__20230608__v2.1.0/1001e_to_zarr.py +++ b/data/1001e__10X__Visium__Mouse__embryo__20230608__v2.1.0/1001e_to_zarr.py @@ -1,10 +1,11 @@ uid = "1001e_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Mouse_Embryo", counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_Embryo_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10040__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedBoneMarrow/10040_to_zarr.py b/data/10040__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedBoneMarrow/10040_to_zarr.py index 196cd4b..37b913b 100644 --- a/data/10040__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedBoneMarrow/10040_to_zarr.py +++ b/data/10040__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedBoneMarrow/10040_to_zarr.py @@ -1,10 +1,11 @@ uid = "10040_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10053__10X__Visium__Mouse__brain__20220329__v1.3.0/10053_to_zarr.py b/data/10053__10X__Visium__Mouse__brain__20220329__v1.3.0/10053_to_zarr.py index 2ac1ddd..0a8accb 100644 --- a/data/10053__10X__Visium__Mouse__brain__20220329__v1.3.0/10053_to_zarr.py +++ b/data/10053__10X__Visium__Mouse__brain__20220329__v1.3.0/10053_to_zarr.py @@ -1,10 +1,11 @@ uid = "10053_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10056__10X__Visium__Mouse__brain__20230417__v2.0.1/10056_to_zarr.py b/data/10056__10X__Visium__Mouse__brain__20230417__v2.0.1/10056_to_zarr.py index 2e42fa8..677a6a8 100644 --- a/data/10056__10X__Visium__Mouse__brain__20230417__v2.0.1/10056_to_zarr.py +++ b/data/10056__10X__Visium__Mouse__brain__20230417__v2.0.1/10056_to_zarr.py @@ -1,10 +1,11 @@ uid = "10056_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1005m__10X__Visium__Human__prostate__20210609__v1.3.0/1005m_to_zarr.py b/data/1005m__10X__Visium__Human__prostate__20210609__v1.3.0/1005m_to_zarr.py index a6803ed..09b1ef2 100644 --- a/data/1005m__10X__Visium__Human__prostate__20210609__v1.3.0/1005m_to_zarr.py +++ b/data/1005m__10X__Visium__Human__prostate__20210609__v1.3.0/1005m_to_zarr.py @@ -1,10 +1,11 @@ uid = "1005m_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Normal_Prostate", counts_file=str(path_read / "Visium_FFPE_Human_Normal_Prostate_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/100my__10X__Visium__Human__breast__20230106__v2.0.1/100my_to_zarr.py b/data/100my__10X__Visium__Human__breast__20230106__v2.0.1/100my_to_zarr.py index ab741a3..8e74408 100644 --- a/data/100my__10X__Visium__Human__breast__20230106__v2.0.1/100my_to_zarr.py +++ b/data/100my__10X__Visium__Human__breast__20230106__v2.0.1/100my_to_zarr.py @@ -1,10 +1,11 @@ uid = "100my_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fresh_Frozen_Human_Breast_Cancer", counts_file=str(path_read / "CytAssist_Fresh_Frozen_Human_Breast_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/100w1__10X__Visium__Human__prostate__20210727__v1.3.0/100w1_to_zarr.py b/data/100w1__10X__Visium__Human__prostate__20210727__v1.3.0/100w1_to_zarr.py index 777c9e8..5c65d5c 100644 --- a/data/100w1__10X__Visium__Human__prostate__20210727__v1.3.0/100w1_to_zarr.py +++ b/data/100w1__10X__Visium__Human__prostate__20210727__v1.3.0/100w1_to_zarr.py @@ -1,10 +1,11 @@ uid = "100w1_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_IF", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_IF_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/100wk__10X__Visium__Mouse__brain__20200623__v1.1.0/100wk_to_zarr.py b/data/100wk__10X__Visium__Mouse__brain__20200623__v1.1.0/100wk_to_zarr.py index fc4ae09..2a0f93e 100644 --- a/data/100wk__10X__Visium__Mouse__brain__20200623__v1.1.0/100wk_to_zarr.py +++ b/data/100wk__10X__Visium__Mouse__brain__20200623__v1.1.0/100wk_to_zarr.py @@ -1,10 +1,11 @@ uid = "100wk_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1012t__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/1012t_to_zarr.py b/data/1012t__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/1012t_to_zarr.py index 0b32223..f444c89 100644 --- a/data/1012t__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/1012t_to_zarr.py +++ b/data/1012t__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/1012t_to_zarr.py @@ -1,10 +1,11 @@ uid = "1012t_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_Cerebellum_Neuroscience", counts_file=str(path_read / "Targeted_Visium_Human_Cerebellum_Neuroscience_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1015d__10X__Xenium__Human__breast__20230418__v1.3.0__InputsSlide/1015d_to_zarr.py b/data/1015d__10X__Xenium__Human__breast__20230418__v1.3.0__InputsSlide/1015d_to_zarr.py index 99f1089..044a482 100644 --- a/data/1015d__10X__Xenium__Human__breast__20230418__v1.3.0__InputsSlide/1015d_to_zarr.py +++ b/data/1015d__10X__Xenium__Human__breast__20230418__v1.3.0__InputsSlide/1015d_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/101cw__10X__Visium__Human__spinal_cord__20201027__v1.2.0/101cw_to_zarr.py b/data/101cw__10X__Visium__Human__spinal_cord__20201027__v1.2.0/101cw_to_zarr.py index 65739a3..f714fe5 100644 --- a/data/101cw__10X__Visium__Human__spinal_cord__20201027__v1.2.0/101cw_to_zarr.py +++ b/data/101cw__10X__Visium__Human__spinal_cord__20201027__v1.2.0/101cw_to_zarr.py @@ -1,10 +1,11 @@ uid = "101cw_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_SpinalCord", counts_file=str(path_read / "Parent_Visium_Human_SpinalCord_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/101in__10X__Visium__Mouse__kidney__20200623__v1.1.0/101in_to_zarr.py b/data/101in__10X__Visium__Mouse__kidney__20200623__v1.1.0/101in_to_zarr.py index 25e2176..6e0a8be 100644 --- a/data/101in__10X__Visium__Mouse__kidney__20200623__v1.1.0/101in_to_zarr.py +++ b/data/101in__10X__Visium__Mouse__kidney__20200623__v1.1.0/101in_to_zarr.py @@ -1,10 +1,11 @@ uid = "101in_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Kidney", counts_file=str(path_read / "V1_Mouse_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/101s6__10X__Visium__Mouse__brain__20230417__v2.0.1/101s6_to_zarr.py b/data/101s6__10X__Visium__Mouse__brain__20230417__v2.0.1/101s6_to_zarr.py index c790dab..13ce2ad 100644 --- a/data/101s6__10X__Visium__Mouse__brain__20230417__v2.0.1/101s6_to_zarr.py +++ b/data/101s6__10X__Visium__Mouse__brain__20230417__v2.0.1/101s6_to_zarr.py @@ -1,10 +1,11 @@ uid = "101s6_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/101t3__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designed+add-onpanel/101t3_to_zarr.py b/data/101t3__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designed+add-onpanel/101t3_to_zarr.py index b7173fd..ad1ebb9 100644 --- a/data/101t3__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designed+add-onpanel/101t3_to_zarr.py +++ b/data/101t3__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designed+add-onpanel/101t3_to_zarr.py @@ -1,10 +1,11 @@ uid = "101t3_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/101tu__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate1/101tu_to_zarr.py b/data/101tu__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate1/101tu_to_zarr.py index fbced9a..0ae4093 100644 --- a/data/101tu__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate1/101tu_to_zarr.py +++ b/data/101tu__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate1/101tu_to_zarr.py @@ -1,10 +1,11 @@ uid = "101tu_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/101x5__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/101x5_to_zarr.py b/data/101x5__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/101x5_to_zarr.py index 2e670d3..60031aa 100644 --- a/data/101x5__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/101x5_to_zarr.py +++ b/data/101x5__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/101x5_to_zarr.py @@ -1,10 +1,11 @@ uid = "101x5_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1020c__10X__Visium__Mouse__brain__20191202__v1.0.0/1020c_to_zarr.py b/data/1020c__10X__Visium__Mouse__brain__20191202__v1.0.0/1020c_to_zarr.py index 66b9ce3..02c2198 100644 --- a/data/1020c__10X__Visium__Mouse__brain__20191202__v1.0.0/1020c_to_zarr.py +++ b/data/1020c__10X__Visium__Mouse__brain__20191202__v1.0.0/1020c_to_zarr.py @@ -1,10 +1,11 @@ uid = "1020c_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1020d__10X__Xenium__Human__tonsil__20240305__v1.9.0__Follicularlymphoidhyperplasia/1020d_to_zarr.py b/data/1020d__10X__Xenium__Human__tonsil__20240305__v1.9.0__Follicularlymphoidhyperplasia/1020d_to_zarr.py index 9fc7e9b..73a67df 100644 --- a/data/1020d__10X__Xenium__Human__tonsil__20240305__v1.9.0__Follicularlymphoidhyperplasia/1020d_to_zarr.py +++ b/data/1020d__10X__Xenium__Human__tonsil__20240305__v1.9.0__Follicularlymphoidhyperplasia/1020d_to_zarr.py @@ -1,10 +1,11 @@ uid = "1020d_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10224__10X__Visium__Mouse__brain__20191202__v1.0.0/10224_to_zarr.py b/data/10224__10X__Visium__Mouse__brain__20191202__v1.0.0/10224_to_zarr.py index 949f45f..06564ae 100644 --- a/data/10224__10X__Visium__Mouse__brain__20191202__v1.0.0/10224_to_zarr.py +++ b/data/10224__10X__Visium__Mouse__brain__20191202__v1.0.0/10224_to_zarr.py @@ -1,10 +1,11 @@ uid = "10224_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1025z__10X__Visium__Human__heart__20200623__v1.1.0/1025z_to_zarr.py b/data/1025z__10X__Visium__Human__heart__20200623__v1.1.0/1025z_to_zarr.py index e227f42..f07345f 100644 --- a/data/1025z__10X__Visium__Human__heart__20200623__v1.1.0/1025z_to_zarr.py +++ b/data/1025z__10X__Visium__Human__heart__20200623__v1.1.0/1025z_to_zarr.py @@ -1,10 +1,11 @@ uid = "1025z_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Heart", counts_file=str(path_read / "V1_Human_Heart_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/102cy__10X__Xenium__Human__skin__20230918__v1.6.0/102cy_to_zarr.py b/data/102cy__10X__Xenium__Human__skin__20230918__v1.6.0/102cy_to_zarr.py index 1f04e29..1a72652 100644 --- a/data/102cy__10X__Xenium__Human__skin__20230918__v1.6.0/102cy_to_zarr.py +++ b/data/102cy__10X__Xenium__Human__skin__20230918__v1.6.0/102cy_to_zarr.py @@ -1,10 +1,11 @@ uid = "102cy_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/102hp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate5/102hp_to_zarr.py b/data/102hp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate5/102hp_to_zarr.py index f8a882f..04a1be7 100644 --- a/data/102hp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate5/102hp_to_zarr.py +++ b/data/102hp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate5/102hp_to_zarr.py @@ -1,10 +1,11 @@ uid = "102hp_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep5", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep5_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1031a__10X__Visium__Mouse__kidney__20191202__v1.0.0/1031a_to_zarr.py b/data/1031a__10X__Visium__Mouse__kidney__20191202__v1.0.0/1031a_to_zarr.py index 82b1d77..9053b81 100644 --- a/data/1031a__10X__Visium__Mouse__kidney__20191202__v1.0.0/1031a_to_zarr.py +++ b/data/1031a__10X__Visium__Mouse__kidney__20191202__v1.0.0/1031a_to_zarr.py @@ -1,10 +1,11 @@ uid = "1031a_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Kidney", counts_file=str(path_read / "V1_Mouse_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1033x__10X__Visium__Human__breast__20201027__v1.2.0/1033x_to_zarr.py b/data/1033x__10X__Visium__Human__breast__20201027__v1.2.0/1033x_to_zarr.py index 8a9ec6c..a9032fa 100644 --- a/data/1033x__10X__Visium__Human__breast__20201027__v1.2.0/1033x_to_zarr.py +++ b/data/1033x__10X__Visium__Human__breast__20201027__v1.2.0/1033x_to_zarr.py @@ -1,10 +1,11 @@ uid = "1033x_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_BreastCancer_Immunology", counts_file=str(path_read / "Targeted_Visium_Human_BreastCancer_Immunology_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1039v__10X__Visium__Mouse__brain__20200623__v1.1.0/1039v_to_zarr.py b/data/1039v__10X__Visium__Mouse__brain__20200623__v1.1.0/1039v_to_zarr.py index 63cfd42..60323c6 100644 --- a/data/1039v__10X__Visium__Mouse__brain__20200623__v1.1.0/1039v_to_zarr.py +++ b/data/1039v__10X__Visium__Mouse__brain__20200623__v1.1.0/1039v_to_zarr.py @@ -1,10 +1,11 @@ uid = "1039v_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103da__10X__Visium__Mouse__brain__20220714__v2.0.0/103da_to_zarr.py b/data/103da__10X__Visium__Mouse__brain__20220714__v2.0.0/103da_to_zarr.py index 99f1089..044a482 100644 --- a/data/103da__10X__Visium__Mouse__brain__20220714__v2.0.0/103da_to_zarr.py +++ b/data/103da__10X__Visium__Mouse__brain__20220714__v2.0.0/103da_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/103mc__10X__Visium__Mouse__kidney__20210816__v1.3.0/103mc_to_zarr.py b/data/103mc__10X__Visium__Mouse__kidney__20210816__v1.3.0/103mc_to_zarr.py index 722b381..043caaa 100644 --- a/data/103mc__10X__Visium__Mouse__kidney__20210816__v1.3.0/103mc_to_zarr.py +++ b/data/103mc__10X__Visium__Mouse__kidney__20210816__v1.3.0/103mc_to_zarr.py @@ -1,10 +1,11 @@ uid = "103mc_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Mouse_Kidney", counts_file=str(path_read / "Visium_FFPE_Mouse_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103mf__10X__Xenium__Human__lymph_node__20230717__v1.5.0/103mf_to_zarr.py b/data/103mf__10X__Xenium__Human__lymph_node__20230717__v1.5.0/103mf_to_zarr.py index 7bedbb8..367565d 100644 --- a/data/103mf__10X__Xenium__Human__lymph_node__20230717__v1.5.0/103mf_to_zarr.py +++ b/data/103mf__10X__Xenium__Human__lymph_node__20230717__v1.5.0/103mf_to_zarr.py @@ -1,10 +1,11 @@ uid = "103mf_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103sf__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/103sf_to_zarr.py b/data/103sf__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/103sf_to_zarr.py index b6c6896..6321b40 100644 --- a/data/103sf__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/103sf_to_zarr.py +++ b/data/103sf__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/103sf_to_zarr.py @@ -1,10 +1,11 @@ uid = "103sf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Mouse_Olfactory_Bulb", counts_file=str(path_read / "Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103sm__10X__Visium__Mouse__brain__20200623__v1.1.0/103sm_to_zarr.py b/data/103sm__10X__Visium__Mouse__brain__20200623__v1.1.0/103sm_to_zarr.py index f7c70e7..8a6aeeb 100644 --- a/data/103sm__10X__Visium__Mouse__brain__20200623__v1.1.0/103sm_to_zarr.py +++ b/data/103sm__10X__Visium__Mouse__brain__20200623__v1.1.0/103sm_to_zarr.py @@ -1,10 +1,11 @@ uid = "103sm_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103te__10X__Visium__Mouse__brain__20200623__v1.1.0/103te_to_zarr.py b/data/103te__10X__Visium__Mouse__brain__20200623__v1.1.0/103te_to_zarr.py index d44debb..14df7d7 100644 --- a/data/103te__10X__Visium__Mouse__brain__20200623__v1.1.0/103te_to_zarr.py +++ b/data/103te__10X__Visium__Mouse__brain__20200623__v1.1.0/103te_to_zarr.py @@ -1,10 +1,11 @@ uid = "103te_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/103uy__10X__Visium__Mouse__brain__20230608__v2.1.0/103uy_to_zarr.py b/data/103uy__10X__Visium__Mouse__brain__20230608__v2.1.0/103uy_to_zarr.py index c4f123d..cd1eff5 100644 --- a/data/103uy__10X__Visium__Mouse__brain__20230608__v2.1.0/103uy_to_zarr.py +++ b/data/103uy__10X__Visium__Mouse__brain__20230608__v2.1.0/103uy_to_zarr.py @@ -1,10 +1,11 @@ uid = "103uy_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/104cz__10X__Xenium__Mouse__brain__20230122__v1.0.2__Tinysubset/104cz_to_zarr.py b/data/104cz__10X__Xenium__Mouse__brain__20230122__v1.0.2__Tinysubset/104cz_to_zarr.py index ab88c31..1c43eaa 100644 --- a/data/104cz__10X__Xenium__Mouse__brain__20230122__v1.0.2__Tinysubset/104cz_to_zarr.py +++ b/data/104cz__10X__Xenium__Mouse__brain__20230122__v1.0.2__Tinysubset/104cz_to_zarr.py @@ -1,10 +1,11 @@ uid = "104cz_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/104dm__10X__Visium__Mouse__brain__20200623__v1.1.0/104dm_to_zarr.py b/data/104dm__10X__Visium__Mouse__brain__20200623__v1.1.0/104dm_to_zarr.py index 8004eb1..da61297 100644 --- a/data/104dm__10X__Visium__Mouse__brain__20200623__v1.1.0/104dm_to_zarr.py +++ b/data/104dm__10X__Visium__Mouse__brain__20200623__v1.1.0/104dm_to_zarr.py @@ -1,10 +1,11 @@ uid = "104dm_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain_Coronal_Section_2", counts_file=str(path_read / "V1_Adult_Mouse_Brain_Coronal_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/104dy__10X__Xenium__unknown__unknown__20230420__v1.3.0__HealthyBrain/104dy_to_zarr.py b/data/104dy__10X__Xenium__unknown__unknown__20230420__v1.3.0__HealthyBrain/104dy_to_zarr.py index 3be9e7f..10bc3d2 100644 --- a/data/104dy__10X__Xenium__unknown__unknown__20230420__v1.3.0__HealthyBrain/104dy_to_zarr.py +++ b/data/104dy__10X__Xenium__unknown__unknown__20230420__v1.3.0__HealthyBrain/104dy_to_zarr.py @@ -1,10 +1,11 @@ uid = "104dy_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/104ee__10X__Visium__Human__brain__20200623__v1.1.0/104ee_to_zarr.py b/data/104ee__10X__Visium__Human__brain__20200623__v1.1.0/104ee_to_zarr.py index 9abaeaa..93248a2 100644 --- a/data/104ee__10X__Visium__Human__brain__20200623__v1.1.0/104ee_to_zarr.py +++ b/data/104ee__10X__Visium__Human__brain__20200623__v1.1.0/104ee_to_zarr.py @@ -1,10 +1,11 @@ uid = "104ee_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Brain_Section_2", counts_file=str(path_read / "V1_Human_Brain_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/104pe__10X__Visium__Mouse__brain__20220712__v2.0.0/104pe_to_zarr.py b/data/104pe__10X__Visium__Mouse__brain__20220712__v2.0.0/104pe_to_zarr.py index 586cbd3..d55e4e5 100644 --- a/data/104pe__10X__Visium__Mouse__brain__20220712__v2.0.0/104pe_to_zarr.py +++ b/data/104pe__10X__Visium__Mouse__brain__20220712__v2.0.0/104pe_to_zarr.py @@ -1,10 +1,11 @@ uid = "104pe_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105h4__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__InputsLibrary/105h4_to_zarr.py b/data/105h4__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__InputsLibrary/105h4_to_zarr.py index 99f1089..044a482 100644 --- a/data/105h4__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__InputsLibrary/105h4_to_zarr.py +++ b/data/105h4__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__InputsLibrary/105h4_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/105jc__10X__Visium__Human__lymph_node__20200623__v1.1.0/105jc_to_zarr.py b/data/105jc__10X__Visium__Human__lymph_node__20200623__v1.1.0/105jc_to_zarr.py index cee387d..620a281 100644 --- a/data/105jc__10X__Visium__Human__lymph_node__20200623__v1.1.0/105jc_to_zarr.py +++ b/data/105jc__10X__Visium__Human__lymph_node__20200623__v1.1.0/105jc_to_zarr.py @@ -1,10 +1,11 @@ uid = "105jc_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Lymph_Node", counts_file=str(path_read / "V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105k3__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate2/105k3_to_zarr.py b/data/105k3__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate2/105k3_to_zarr.py index dba56b9..ca45772 100644 --- a/data/105k3__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate2/105k3_to_zarr.py +++ b/data/105k3__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate2/105k3_to_zarr.py @@ -1,10 +1,11 @@ uid = "105k3_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2", counts_file=str(path_read / "CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105ka__10X__Visium__Human__breast__20191212__v1.0.0/105ka_to_zarr.py b/data/105ka__10X__Visium__Human__breast__20191212__v1.0.0/105ka_to_zarr.py index 8e50b3a..9d46fcc 100644 --- a/data/105ka__10X__Visium__Human__breast__20191212__v1.0.0/105ka_to_zarr.py +++ b/data/105ka__10X__Visium__Human__breast__20191212__v1.0.0/105ka_to_zarr.py @@ -1,10 +1,11 @@ uid = "105ka_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_1", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105tt__10X__Visium__Mouse__brain__20220712__v2.0.0/105tt_to_zarr.py b/data/105tt__10X__Visium__Mouse__brain__20220712__v2.0.0/105tt_to_zarr.py index 4368eff..7c0de9d 100644 --- a/data/105tt__10X__Visium__Mouse__brain__20220712__v2.0.0/105tt_to_zarr.py +++ b/data/105tt__10X__Visium__Mouse__brain__20220712__v2.0.0/105tt_to_zarr.py @@ -1,10 +1,11 @@ uid = "105tt_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105vj__10X__Visium__Human__lymph_node__20200623__v1.1.0/105vj_to_zarr.py b/data/105vj__10X__Visium__Human__lymph_node__20200623__v1.1.0/105vj_to_zarr.py index 92dc8af..f68b53c 100644 --- a/data/105vj__10X__Visium__Human__lymph_node__20200623__v1.1.0/105vj_to_zarr.py +++ b/data/105vj__10X__Visium__Human__lymph_node__20200623__v1.1.0/105vj_to_zarr.py @@ -1,10 +1,11 @@ uid = "105vj_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Lymph_Node", counts_file=str(path_read / "V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/105yf__10X__Visium__Mouse__kidney__20200623__v1.1.0/105yf_to_zarr.py b/data/105yf__10X__Visium__Mouse__kidney__20200623__v1.1.0/105yf_to_zarr.py index a7fb85c..4098fee 100644 --- a/data/105yf__10X__Visium__Mouse__kidney__20200623__v1.1.0/105yf_to_zarr.py +++ b/data/105yf__10X__Visium__Mouse__kidney__20200623__v1.1.0/105yf_to_zarr.py @@ -1,10 +1,11 @@ uid = "105yf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Kidney", counts_file=str(path_read / "V1_Mouse_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1063i__10X__Xenium__Human__kidney__20230717__v1.5.0__Non-diseasedKidney/1063i_to_zarr.py b/data/1063i__10X__Xenium__Human__kidney__20230717__v1.5.0__Non-diseasedKidney/1063i_to_zarr.py index d5f6952..39d0023 100644 --- a/data/1063i__10X__Xenium__Human__kidney__20230717__v1.5.0__Non-diseasedKidney/1063i_to_zarr.py +++ b/data/1063i__10X__Xenium__Human__kidney__20230717__v1.5.0__Non-diseasedKidney/1063i_to_zarr.py @@ -1,10 +1,11 @@ uid = "1063i_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1065r__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate2/1065r_to_zarr.py b/data/1065r__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate2/1065r_to_zarr.py index 4f0c425..ac17e08 100644 --- a/data/1065r__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate2/1065r_to_zarr.py +++ b/data/1065r__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate2/1065r_to_zarr.py @@ -1,10 +1,11 @@ uid = "1065r_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Colon_Rep2", counts_file=str(path_read / "CytAssist_FFPE_Human_Colon_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10676__10X__Visium__Mouse__brain__20220712__v2.0.0/10676_to_zarr.py b/data/10676__10X__Visium__Mouse__brain__20220712__v2.0.0/10676_to_zarr.py index 9fbba97..315add3 100644 --- a/data/10676__10X__Visium__Mouse__brain__20220712__v2.0.0/10676_to_zarr.py +++ b/data/10676__10X__Visium__Mouse__brain__20220712__v2.0.0/10676_to_zarr.py @@ -1,10 +1,11 @@ uid = "10676_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106ip__10X__Visium__Human__brain__20230214__v2.0.1/106ip_to_zarr.py b/data/106ip__10X__Visium__Human__brain__20230214__v2.0.1/106ip_to_zarr.py index 525afb2..5ea98fc 100644 --- a/data/106ip__10X__Visium__Human__brain__20230214__v2.0.1/106ip_to_zarr.py +++ b/data/106ip__10X__Visium__Human__brain__20230214__v2.0.1/106ip_to_zarr.py @@ -1,10 +1,11 @@ uid = "106ip_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Human_Glioblastoma", counts_file=str(path_read / "CytAssist_11mm_FFPE_Human_Glioblastoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106ru__10X__Visium__Human__prostate__20220712__v2.0.0/106ru_to_zarr.py b/data/106ru__10X__Visium__Human__prostate__20220712__v2.0.0/106ru_to_zarr.py index add1414..0fdaa13 100644 --- a/data/106ru__10X__Visium__Human__prostate__20220712__v2.0.0/106ru_to_zarr.py +++ b/data/106ru__10X__Visium__Human__prostate__20220712__v2.0.0/106ru_to_zarr.py @@ -1,10 +1,11 @@ uid = "106ru_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_IF", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_IF_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106s5__10X__Visium__Mouse__brain__20230608__v2.1.0/106s5_to_zarr.py b/data/106s5__10X__Visium__Mouse__brain__20230608__v2.1.0/106s5_to_zarr.py index 1b683a6..4151df4 100644 --- a/data/106s5__10X__Visium__Mouse__brain__20230608__v2.1.0/106s5_to_zarr.py +++ b/data/106s5__10X__Visium__Mouse__brain__20230608__v2.1.0/106s5_to_zarr.py @@ -1,10 +1,11 @@ uid = "106s5_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106v2__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/106v2_to_zarr.py b/data/106v2__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/106v2_to_zarr.py index e3c17f4..c869aa0 100644 --- a/data/106v2__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/106v2_to_zarr.py +++ b/data/106v2__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/106v2_to_zarr.py @@ -1,10 +1,11 @@ uid = "106v2_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Mouse_Olfactory_Bulb", counts_file=str(path_read / "Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106ws__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype13.4months/106ws_to_zarr.py b/data/106ws__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype13.4months/106ws_to_zarr.py index a80e11f..c7a7779 100644 --- a/data/106ws__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype13.4months/106ws_to_zarr.py +++ b/data/106ws__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype13.4months/106ws_to_zarr.py @@ -1,10 +1,11 @@ uid = "106ws_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/106xa__10X__Xenium__Mouse__bone__20240403__v1.9.0__10Formicaciddecalcification/106xa_to_zarr.py b/data/106xa__10X__Xenium__Mouse__bone__20240403__v1.9.0__10Formicaciddecalcification/106xa_to_zarr.py index 45528ae..ef5db40 100644 --- a/data/106xa__10X__Xenium__Mouse__bone__20240403__v1.9.0__10Formicaciddecalcification/106xa_to_zarr.py +++ b/data/106xa__10X__Xenium__Mouse__bone__20240403__v1.9.0__10Formicaciddecalcification/106xa_to_zarr.py @@ -1,10 +1,11 @@ uid = "106xa_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1074f__10X__Xenium__Human__liver__20240305__v1.9.0__Non-diseased/1074f_to_zarr.py b/data/1074f__10X__Xenium__Human__liver__20240305__v1.9.0__Non-diseased/1074f_to_zarr.py index 494d4a4..c76492a 100644 --- a/data/1074f__10X__Xenium__Human__liver__20240305__v1.9.0__Non-diseased/1074f_to_zarr.py +++ b/data/1074f__10X__Xenium__Human__liver__20240305__v1.9.0__Non-diseased/1074f_to_zarr.py @@ -1,10 +1,11 @@ uid = "1074f_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/107rk__10X__Visium__Mouse__brain__20221018__v2.0.0/107rk_to_zarr.py b/data/107rk__10X__Visium__Mouse__brain__20221018__v2.0.0/107rk_to_zarr.py index 6b38889..efdbaf3 100644 --- a/data/107rk__10X__Visium__Mouse__brain__20221018__v2.0.0/107rk_to_zarr.py +++ b/data/107rk__10X__Visium__Mouse__brain__20221018__v2.0.0/107rk_to_zarr.py @@ -1,10 +1,11 @@ uid = "107rk_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/107rw__10X__Visium__Mouse__brain__20200623__v1.1.0/107rw_to_zarr.py b/data/107rw__10X__Visium__Mouse__brain__20200623__v1.1.0/107rw_to_zarr.py index e4ddd3c..737d41b 100644 --- a/data/107rw__10X__Visium__Mouse__brain__20200623__v1.1.0/107rw_to_zarr.py +++ b/data/107rw__10X__Visium__Mouse__brain__20200623__v1.1.0/107rw_to_zarr.py @@ -1,10 +1,11 @@ uid = "107rw_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/107sr__10X__Xenium__Human__lung__20230717__v1.5.0/107sr_to_zarr.py b/data/107sr__10X__Xenium__Human__lung__20230717__v1.5.0/107sr_to_zarr.py index c73d760..de0c3b4 100644 --- a/data/107sr__10X__Xenium__Human__lung__20230717__v1.5.0/107sr_to_zarr.py +++ b/data/107sr__10X__Xenium__Human__lung__20230717__v1.5.0/107sr_to_zarr.py @@ -1,10 +1,11 @@ uid = "107sr_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/107yk__10X__Xenium__Human__pancreas__20230717__v1.5.0/107yk_to_zarr.py b/data/107yk__10X__Xenium__Human__pancreas__20230717__v1.5.0/107yk_to_zarr.py index 551926b..3631fd7 100644 --- a/data/107yk__10X__Xenium__Human__pancreas__20230717__v1.5.0/107yk_to_zarr.py +++ b/data/107yk__10X__Xenium__Human__pancreas__20230717__v1.5.0/107yk_to_zarr.py @@ -1,10 +1,11 @@ uid = "107yk_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/107z9__10X__VisiumHD__Human__colon__20240325__v3.0.0/107z9_to_zarr.py b/data/107z9__10X__VisiumHD__Human__colon__20240325__v3.0.0/107z9_to_zarr.py index 99f1089..044a482 100644 --- a/data/107z9__10X__VisiumHD__Human__colon__20240325__v3.0.0/107z9_to_zarr.py +++ b/data/107z9__10X__VisiumHD__Human__colon__20240325__v3.0.0/107z9_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10817__10X__Visium__Mouse__brain__20191202__v1.0.0/10817_to_zarr.py b/data/10817__10X__Visium__Mouse__brain__20191202__v1.0.0/10817_to_zarr.py index 51ee894..be9b581 100644 --- a/data/10817__10X__Visium__Mouse__brain__20191202__v1.0.0/10817_to_zarr.py +++ b/data/10817__10X__Visium__Mouse__brain__20191202__v1.0.0/10817_to_zarr.py @@ -1,10 +1,11 @@ uid = "10817_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10834__10X__Visium__Mouse__brain__20220713__v2.0.0/10834_to_zarr.py b/data/10834__10X__Visium__Mouse__brain__20220713__v2.0.0/10834_to_zarr.py index ead4fdc..bbd0c45 100644 --- a/data/10834__10X__Visium__Mouse__brain__20220713__v2.0.0/10834_to_zarr.py +++ b/data/10834__10X__Visium__Mouse__brain__20220713__v2.0.0/10834_to_zarr.py @@ -1,10 +1,11 @@ uid = "10834_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_Brain_Rep2", counts_file=str(path_read / "CytAssist_FFPE_Mouse_Brain_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108d3__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype5.7months/108d3_to_zarr.py b/data/108d3__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype5.7months/108d3_to_zarr.py index 36a6f22..3079fd3 100644 --- a/data/108d3__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype5.7months/108d3_to_zarr.py +++ b/data/108d3__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype5.7months/108d3_to_zarr.py @@ -1,10 +1,11 @@ uid = "108d3_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108dr__10X__Xenium__Human__liver__20240305__v1.9.0__Livercancer/108dr_to_zarr.py b/data/108dr__10X__Xenium__Human__liver__20240305__v1.9.0__Livercancer/108dr_to_zarr.py index 80dddfd..9c9c407 100644 --- a/data/108dr__10X__Xenium__Human__liver__20240305__v1.9.0__Livercancer/108dr_to_zarr.py +++ b/data/108dr__10X__Xenium__Human__liver__20240305__v1.9.0__Livercancer/108dr_to_zarr.py @@ -1,10 +1,11 @@ uid = "108dr_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108h0__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate3/108h0_to_zarr.py b/data/108h0__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate3/108h0_to_zarr.py index 5f8537e..aaf4f82 100644 --- a/data/108h0__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate3/108h0_to_zarr.py +++ b/data/108h0__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate3/108h0_to_zarr.py @@ -1,10 +1,11 @@ uid = "108h0_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108r9__10X__Visium__Human__breast__20200623__v1.1.0/108r9_to_zarr.py b/data/108r9__10X__Visium__Human__breast__20200623__v1.1.0/108r9_to_zarr.py index 9a330b9..66397b5 100644 --- a/data/108r9__10X__Visium__Human__breast__20200623__v1.1.0/108r9_to_zarr.py +++ b/data/108r9__10X__Visium__Human__breast__20200623__v1.1.0/108r9_to_zarr.py @@ -1,10 +1,11 @@ uid = "108r9_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_1", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108rf__10X__Visium__Human__ovary__20220714__v2.0.0/108rf_to_zarr.py b/data/108rf__10X__Visium__Human__ovary__20220714__v2.0.0/108rf_to_zarr.py index 5fdd0ec..065e991 100644 --- a/data/108rf__10X__Visium__Human__ovary__20220714__v2.0.0/108rf_to_zarr.py +++ b/data/108rf__10X__Visium__Human__ovary__20220714__v2.0.0/108rf_to_zarr.py @@ -1,10 +1,11 @@ uid = "108rf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Human_Ovarian_Carcinoma", counts_file=str(path_read / "CytAssist_11mm_FFPE_Human_Ovarian_Carcinoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108ty__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate1/108ty_to_zarr.py b/data/108ty__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate1/108ty_to_zarr.py index 783cdfc..f7304b8 100644 --- a/data/108ty__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate1/108ty_to_zarr.py +++ b/data/108ty__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate1/108ty_to_zarr.py @@ -1,10 +1,11 @@ uid = "108ty_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep1", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/108x2__10X__VisiumHD__Mouse__brain__20240329__v3.0.0/108x2_to_zarr.py b/data/108x2__10X__VisiumHD__Mouse__brain__20240329__v3.0.0/108x2_to_zarr.py index 99f1089..044a482 100644 --- a/data/108x2__10X__VisiumHD__Mouse__brain__20240329__v3.0.0/108x2_to_zarr.py +++ b/data/108x2__10X__VisiumHD__Mouse__brain__20240329__v3.0.0/108x2_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/1090h__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate4/1090h_to_zarr.py b/data/1090h__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate4/1090h_to_zarr.py index e99e464..9a83856 100644 --- a/data/1090h__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate4/1090h_to_zarr.py +++ b/data/1090h__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate4/1090h_to_zarr.py @@ -1,10 +1,11 @@ uid = "1090h_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep4", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep4_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1091x__10X__Xenium__unknown__unknown__20230420__v1.3.0__Glioblastoma/1091x_to_zarr.py b/data/1091x__10X__Xenium__unknown__unknown__20230420__v1.3.0__Glioblastoma/1091x_to_zarr.py index 406ff96..d63bcd7 100644 --- a/data/1091x__10X__Xenium__unknown__unknown__20230420__v1.3.0__Glioblastoma/1091x_to_zarr.py +++ b/data/1091x__10X__Xenium__unknown__unknown__20230420__v1.3.0__Glioblastoma/1091x_to_zarr.py @@ -1,10 +1,11 @@ uid = "1091x_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1094t__10X__Visium__Mouse__kidney__20191202__v1.0.0/1094t_to_zarr.py b/data/1094t__10X__Visium__Mouse__kidney__20191202__v1.0.0/1094t_to_zarr.py index 5df7f72..4ad4fd4 100644 --- a/data/1094t__10X__Visium__Mouse__kidney__20191202__v1.0.0/1094t_to_zarr.py +++ b/data/1094t__10X__Visium__Mouse__kidney__20191202__v1.0.0/1094t_to_zarr.py @@ -1,10 +1,11 @@ uid = "1094t_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Kidney", counts_file=str(path_read / "V1_Mouse_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/1097y__10X__Visium__Human__breast__20191212__v1.0.0/1097y_to_zarr.py b/data/1097y__10X__Visium__Human__breast__20191212__v1.0.0/1097y_to_zarr.py index 99c7f74..fef4206 100644 --- a/data/1097y__10X__Visium__Human__breast__20191212__v1.0.0/1097y_to_zarr.py +++ b/data/1097y__10X__Visium__Human__breast__20191212__v1.0.0/1097y_to_zarr.py @@ -1,10 +1,11 @@ uid = "1097y_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_2", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/109k1__10X__Xenium__Human__lung__20230518__v1.3.0__LungCancer/109k1_to_zarr.py b/data/109k1__10X__Xenium__Human__lung__20230518__v1.3.0__LungCancer/109k1_to_zarr.py index a49b9f8..1a75078 100644 --- a/data/109k1__10X__Xenium__Human__lung__20230518__v1.3.0__LungCancer/109k1_to_zarr.py +++ b/data/109k1__10X__Xenium__Human__lung__20230518__v1.3.0__LungCancer/109k1_to_zarr.py @@ -1,10 +1,11 @@ uid = "109k1_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/109pp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate2/109pp_to_zarr.py b/data/109pp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate2/109pp_to_zarr.py index c17ee2f..f93b1ac 100644 --- a/data/109pp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate2/109pp_to_zarr.py +++ b/data/109pp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate2/109pp_to_zarr.py @@ -1,10 +1,11 @@ uid = "109pp_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep2", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/109zw__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/109zw_to_zarr.py b/data/109zw__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/109zw_to_zarr.py index ac23c18..fe3bb76 100644 --- a/data/109zw__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/109zw_to_zarr.py +++ b/data/109zw__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/109zw_to_zarr.py @@ -1,10 +1,11 @@ uid = "109zw_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10a6w__10X__Visium__Mouse__brain__20191202__v1.0.0/10a6w_to_zarr.py b/data/10a6w__10X__Visium__Mouse__brain__20191202__v1.0.0/10a6w_to_zarr.py index 071d327..9f08334 100644 --- a/data/10a6w__10X__Visium__Mouse__brain__20191202__v1.0.0/10a6w_to_zarr.py +++ b/data/10a6w__10X__Visium__Mouse__brain__20191202__v1.0.0/10a6w_to_zarr.py @@ -1,10 +1,11 @@ uid = "10a6w_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Adult_Mouse_Brain", counts_file=str(path_read / "Visium_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10a7t__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10a7t_to_zarr.py b/data/10a7t__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10a7t_to_zarr.py index 99f1089..044a482 100644 --- a/data/10a7t__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10a7t_to_zarr.py +++ b/data/10a7t__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10a7t_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10ae2__10X__Xenium__Human__skin__20240305__v1.9.0__Sample2/10ae2_to_zarr.py b/data/10ae2__10X__Xenium__Human__skin__20240305__v1.9.0__Sample2/10ae2_to_zarr.py index 0472f7b..6486338 100644 --- a/data/10ae2__10X__Xenium__Human__skin__20240305__v1.9.0__Sample2/10ae2_to_zarr.py +++ b/data/10ae2__10X__Xenium__Human__skin__20240305__v1.9.0__Sample2/10ae2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ae2_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ah4__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designedpanel/10ah4_to_zarr.py b/data/10ah4__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designedpanel/10ah4_to_zarr.py index 2fe7a36..40f1bfa 100644 --- a/data/10ah4__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designedpanel/10ah4_to_zarr.py +++ b/data/10ah4__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designedpanel/10ah4_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ah4_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ake__10X__Visium__Mouse__brain__20230106__v2.0.1/10ake_to_zarr.py b/data/10ake__10X__Visium__Mouse__brain__20230106__v2.0.1/10ake_to_zarr.py index 6dd558f..bda8451 100644 --- a/data/10ake__10X__Visium__Mouse__brain__20230106__v2.0.1/10ake_to_zarr.py +++ b/data/10ake__10X__Visium__Mouse__brain__20230106__v2.0.1/10ake_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ake_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_Fresh_Frozen_Mouse_Brain", counts_file=str(path_read / "CytAssist_Fresh_Frozen_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10amj__10X__Visium__Mouse__brain__20200623__v1.1.0/10amj_to_zarr.py b/data/10amj__10X__Visium__Mouse__brain__20200623__v1.1.0/10amj_to_zarr.py index 252f81e..10d5c95 100644 --- a/data/10amj__10X__Visium__Mouse__brain__20200623__v1.1.0/10amj_to_zarr.py +++ b/data/10amj__10X__Visium__Mouse__brain__20200623__v1.1.0/10amj_to_zarr.py @@ -1,10 +1,11 @@ uid = "10amj_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ant__10X__Visium__Mouse__brain__20230417__v2.0.1/10ant_to_zarr.py b/data/10ant__10X__Visium__Mouse__brain__20230417__v2.0.1/10ant_to_zarr.py index c7cf9ea..6bbd9a5 100644 --- a/data/10ant__10X__Visium__Mouse__brain__20230417__v2.0.1/10ant_to_zarr.py +++ b/data/10ant__10X__Visium__Mouse__brain__20230417__v2.0.1/10ant_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ant_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_FFPE_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10arp__10X__Xenium__Human__tonsil__20240305__v1.9.0__Reactivefollicularhyperplasia/10arp_to_zarr.py b/data/10arp__10X__Xenium__Human__tonsil__20240305__v1.9.0__Reactivefollicularhyperplasia/10arp_to_zarr.py index 5f7de3d..838ff61 100644 --- a/data/10arp__10X__Xenium__Human__tonsil__20240305__v1.9.0__Reactivefollicularhyperplasia/10arp_to_zarr.py +++ b/data/10arp__10X__Xenium__Human__tonsil__20240305__v1.9.0__Reactivefollicularhyperplasia/10arp_to_zarr.py @@ -1,10 +1,11 @@ uid = "10arp_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10c6u__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate2/10c6u_to_zarr.py b/data/10c6u__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate2/10c6u_to_zarr.py index 8246dad..c584a29 100644 --- a/data/10c6u__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate2/10c6u_to_zarr.py +++ b/data/10c6u__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate2/10c6u_to_zarr.py @@ -1,10 +1,11 @@ uid = "10c6u_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10caf__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate1/10caf_to_zarr.py b/data/10caf__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate1/10caf_to_zarr.py index c21e28a..5903151 100644 --- a/data/10caf__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate1/10caf_to_zarr.py +++ b/data/10caf__10X__Visium__Mouse__brain__20231005__v2.1.0__Post-XeniumReplicate1/10caf_to_zarr.py @@ -1,10 +1,11 @@ uid = "10caf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep1", counts_file=str(path_read / "CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ci4__10X__Visium__Mouse__brain__20200623__v1.1.0/10ci4_to_zarr.py b/data/10ci4__10X__Visium__Mouse__brain__20200623__v1.1.0/10ci4_to_zarr.py index fdebd75..ab3051f 100644 --- a/data/10ci4__10X__Visium__Mouse__brain__20200623__v1.1.0/10ci4_to_zarr.py +++ b/data/10ci4__10X__Visium__Mouse__brain__20200623__v1.1.0/10ci4_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ci4_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ckr__10X__Visium__Mouse__brain__20230525__v2.1.0/10ckr_to_zarr.py b/data/10ckr__10X__Visium__Mouse__brain__20230525__v2.1.0/10ckr_to_zarr.py index d06f7f0..777a5d8 100644 --- a/data/10ckr__10X__Visium__Mouse__brain__20230525__v2.1.0/10ckr_to_zarr.py +++ b/data/10ckr__10X__Visium__Mouse__brain__20230525__v2.1.0/10ckr_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ckr_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10d9e__10X__Visium__Mouse__brain__20221018__v2.0.0/10d9e_to_zarr.py b/data/10d9e__10X__Visium__Mouse__brain__20221018__v2.0.0/10d9e_to_zarr.py index 7065a48..cc07c9e 100644 --- a/data/10d9e__10X__Visium__Mouse__brain__20221018__v2.0.0/10d9e_to_zarr.py +++ b/data/10d9e__10X__Visium__Mouse__brain__20221018__v2.0.0/10d9e_to_zarr.py @@ -1,10 +1,11 @@ uid = "10d9e_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Fresh_Frozen_Adult_Mouse_Brain", counts_file=str(path_read / "Visium_Fresh_Frozen_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10dcv__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/10dcv_to_zarr.py b/data/10dcv__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/10dcv_to_zarr.py index b138f3c..19fb627 100644 --- a/data/10dcv__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/10dcv_to_zarr.py +++ b/data/10dcv__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample1/10dcv_to_zarr.py @@ -1,10 +1,11 @@ uid = "10dcv_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10drc__10X__Visium__Human__colorectal__20230214__v2.0.1/10drc_to_zarr.py b/data/10drc__10X__Visium__Human__colorectal__20230214__v2.0.1/10drc_to_zarr.py index cef49bd..b25bdee 100644 --- a/data/10drc__10X__Visium__Human__colorectal__20230214__v2.0.1/10drc_to_zarr.py +++ b/data/10drc__10X__Visium__Human__colorectal__20230214__v2.0.1/10drc_to_zarr.py @@ -1,10 +1,11 @@ uid = "10drc_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Human_Colorectal_Cancer", counts_file=str(path_read / "CytAssist_11mm_FFPE_Human_Colorectal_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10dvd__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10dvd_to_zarr.py b/data/10dvd__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10dvd_to_zarr.py index 99f1089..044a482 100644 --- a/data/10dvd__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10dvd_to_zarr.py +++ b/data/10dvd__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10dvd_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10e4w__10X__Visium__Mouse__kidney_brain__20230221__v2.0.1/10e4w_to_zarr.py b/data/10e4w__10X__Visium__Mouse__kidney_brain__20230221__v2.0.1/10e4w_to_zarr.py index 7ba83e2..3b3904c 100644 --- a/data/10e4w__10X__Visium__Mouse__kidney_brain__20230221__v2.0.1/10e4w_to_zarr.py +++ b/data/10e4w__10X__Visium__Mouse__kidney_brain__20230221__v2.0.1/10e4w_to_zarr.py @@ -1,10 +1,11 @@ uid = "10e4w_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Mouse_TMA_5x5_1mm", counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_TMA_5x5_1mm_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10e4x__10X__Visium__Mouse__embryo__20220714__v2.0.0/10e4x_to_zarr.py b/data/10e4x__10X__Visium__Mouse__embryo__20220714__v2.0.0/10e4x_to_zarr.py index 4cbe86b..a71780d 100644 --- a/data/10e4x__10X__Visium__Mouse__embryo__20220714__v2.0.0/10e4x_to_zarr.py +++ b/data/10e4x__10X__Visium__Mouse__embryo__20220714__v2.0.0/10e4x_to_zarr.py @@ -1,10 +1,11 @@ uid = "10e4x_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Mouse_Embryo", counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_Embryo_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10e5i__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate1/10e5i_to_zarr.py b/data/10e5i__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate1/10e5i_to_zarr.py index dd67436..68fad08 100644 --- a/data/10e5i__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate1/10e5i_to_zarr.py +++ b/data/10e5i__10X__Visium__Human__colon__20231005__v2.1.0__ControlReplicate1/10e5i_to_zarr.py @@ -1,10 +1,11 @@ uid = "10e5i_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Colon_Rep1", counts_file=str(path_read / "CytAssist_FFPE_Human_Colon_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10e9s__10X__Visium__Human__heart__20200623__v1.1.0/10e9s_to_zarr.py b/data/10e9s__10X__Visium__Human__heart__20200623__v1.1.0/10e9s_to_zarr.py index ee281f0..19d326b 100644 --- a/data/10e9s__10X__Visium__Human__heart__20200623__v1.1.0/10e9s_to_zarr.py +++ b/data/10e9s__10X__Visium__Human__heart__20200623__v1.1.0/10e9s_to_zarr.py @@ -1,10 +1,11 @@ uid = "10e9s_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Heart", counts_file=str(path_read / "V1_Human_Heart_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ekd__10X__CytAssist__Human__tonsil__20230515__v2.1.0/10ekd_to_zarr.py b/data/10ekd__10X__CytAssist__Human__tonsil__20230515__v2.1.0/10ekd_to_zarr.py index 727d0ca..e2c21cf 100644 --- a/data/10ekd__10X__CytAssist__Human__tonsil__20230515__v2.1.0/10ekd_to_zarr.py +++ b/data/10ekd__10X__CytAssist__Human__tonsil__20230515__v2.1.0/10ekd_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ekd_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Protein_Expression_Human_Tonsil", counts_file=str(path_read / "CytAssist_FFPE_Protein_Expression_Human_Tonsil_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10etk__10X__Visium__Human__cerebellum__20220712__v2.0.0/10etk_to_zarr.py b/data/10etk__10X__Visium__Human__cerebellum__20220712__v2.0.0/10etk_to_zarr.py index 5b0d018..1e2dd95 100644 --- a/data/10etk__10X__Visium__Human__cerebellum__20220712__v2.0.0/10etk_to_zarr.py +++ b/data/10etk__10X__Visium__Human__cerebellum__20220712__v2.0.0/10etk_to_zarr.py @@ -1,10 +1,11 @@ uid = "10etk_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_Cerebellum_Neuroscience", counts_file=str(path_read / "Targeted_Visium_Human_Cerebellum_Neuroscience_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10evh__10X__Visium__Human__breast__20200623__v1.1.0/10evh_to_zarr.py b/data/10evh__10X__Visium__Human__breast__20200623__v1.1.0/10evh_to_zarr.py index 0cd00be..b64d09f 100644 --- a/data/10evh__10X__Visium__Human__breast__20200623__v1.1.0/10evh_to_zarr.py +++ b/data/10evh__10X__Visium__Human__breast__20200623__v1.1.0/10evh_to_zarr.py @@ -1,10 +1,11 @@ uid = "10evh_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_2", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10f2z__10X__Visium__Human__prostate__20211008__v1.3.0/10f2z_to_zarr.py b/data/10f2z__10X__Visium__Human__prostate__20211008__v1.3.0/10f2z_to_zarr.py index 5decfa0..1f40c7c 100644 --- a/data/10f2z__10X__Visium__Human__prostate__20211008__v1.3.0/10f2z_to_zarr.py +++ b/data/10f2z__10X__Visium__Human__prostate__20211008__v1.3.0/10f2z_to_zarr.py @@ -1,10 +1,11 @@ uid = "10f2z_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fc7__10X__Visium__Mouse__brain__20200623__v1.1.0/10fc7_to_zarr.py b/data/10fc7__10X__Visium__Mouse__brain__20200623__v1.1.0/10fc7_to_zarr.py index a6359ff..a346731 100644 --- a/data/10fc7__10X__Visium__Mouse__brain__20200623__v1.1.0/10fc7_to_zarr.py +++ b/data/10fc7__10X__Visium__Mouse__brain__20200623__v1.1.0/10fc7_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fc7_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fmm__10X__Visium__Human__breast__20200623__v1.1.0/10fmm_to_zarr.py b/data/10fmm__10X__Visium__Human__breast__20200623__v1.1.0/10fmm_to_zarr.py index e6d7eee..e4854b0 100644 --- a/data/10fmm__10X__Visium__Human__breast__20200623__v1.1.0/10fmm_to_zarr.py +++ b/data/10fmm__10X__Visium__Human__breast__20200623__v1.1.0/10fmm_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fmm_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_2", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fn9__10X__Visium__Mouse__brain__20200623__v1.1.0/10fn9_to_zarr.py b/data/10fn9__10X__Visium__Mouse__brain__20200623__v1.1.0/10fn9_to_zarr.py index a866404..52fc5d3 100644 --- a/data/10fn9__10X__Visium__Mouse__brain__20200623__v1.1.0/10fn9_to_zarr.py +++ b/data/10fn9__10X__Visium__Mouse__brain__20200623__v1.1.0/10fn9_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fn9_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fna__10X__Visium__Mouse__brain__20191202__v1.0.0/10fna_to_zarr.py b/data/10fna__10X__Visium__Mouse__brain__20191202__v1.0.0/10fna_to_zarr.py index 46a9b95..3fefe53 100644 --- a/data/10fna__10X__Visium__Mouse__brain__20191202__v1.0.0/10fna_to_zarr.py +++ b/data/10fna__10X__Visium__Mouse__brain__20191202__v1.0.0/10fna_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fna_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fpp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND85.7months/10fpp_to_zarr.py b/data/10fpp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND85.7months/10fpp_to_zarr.py index 4841b4d..cff15d6 100644 --- a/data/10fpp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND85.7months/10fpp_to_zarr.py +++ b/data/10fpp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND85.7months/10fpp_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fpp_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fri__10X__Xenium__Human__lung__20230518__v1.3.0__Non-diseasedLung/10fri_to_zarr.py b/data/10fri__10X__Xenium__Human__lung__20230518__v1.3.0__Non-diseasedLung/10fri_to_zarr.py index 38999b5..41f7e3d 100644 --- a/data/10fri__10X__Xenium__Human__lung__20230518__v1.3.0__Non-diseasedLung/10fri_to_zarr.py +++ b/data/10fri__10X__Xenium__Human__lung__20230518__v1.3.0__Non-diseasedLung/10fri_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fri_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fty__10X__Visium__Human__breast__20200623__v1.1.0/10fty_to_zarr.py b/data/10fty__10X__Visium__Human__breast__20200623__v1.1.0/10fty_to_zarr.py index e0ee39a..7f9c9f9 100644 --- a/data/10fty__10X__Visium__Human__breast__20200623__v1.1.0/10fty_to_zarr.py +++ b/data/10fty__10X__Visium__Human__breast__20200623__v1.1.0/10fty_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fty_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_1", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10fyx__10X__Xenium__Human__pancreas__20231116__v1.6.0/10fyx_to_zarr.py b/data/10fyx__10X__Xenium__Human__pancreas__20231116__v1.6.0/10fyx_to_zarr.py index ca070cd..80232da 100644 --- a/data/10fyx__10X__Xenium__Human__pancreas__20231116__v1.6.0/10fyx_to_zarr.py +++ b/data/10fyx__10X__Xenium__Human__pancreas__20231116__v1.6.0/10fyx_to_zarr.py @@ -1,10 +1,11 @@ uid = "10fyx_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10h3h__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10h3h_to_zarr.py b/data/10h3h__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10h3h_to_zarr.py index 99f1089..044a482 100644 --- a/data/10h3h__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10h3h_to_zarr.py +++ b/data/10h3h__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10h3h_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10ha9__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate2/10ha9_to_zarr.py b/data/10ha9__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate2/10ha9_to_zarr.py index 3bd7622..66d443b 100644 --- a/data/10ha9__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate2/10ha9_to_zarr.py +++ b/data/10ha9__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate2/10ha9_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ha9_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FreshFrozen_Mouse_Brain_Rep2", counts_file=str(path_read / "CytAssist_FreshFrozen_Mouse_Brain_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10hay__10X__Visium__Human__heart__20191212__v1.0.0/10hay_to_zarr.py b/data/10hay__10X__Visium__Human__heart__20191212__v1.0.0/10hay_to_zarr.py index b77ff9e..91ca77c 100644 --- a/data/10hay__10X__Visium__Human__heart__20191212__v1.0.0/10hay_to_zarr.py +++ b/data/10hay__10X__Visium__Human__heart__20191212__v1.0.0/10hay_to_zarr.py @@ -1,10 +1,11 @@ uid = "10hay_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Heart", counts_file=str(path_read / "V1_Human_Heart_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10hhx__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND817.9months/10hhx_to_zarr.py b/data/10hhx__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND817.9months/10hhx_to_zarr.py index b872c95..e4f9324 100644 --- a/data/10hhx__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND817.9months/10hhx_to_zarr.py +++ b/data/10hhx__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND817.9months/10hhx_to_zarr.py @@ -1,10 +1,11 @@ uid = "10hhx_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10hm6__10X__Visium__Human__cervix__20220328__v1.3.0/10hm6_to_zarr.py b/data/10hm6__10X__Visium__Human__cervix__20220328__v1.3.0/10hm6_to_zarr.py index ff55037..c35edef 100644 --- a/data/10hm6__10X__Visium__Human__cervix__20220328__v1.3.0/10hm6_to_zarr.py +++ b/data/10hm6__10X__Visium__Human__cervix__20220328__v1.3.0/10hm6_to_zarr.py @@ -1,10 +1,11 @@ uid = "10hm6_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Cervical_Cancer", counts_file=str(path_read / "Visium_FFPE_Human_Cervical_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10hmw__10X__Visium__Mouse__brain__20191202__v1.0.0/10hmw_to_zarr.py b/data/10hmw__10X__Visium__Mouse__brain__20191202__v1.0.0/10hmw_to_zarr.py index b27e5b1..02b3fed 100644 --- a/data/10hmw__10X__Visium__Mouse__brain__20191202__v1.0.0/10hmw_to_zarr.py +++ b/data/10hmw__10X__Visium__Mouse__brain__20191202__v1.0.0/10hmw_to_zarr.py @@ -1,10 +1,11 @@ uid = "10hmw_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10huw__10X__Visium__Mouse__brain__20191202__v1.0.0/10huw_to_zarr.py b/data/10huw__10X__Visium__Mouse__brain__20191202__v1.0.0/10huw_to_zarr.py index 9b9fecc..0a5c081 100644 --- a/data/10huw__10X__Visium__Mouse__brain__20191202__v1.0.0/10huw_to_zarr.py +++ b/data/10huw__10X__Visium__Mouse__brain__20191202__v1.0.0/10huw_to_zarr.py @@ -1,10 +1,11 @@ uid = "10huw_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10hxz__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10hxz_to_zarr.py b/data/10hxz__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10hxz_to_zarr.py index 41615a1..26e12cd 100644 --- a/data/10hxz__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10hxz_to_zarr.py +++ b/data/10hxz__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10hxz_to_zarr.py @@ -1,10 +1,11 @@ uid = "10hxz_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_Cerebellum_Neuroscience", counts_file=str(path_read / "Targeted_Visium_Human_Cerebellum_Neuroscience_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10i70__10X__Xenium__Human__pancreas__20240319__v2.0.0/10i70_to_zarr.py b/data/10i70__10X__Xenium__Human__pancreas__20240319__v2.0.0/10i70_to_zarr.py index 66599aa..87afaeb 100644 --- a/data/10i70__10X__Xenium__Human__pancreas__20240319__v2.0.0/10i70_to_zarr.py +++ b/data/10i70__10X__Xenium__Human__pancreas__20240319__v2.0.0/10i70_to_zarr.py @@ -1,10 +1,11 @@ uid = "10i70_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10i8s__10X__Visium__Mouse__brain__20191202__v1.0.0/10i8s_to_zarr.py b/data/10i8s__10X__Visium__Mouse__brain__20191202__v1.0.0/10i8s_to_zarr.py index b0b0dad..000244f 100644 --- a/data/10i8s__10X__Visium__Mouse__brain__20191202__v1.0.0/10i8s_to_zarr.py +++ b/data/10i8s__10X__Visium__Mouse__brain__20191202__v1.0.0/10i8s_to_zarr.py @@ -1,10 +1,11 @@ uid = "10i8s_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ieh__10X__Visium__Human__skin__20220713__v2.0.0/10ieh_to_zarr.py b/data/10ieh__10X__Visium__Human__skin__20220713__v2.0.0/10ieh_to_zarr.py index 82c347e..257dfc6 100644 --- a/data/10ieh__10X__Visium__Human__skin__20220713__v2.0.0/10ieh_to_zarr.py +++ b/data/10ieh__10X__Visium__Human__skin__20220713__v2.0.0/10ieh_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ieh_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Skin_Melanoma", counts_file=str(path_read / "CytAssist_FFPE_Human_Skin_Melanoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10if2__10X__CytAssist__Human__breast__20230515__v2.1.0/10if2_to_zarr.py b/data/10if2__10X__CytAssist__Human__breast__20230515__v2.1.0/10if2_to_zarr.py index 77a41d2..c8e14c4 100644 --- a/data/10if2__10X__CytAssist__Human__breast__20230515__v2.1.0/10if2_to_zarr.py +++ b/data/10if2__10X__CytAssist__Human__breast__20230515__v2.1.0/10if2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10if2_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer", counts_file=str(path_read / "CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10iky__10X__Visium__Human__kidney__20230214__v2.0.1/10iky_to_zarr.py b/data/10iky__10X__Visium__Human__kidney__20230214__v2.0.1/10iky_to_zarr.py index 2245144..88ff399 100644 --- a/data/10iky__10X__Visium__Human__kidney__20230214__v2.0.1/10iky_to_zarr.py +++ b/data/10iky__10X__Visium__Human__kidney__20230214__v2.0.1/10iky_to_zarr.py @@ -1,10 +1,11 @@ uid = "10iky_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Human_Kidney", counts_file=str(path_read / "CytAssist_11mm_FFPE_Human_Kidney_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ipu__10X__Visium__Mouse__brain__20220311__v1.3.1/10ipu_to_zarr.py b/data/10ipu__10X__Visium__Mouse__brain__20220311__v1.3.1/10ipu_to_zarr.py index 99f1089..044a482 100644 --- a/data/10ipu__10X__Visium__Mouse__brain__20220311__v1.3.1/10ipu_to_zarr.py +++ b/data/10ipu__10X__Visium__Mouse__brain__20220311__v1.3.1/10ipu_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10j0z__10X__Visium__Human__ovary__20201027__v1.2.0/10j0z_to_zarr.py b/data/10j0z__10X__Visium__Human__ovary__20201027__v1.2.0/10j0z_to_zarr.py index cbceb17..b55fd5d 100644 --- a/data/10j0z__10X__Visium__Human__ovary__20201027__v1.2.0/10j0z_to_zarr.py +++ b/data/10j0z__10X__Visium__Human__ovary__20201027__v1.2.0/10j0z_to_zarr.py @@ -1,10 +1,11 @@ uid = "10j0z_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_OvarianCancer_Immunology", counts_file=str(path_read / "Targeted_Visium_Human_OvarianCancer_Immunology_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jcz__10X__Visium__Human__breast__20210609__v1.3.0/10jcz_to_zarr.py b/data/10jcz__10X__Visium__Human__breast__20210609__v1.3.0/10jcz_to_zarr.py index c336856..3c0a08f 100644 --- a/data/10jcz__10X__Visium__Human__breast__20210609__v1.3.0/10jcz_to_zarr.py +++ b/data/10jcz__10X__Visium__Human__breast__20210609__v1.3.0/10jcz_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jcz_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Breast_Cancer", counts_file=str(path_read / "Visium_FFPE_Human_Breast_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jdw__10X__Visium__Mouse__brain__20220714__v2.0.0/10jdw_to_zarr.py b/data/10jdw__10X__Visium__Mouse__brain__20220714__v2.0.0/10jdw_to_zarr.py index 99f1089..044a482 100644 --- a/data/10jdw__10X__Visium__Mouse__brain__20220714__v2.0.0/10jdw_to_zarr.py +++ b/data/10jdw__10X__Visium__Mouse__brain__20220714__v2.0.0/10jdw_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10jfe__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate2/10jfe_to_zarr.py b/data/10jfe__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate2/10jfe_to_zarr.py index 2308640..0ded74f 100644 --- a/data/10jfe__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate2/10jfe_to_zarr.py +++ b/data/10jfe__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate2/10jfe_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jfe_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Colon_Post_Xenium_Rep2", counts_file=str(path_read / "CytAssist_FFPE_Human_Colon_Post_Xenium_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jff__10X__Visium__Mouse__brain__20191202__v1.0.0/10jff_to_zarr.py b/data/10jff__10X__Visium__Mouse__brain__20191202__v1.0.0/10jff_to_zarr.py index b5df78a..54f767c 100644 --- a/data/10jff__10X__Visium__Mouse__brain__20191202__v1.0.0/10jff_to_zarr.py +++ b/data/10jff__10X__Visium__Mouse__brain__20191202__v1.0.0/10jff_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jff_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jft__10X__Visium__Mouse__brain__20200623__v1.1.0/10jft_to_zarr.py b/data/10jft__10X__Visium__Mouse__brain__20200623__v1.1.0/10jft_to_zarr.py index 5805791..efbb53a 100644 --- a/data/10jft__10X__Visium__Mouse__brain__20200623__v1.1.0/10jft_to_zarr.py +++ b/data/10jft__10X__Visium__Mouse__brain__20200623__v1.1.0/10jft_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jft_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jr4__10X__CytAssist__Human__tonsil__20230824__v2.1.0/10jr4_to_zarr.py b/data/10jr4__10X__CytAssist__Human__tonsil__20230824__v2.1.0/10jr4_to_zarr.py index fd27c0c..e61a2d6 100644 --- a/data/10jr4__10X__CytAssist__Human__tonsil__20230824__v2.1.0/10jr4_to_zarr.py +++ b/data/10jr4__10X__CytAssist__Human__tonsil__20230824__v2.1.0/10jr4_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jr4_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Protein_Expression_Human_Tonsil_AddOns", counts_file=str(path_read / "CytAssist_FFPE_Protein_Expression_Human_Tonsil_AddOns_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10jss__10X__Visium__Mouse__brain__20191202__v1.0.0/10jss_to_zarr.py b/data/10jss__10X__Visium__Mouse__brain__20191202__v1.0.0/10jss_to_zarr.py index 67f6809..fd42338 100644 --- a/data/10jss__10X__Visium__Mouse__brain__20191202__v1.0.0/10jss_to_zarr.py +++ b/data/10jss__10X__Visium__Mouse__brain__20191202__v1.0.0/10jss_to_zarr.py @@ -1,10 +1,11 @@ uid = "10jss_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10k3x__10X__Xenium__Human__skin__20240305__v1.9.0__Sample1/10k3x_to_zarr.py b/data/10k3x__10X__Xenium__Human__skin__20240305__v1.9.0__Sample1/10k3x_to_zarr.py index a79a831..ad7fe0e 100644 --- a/data/10k3x__10X__Xenium__Human__skin__20240305__v1.9.0__Sample1/10k3x_to_zarr.py +++ b/data/10k3x__10X__Xenium__Human__skin__20240305__v1.9.0__Sample1/10k3x_to_zarr.py @@ -1,10 +1,11 @@ uid = "10k3x_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10k5p__10X__Visium__Human__breast__20220701__v1.3.0/10k5p_to_zarr.py b/data/10k5p__10X__Visium__Human__breast__20220701__v1.3.0/10k5p_to_zarr.py index b349194..24d6e36 100644 --- a/data/10k5p__10X__Visium__Human__breast__20220701__v1.3.0/10k5p_to_zarr.py +++ b/data/10k5p__10X__Visium__Human__breast__20220701__v1.3.0/10k5p_to_zarr.py @@ -1,10 +1,11 @@ uid = "10k5p_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Human_Breast_Cancer", counts_file=str(path_read / "Visium_Human_Breast_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kia__10X__Visium__Human__large_intestine__20201027__v1.2.0/10kia_to_zarr.py b/data/10kia__10X__Visium__Human__large_intestine__20201027__v1.2.0/10kia_to_zarr.py index 96c9aaa..172dc8f 100644 --- a/data/10kia__10X__Visium__Human__large_intestine__20201027__v1.2.0/10kia_to_zarr.py +++ b/data/10kia__10X__Visium__Human__large_intestine__20201027__v1.2.0/10kia_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kia_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_ColorectalCancer_GeneSignature", counts_file=str(path_read / "Targeted_Visium_Human_ColorectalCancer_GeneSignature_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kmy__10X__Visium__Human__lung__20230214__v2.0.1/10kmy_to_zarr.py b/data/10kmy__10X__Visium__Human__lung__20230214__v2.0.1/10kmy_to_zarr.py index 5064c4c..8ca1a48 100644 --- a/data/10kmy__10X__Visium__Human__lung__20230214__v2.0.1/10kmy_to_zarr.py +++ b/data/10kmy__10X__Visium__Human__lung__20230214__v2.0.1/10kmy_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kmy_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Human_Lung_Cancer", counts_file=str(path_read / "CytAssist_11mm_FFPE_Human_Lung_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py index 3dd3a13..7f2cd19 100644 --- a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py +++ b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py @@ -4,39 +4,25 @@ ln.context.track("5PYtTxDE7LvE") -from vitessce import ( - VitessceConfig, - Component as cm, - CoordinationType as ct, - CoordinationLevel as CL, - AbstractWrapper, - SpatialDataWrapper, - get_initial_coordination_scope_prefix -) -from vitessce.data_utils import ( - optimize_adata, - VAR_CHUNK_SIZE, -) -import spatialdata as sd from lamindb.integrations import save_vitessce_config - +from vitessce import SpatialDataWrapper, VitessceConfig artifact = ln.Artifact.filter(ulabels__name=theislab_uid).one() vc = VitessceConfig( schema_version="1.0.16", - name='Visium + Xenium demo', - description='From https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html' + name="Visium + Xenium demo", + description="From https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html", ) wrapper = SpatialDataWrapper( spatialdata_url=artifact.path.to_url(), image_elem="images/Visium_Adult_Mouse_Brain_hires_image", - shapes_elem = "shapes/Visium_Adult_Mouse_Brain", - table_path = "tables/table", + shapes_elem="shapes/Visium_Adult_Mouse_Brain", + table_path="tables/table", ) -dataset = vc.add_dataset(name='Visium demo').add_object(wrapper) +dataset = vc.add_dataset(name="Visium demo").add_object(wrapper) spatial = vc.add_view("spatialBeta", dataset=dataset) vc.layout(spatial) view = save_vitessce_config(vc, description="Visium HD demo vitessce config") diff --git a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py index ccf2425..45fde3e 100644 --- a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py +++ b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py @@ -1,6 +1,7 @@ theislab_uid = "10ktp" import lamindb as ln + from spatialdata_db import load_10x_metadata ln.track("KgGzOw8PUYKO7CpM") diff --git a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_zarr.py b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_zarr.py index bd3de88..0bf835f 100644 --- a/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_zarr.py +++ b/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_zarr.py @@ -2,10 +2,11 @@ uid = "10ktp_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -20,8 +21,8 @@ ## print("parsing the data... ", end="") -# had to extract -# - Visium_Adult_Mouse_Brain_spatial.tar.gz +# had to extract +# - Visium_Adult_Mouse_Brain_spatial.tar.gz sdata = visium( path=path_read, dataset_id="Visium_Adult_Mouse_Brain", @@ -42,7 +43,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kxi__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10kxi_to_zarr.py b/data/10kxi__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10kxi_to_zarr.py index 99f1089..044a482 100644 --- a/data/10kxi__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10kxi_to_zarr.py +++ b/data/10kxi__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10kxi_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10kyn__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10kyn_to_zarr.py b/data/10kyn__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10kyn_to_zarr.py index 3c1bc3b..ebee900 100644 --- a/data/10kyn__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10kyn_to_zarr.py +++ b/data/10kyn__10X__Visium__Human__brain_cerebellum__20201027__v1.2.0/10kyn_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kyn_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_Cerebellum", counts_file=str(path_read / "Parent_Visium_Human_Cerebellum_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kyp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND82.5months/10kyp_to_zarr.py b/data/10kyp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND82.5months/10kyp_to_zarr.py index 62a7d84..7c2f0af 100644 --- a/data/10kyp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND82.5months/10kyp_to_zarr.py +++ b/data/10kyp__10X__Xenium__Mouse__brain__20230713__v1.4.0__TgCRND82.5months/10kyp_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kyp_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kz2__10X__Visium__Human__prostate__20210727__v1.3.0/10kz2_to_zarr.py b/data/10kz2__10X__Visium__Human__prostate__20210727__v1.3.0/10kz2_to_zarr.py index 17701be..aa78cc5 100644 --- a/data/10kz2__10X__Visium__Human__prostate__20210727__v1.3.0/10kz2_to_zarr.py +++ b/data/10kz2__10X__Visium__Human__prostate__20210727__v1.3.0/10kz2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kz2_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_IF", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_IF_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10kz7__10X__Visium__Mouse__brain__20210816__v1.3.0/10kz7_to_zarr.py b/data/10kz7__10X__Visium__Mouse__brain__20210816__v1.3.0/10kz7_to_zarr.py index e36b40e..18acdc8 100644 --- a/data/10kz7__10X__Visium__Mouse__brain__20210816__v1.3.0/10kz7_to_zarr.py +++ b/data/10kz7__10X__Visium__Mouse__brain__20210816__v1.3.0/10kz7_to_zarr.py @@ -1,10 +1,11 @@ uid = "10kz7_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Mouse_Brain_IF", counts_file=str(path_read / "Visium_FFPE_Mouse_Brain_IF_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10m16__10X__Visium__Mouse__brain__20200623__v1.1.0/10m16_to_zarr.py b/data/10m16__10X__Visium__Mouse__brain__20200623__v1.1.0/10m16_to_zarr.py index ab1a4c5..e599017 100644 --- a/data/10m16__10X__Visium__Mouse__brain__20200623__v1.1.0/10m16_to_zarr.py +++ b/data/10m16__10X__Visium__Mouse__brain__20200623__v1.1.0/10m16_to_zarr.py @@ -1,10 +1,11 @@ uid = "10m16_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10m49__10X__Visium__Mouse__brain__20220329__v1.3.0/10m49_to_zarr.py b/data/10m49__10X__Visium__Mouse__brain__20220329__v1.3.0/10m49_to_zarr.py index efa006f..3b514da 100644 --- a/data/10m49__10X__Visium__Mouse__brain__20220329__v1.3.0/10m49_to_zarr.py +++ b/data/10m49__10X__Visium__Mouse__brain__20220329__v1.3.0/10m49_to_zarr.py @@ -1,10 +1,11 @@ uid = "10m49_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10mda__10X__Visium__Mouse__brain__20230608__v2.1.0/10mda_to_zarr.py b/data/10mda__10X__Visium__Mouse__brain__20230608__v2.1.0/10mda_to_zarr.py index 4649ee6..79257f0 100644 --- a/data/10mda__10X__Visium__Mouse__brain__20230608__v2.1.0/10mda_to_zarr.py +++ b/data/10mda__10X__Visium__Mouse__brain__20230608__v2.1.0/10mda_to_zarr.py @@ -1,10 +1,11 @@ uid = "10mda_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Sagittal_Mouse_Brain", counts_file=str(path_read / "CytAssist_FFPE_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10mx9__10X__Visium__Human__lymph_node__20191212__v1.0.0/10mx9_to_zarr.py b/data/10mx9__10X__Visium__Human__lymph_node__20191212__v1.0.0/10mx9_to_zarr.py index 485e920..4aa3427 100644 --- a/data/10mx9__10X__Visium__Human__lymph_node__20191212__v1.0.0/10mx9_to_zarr.py +++ b/data/10mx9__10X__Visium__Human__lymph_node__20191212__v1.0.0/10mx9_to_zarr.py @@ -1,10 +1,11 @@ uid = "10mx9_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Lymph_Node", counts_file=str(path_read / "V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10n1k__10X__Xenium__Mouse__bone__20240403__v1.9.0__0.5MEDTAdecalcification/10n1k_to_zarr.py b/data/10n1k__10X__Xenium__Mouse__bone__20240403__v1.9.0__0.5MEDTAdecalcification/10n1k_to_zarr.py index 412b2a4..f59b571 100644 --- a/data/10n1k__10X__Xenium__Mouse__bone__20240403__v1.9.0__0.5MEDTAdecalcification/10n1k_to_zarr.py +++ b/data/10n1k__10X__Xenium__Mouse__bone__20240403__v1.9.0__0.5MEDTAdecalcification/10n1k_to_zarr.py @@ -1,10 +1,11 @@ uid = "10n1k_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10nc2__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10nc2_to_zarr.py b/data/10nc2__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10nc2_to_zarr.py index 99f1089..044a482 100644 --- a/data/10nc2__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10nc2_to_zarr.py +++ b/data/10nc2__10X__Xenium__Mouse__brain__20230122__v1.0.2__InputsSlide/10nc2_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10ndj__10X__Visium__Mouse__brain__20220713__v2.0.0/10ndj_to_zarr.py b/data/10ndj__10X__Visium__Mouse__brain__20220713__v2.0.0/10ndj_to_zarr.py index 6461c9a..110069d 100644 --- a/data/10ndj__10X__Visium__Mouse__brain__20220713__v2.0.0/10ndj_to_zarr.py +++ b/data/10ndj__10X__Visium__Mouse__brain__20220713__v2.0.0/10ndj_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ndj_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_Brain_Rep1", counts_file=str(path_read / "CytAssist_FFPE_Mouse_Brain_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ndm__10X__Xenium__Mouse__bone__20240403__v1.9.0__15EDTA0.4PFAdecalcification/10ndm_to_zarr.py b/data/10ndm__10X__Xenium__Mouse__bone__20240403__v1.9.0__15EDTA0.4PFAdecalcification/10ndm_to_zarr.py index aa57e19..9ea48ec 100644 --- a/data/10ndm__10X__Xenium__Mouse__bone__20240403__v1.9.0__15EDTA0.4PFAdecalcification/10ndm_to_zarr.py +++ b/data/10ndm__10X__Xenium__Mouse__bone__20240403__v1.9.0__15EDTA0.4PFAdecalcification/10ndm_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ndm_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10nfy__10X__Visium__Mouse__brain__20220712__v2.0.0/10nfy_to_zarr.py b/data/10nfy__10X__Visium__Mouse__brain__20220712__v2.0.0/10nfy_to_zarr.py index 36c0bbe..8792756 100644 --- a/data/10nfy__10X__Visium__Mouse__brain__20220712__v2.0.0/10nfy_to_zarr.py +++ b/data/10nfy__10X__Visium__Mouse__brain__20220712__v2.0.0/10nfy_to_zarr.py @@ -1,10 +1,11 @@ uid = "10nfy_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10nsr__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__AcuteLymphoidLeukemiaBoneMarrow/10nsr_to_zarr.py b/data/10nsr__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__AcuteLymphoidLeukemiaBoneMarrow/10nsr_to_zarr.py index 389b05f..247e789 100644 --- a/data/10nsr__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__AcuteLymphoidLeukemiaBoneMarrow/10nsr_to_zarr.py +++ b/data/10nsr__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__AcuteLymphoidLeukemiaBoneMarrow/10nsr_to_zarr.py @@ -1,10 +1,11 @@ uid = "10nsr_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10nzm__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores/10nzm_to_zarr.py b/data/10nzm__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores/10nzm_to_zarr.py index 99f1089..044a482 100644 --- a/data/10nzm__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores/10nzm_to_zarr.py +++ b/data/10nzm__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores/10nzm_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10p19__10X__Visium__Human__breast__20201027__v1.2.0/10p19_to_zarr.py b/data/10p19__10X__Visium__Human__breast__20201027__v1.2.0/10p19_to_zarr.py index 4f5b90e..4faa093 100644 --- a/data/10p19__10X__Visium__Human__breast__20201027__v1.2.0/10p19_to_zarr.py +++ b/data/10p19__10X__Visium__Human__breast__20201027__v1.2.0/10p19_to_zarr.py @@ -1,10 +1,11 @@ uid = "10p19_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_BreastCancer", counts_file=str(path_read / "Parent_Visium_Human_BreastCancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10p4f__10X__Visium__Human__heart__20191212__v1.0.0/10p4f_to_zarr.py b/data/10p4f__10X__Visium__Human__heart__20191212__v1.0.0/10p4f_to_zarr.py index 71e8e4b..2d4ac56 100644 --- a/data/10p4f__10X__Visium__Human__heart__20191212__v1.0.0/10p4f_to_zarr.py +++ b/data/10p4f__10X__Visium__Human__heart__20191212__v1.0.0/10p4f_to_zarr.py @@ -1,10 +1,11 @@ uid = "10p4f_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Heart", counts_file=str(path_read / "V1_Human_Heart_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10p5f__10X__Visium__Mouse__brain__20200623__v1.1.0/10p5f_to_zarr.py b/data/10p5f__10X__Visium__Mouse__brain__20200623__v1.1.0/10p5f_to_zarr.py index 2baeb4b..0e8b425 100644 --- a/data/10p5f__10X__Visium__Mouse__brain__20200623__v1.1.0/10p5f_to_zarr.py +++ b/data/10p5f__10X__Visium__Mouse__brain__20200623__v1.1.0/10p5f_to_zarr.py @@ -1,10 +1,11 @@ uid = "10p5f_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain_Coronal_Section_1", counts_file=str(path_read / "V1_Adult_Mouse_Brain_Coronal_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10pa3__10X__Xenium__Mouse__whole_organism__20230818__v1.6.0/10pa3_to_zarr.py b/data/10pa3__10X__Xenium__Mouse__whole_organism__20230818__v1.6.0/10pa3_to_zarr.py index adb72b3..2a261b4 100644 --- a/data/10pa3__10X__Xenium__Mouse__whole_organism__20230818__v1.6.0/10pa3_to_zarr.py +++ b/data/10pa3__10X__Xenium__Mouse__whole_organism__20230818__v1.6.0/10pa3_to_zarr.py @@ -1,10 +1,11 @@ uid = "10pa3_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10pf0__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/10pf0_to_zarr.py b/data/10pf0__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/10pf0_to_zarr.py index 6a20c09..161f3e6 100644 --- a/data/10pf0__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/10pf0_to_zarr.py +++ b/data/10pf0__10X__Xenium__Human__breast__20230122__v1.0.2__Tissuesample2/10pf0_to_zarr.py @@ -1,10 +1,11 @@ uid = "10pf0_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ps4__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate1/10ps4_to_zarr.py b/data/10ps4__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate1/10ps4_to_zarr.py index af93c64..18a94ce 100644 --- a/data/10ps4__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate1/10ps4_to_zarr.py +++ b/data/10ps4__10X__Visium__Mouse__brain__20231005__v2.1.0__ControlReplicate1/10ps4_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ps4_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FreshFrozen_Mouse_Brain_Rep1", counts_file=str(path_read / "CytAssist_FreshFrozen_Mouse_Brain_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10pui__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedFemurBone/10pui_to_zarr.py b/data/10pui__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedFemurBone/10pui_to_zarr.py index e8f9ee8..b46b421 100644 --- a/data/10pui__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedFemurBone/10pui_to_zarr.py +++ b/data/10pui__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedFemurBone/10pui_to_zarr.py @@ -1,10 +1,11 @@ uid = "10pui_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10rm3__10X__Visium__Mouse__brain__20191202__v1.0.0/10rm3_to_zarr.py b/data/10rm3__10X__Visium__Mouse__brain__20191202__v1.0.0/10rm3_to_zarr.py index d97b974..534e495 100644 --- a/data/10rm3__10X__Visium__Mouse__brain__20191202__v1.0.0/10rm3_to_zarr.py +++ b/data/10rm3__10X__Visium__Mouse__brain__20191202__v1.0.0/10rm3_to_zarr.py @@ -1,10 +1,11 @@ uid = "10rm3_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10rx2__10X__Visium__Mouse__brain__20220712__v2.0.0/10rx2_to_zarr.py b/data/10rx2__10X__Visium__Mouse__brain__20220712__v2.0.0/10rx2_to_zarr.py index 090b38f..3c9ee32 100644 --- a/data/10rx2__10X__Visium__Mouse__brain__20220712__v2.0.0/10rx2_to_zarr.py +++ b/data/10rx2__10X__Visium__Mouse__brain__20220712__v2.0.0/10rx2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10rx2_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Anterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10rxw__10X__Visium__Human__ovary__20201027__v1.2.0/10rxw_to_zarr.py b/data/10rxw__10X__Visium__Human__ovary__20201027__v1.2.0/10rxw_to_zarr.py index 3edacd2..94ed58d 100644 --- a/data/10rxw__10X__Visium__Human__ovary__20201027__v1.2.0/10rxw_to_zarr.py +++ b/data/10rxw__10X__Visium__Human__ovary__20201027__v1.2.0/10rxw_to_zarr.py @@ -1,10 +1,11 @@ uid = "10rxw_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_OvarianCancer", counts_file=str(path_read / "Parent_Visium_Human_OvarianCancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10s7d__10X__VisiumHD__Mouse__intestine__20240325__v3.0.0/10s7d_to_zarr.py b/data/10s7d__10X__VisiumHD__Mouse__intestine__20240325__v3.0.0/10s7d_to_zarr.py index 99f1089..044a482 100644 --- a/data/10s7d__10X__VisiumHD__Mouse__intestine__20240325__v3.0.0/10s7d_to_zarr.py +++ b/data/10s7d__10X__VisiumHD__Mouse__intestine__20240325__v3.0.0/10s7d_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10s8t__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate3/10s8t_to_zarr.py b/data/10s8t__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate3/10s8t_to_zarr.py index f074b4a..d1c47de 100644 --- a/data/10s8t__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate3/10s8t_to_zarr.py +++ b/data/10s8t__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate3/10s8t_to_zarr.py @@ -1,10 +1,11 @@ uid = "10s8t_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep3", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep3_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10sja__10X__Xenium__Mouse__colon__20240319__v2.0.0/10sja_to_zarr.py b/data/10sja__10X__Xenium__Mouse__colon__20240319__v2.0.0/10sja_to_zarr.py index 5c6ccc6..da302ff 100644 --- a/data/10sja__10X__Xenium__Mouse__colon__20240319__v2.0.0/10sja_to_zarr.py +++ b/data/10sja__10X__Xenium__Mouse__colon__20240319__v2.0.0/10sja_to_zarr.py @@ -1,10 +1,11 @@ uid = "10sja_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10sn3__10X__Visium__Human__lung__20220713__v2.0.0/10sn3_to_zarr.py b/data/10sn3__10X__Visium__Human__lung__20220713__v2.0.0/10sn3_to_zarr.py index 0991b49..d9915e3 100644 --- a/data/10sn3__10X__Visium__Human__lung__20220713__v2.0.0/10sn3_to_zarr.py +++ b/data/10sn3__10X__Visium__Human__lung__20220713__v2.0.0/10sn3_to_zarr.py @@ -1,10 +1,11 @@ uid = "10sn3_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma", counts_file=str(path_read / "CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10sph__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate4/10sph_to_zarr.py b/data/10sph__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate4/10sph_to_zarr.py index 8e7147a..35d2fa9 100644 --- a/data/10sph__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate4/10sph_to_zarr.py +++ b/data/10sph__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate4/10sph_to_zarr.py @@ -1,10 +1,11 @@ uid = "10sph_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep4", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep4_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10t8c__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/10t8c_to_zarr.py b/data/10t8c__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/10t8c_to_zarr.py index bbc7480..1c2c545 100644 --- a/data/10t8c__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/10t8c_to_zarr.py +++ b/data/10t8c__10X__Visium__Mouse__olfactory_bulb__20220324__v1.3.0/10t8c_to_zarr.py @@ -1,10 +1,11 @@ uid = "10t8c_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Mouse_Olfactory_Bulb", counts_file=str(path_read / "Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10tei__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate1/10tei_to_zarr.py b/data/10tei__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate1/10tei_to_zarr.py index deea9b5..12aaf1b 100644 --- a/data/10tei__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate1/10tei_to_zarr.py +++ b/data/10tei__10X__Visium__Human__colon__20231005__v2.1.0__Post-XeniumReplicate1/10tei_to_zarr.py @@ -1,10 +1,11 @@ uid = "10tei_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1", counts_file=str(path_read / "CytAssist_FFPE_Human_Colon_Post_Xenium_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10thd__10X__Visium__Human__prostate__20220712__v2.0.0/10thd_to_zarr.py b/data/10thd__10X__Visium__Human__prostate__20220712__v2.0.0/10thd_to_zarr.py index cf38dbe..646e2e6 100644 --- a/data/10thd__10X__Visium__Human__prostate__20220712__v2.0.0/10thd_to_zarr.py +++ b/data/10thd__10X__Visium__Human__prostate__20220712__v2.0.0/10thd_to_zarr.py @@ -1,10 +1,11 @@ uid = "10thd_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_IF", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_IF_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10tsy__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designedpanel/10tsy_to_zarr.py b/data/10tsy__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designedpanel/10tsy_to_zarr.py index 2e38a58..a8740b5 100644 --- a/data/10tsy__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designedpanel/10tsy_to_zarr.py +++ b/data/10tsy__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Non-diseasedpre-designedpanel/10tsy_to_zarr.py @@ -1,10 +1,11 @@ uid = "10tsy_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10ttt__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AllTissueCores/10ttt_to_zarr.py b/data/10ttt__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AllTissueCores/10ttt_to_zarr.py index 20dbc96..868897c 100644 --- a/data/10ttt__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AllTissueCores/10ttt_to_zarr.py +++ b/data/10ttt__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AllTissueCores/10ttt_to_zarr.py @@ -1,10 +1,11 @@ uid = "10ttt_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm", counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10tyd__10X__Visium__Human__ovary__20201027__v1.2.0/10tyd_to_zarr.py b/data/10tyd__10X__Visium__Human__ovary__20201027__v1.2.0/10tyd_to_zarr.py index c1bb218..06c54cc 100644 --- a/data/10tyd__10X__Visium__Human__ovary__20201027__v1.2.0/10tyd_to_zarr.py +++ b/data/10tyd__10X__Visium__Human__ovary__20201027__v1.2.0/10tyd_to_zarr.py @@ -1,10 +1,11 @@ uid = "10tyd_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_OvarianCancer_Pan_Cancer", counts_file=str(path_read / "Targeted_Visium_Human_OvarianCancer_Pan_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10tzs__10X__Visium__Mouse__brain__20191202__v1.0.0/10tzs_to_zarr.py b/data/10tzs__10X__Visium__Mouse__brain__20191202__v1.0.0/10tzs_to_zarr.py index 019624f..ab807cf 100644 --- a/data/10tzs__10X__Visium__Mouse__brain__20191202__v1.0.0/10tzs_to_zarr.py +++ b/data/10tzs__10X__Visium__Mouse__brain__20191202__v1.0.0/10tzs_to_zarr.py @@ -1,10 +1,11 @@ uid = "10tzs_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10u63__10X__Xenium__Human__brain__20240415__v2.0.0/10u63_to_zarr.py b/data/10u63__10X__Xenium__Human__brain__20240415__v2.0.0/10u63_to_zarr.py index 9a61c64..5ae46f4 100644 --- a/data/10u63__10X__Xenium__Human__brain__20240415__v2.0.0/10u63_to_zarr.py +++ b/data/10u63__10X__Xenium__Human__brain__20240415__v2.0.0/10u63_to_zarr.py @@ -1,10 +1,11 @@ uid = "10u63_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10u6u__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/10u6u_to_zarr.py b/data/10u6u__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/10u6u_to_zarr.py index 4933d09..2e28bd8 100644 --- a/data/10u6u__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/10u6u_to_zarr.py +++ b/data/10u6u__10X__Visium__Mouse__olfactory_bulb__20220712__v2.0.0/10u6u_to_zarr.py @@ -1,10 +1,11 @@ uid = "10u6u_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Mouse_Olfactory_Bulb", counts_file=str(path_read / "Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10u89__10X__Xenium__Human__kidney__20230717__v1.5.0__KidneyCancer(PRCC)/10u89_to_zarr.py b/data/10u89__10X__Xenium__Human__kidney__20230717__v1.5.0__KidneyCancer(PRCC)/10u89_to_zarr.py index 6fcaea0..0203a5a 100644 --- a/data/10u89__10X__Xenium__Human__kidney__20230717__v1.5.0__KidneyCancer(PRCC)/10u89_to_zarr.py +++ b/data/10u89__10X__Xenium__Human__kidney__20230717__v1.5.0__KidneyCancer(PRCC)/10u89_to_zarr.py @@ -1,10 +1,11 @@ uid = "10u89_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10uac__10X__Xenium__Human__breast__20230418__v1.3.0__Tissuesample1(IDC)/10uac_to_zarr.py b/data/10uac__10X__Xenium__Human__breast__20230418__v1.3.0__Tissuesample1(IDC)/10uac_to_zarr.py index 6ef2f29..a96bfd6 100644 --- a/data/10uac__10X__Xenium__Human__breast__20230418__v1.3.0__Tissuesample1(IDC)/10uac_to_zarr.py +++ b/data/10uac__10X__Xenium__Human__breast__20230418__v1.3.0__Tissuesample1(IDC)/10uac_to_zarr.py @@ -1,10 +1,11 @@ uid = "10uac_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10uf7__10X__Visium__Mouse__brain__20210816__v1.3.0/10uf7_to_zarr.py b/data/10uf7__10X__Visium__Mouse__brain__20210816__v1.3.0/10uf7_to_zarr.py index 6507bf6..430cad1 100644 --- a/data/10uf7__10X__Visium__Mouse__brain__20210816__v1.3.0/10uf7_to_zarr.py +++ b/data/10uf7__10X__Visium__Mouse__brain__20210816__v1.3.0/10uf7_to_zarr.py @@ -1,10 +1,11 @@ uid = "10uf7_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Mouse_Brain", counts_file=str(path_read / "Visium_FFPE_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10uik__10X__Visium__Human__prostate__20210609__v1.3.0/10uik_to_zarr.py b/data/10uik__10X__Visium__Human__prostate__20210609__v1.3.0/10uik_to_zarr.py index feb8594..8c9a03a 100644 --- a/data/10uik__10X__Visium__Human__prostate__20210609__v1.3.0/10uik_to_zarr.py +++ b/data/10uik__10X__Visium__Human__prostate__20210609__v1.3.0/10uik_to_zarr.py @@ -1,10 +1,11 @@ uid = "10uik_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Prostate_Cancer", counts_file=str(path_read / "Visium_FFPE_Human_Prostate_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10uxy__10X__Xenium__Human__lung__20240205__v2.0.0/10uxy_to_zarr.py b/data/10uxy__10X__Xenium__Human__lung__20240205__v2.0.0/10uxy_to_zarr.py index 91ce4f4..d317c71 100644 --- a/data/10uxy__10X__Xenium__Human__lung__20240205__v2.0.0/10uxy_to_zarr.py +++ b/data/10uxy__10X__Xenium__Human__lung__20240205__v2.0.0/10uxy_to_zarr.py @@ -1,10 +1,11 @@ uid = "10uxy_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10v4k__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate2/10v4k_to_zarr.py b/data/10v4k__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate2/10v4k_to_zarr.py index bd2816b..55b390b 100644 --- a/data/10v4k__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate2/10v4k_to_zarr.py +++ b/data/10v4k__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate2/10v4k_to_zarr.py @@ -1,10 +1,11 @@ uid = "10v4k_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep2", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Brain_Rep2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10v61__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate1/10v61_to_zarr.py b/data/10v61__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate1/10v61_to_zarr.py index 67debbd..ddb803e 100644 --- a/data/10v61__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate1/10v61_to_zarr.py +++ b/data/10v61__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate1/10v61_to_zarr.py @@ -1,10 +1,11 @@ uid = "10v61_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep1", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10vcj__10X__Visium__Human__ovary__20220328__v1.3.0/10vcj_to_zarr.py b/data/10vcj__10X__Visium__Human__ovary__20220328__v1.3.0/10vcj_to_zarr.py index 42a7107..a84df09 100644 --- a/data/10vcj__10X__Visium__Human__ovary__20220328__v1.3.0/10vcj_to_zarr.py +++ b/data/10vcj__10X__Visium__Human__ovary__20220328__v1.3.0/10vcj_to_zarr.py @@ -1,10 +1,11 @@ uid = "10vcj_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_FFPE_Human_Ovarian_Cancer", counts_file=str(path_read / "Visium_FFPE_Human_Ovarian_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10vek__10X__VisiumHD__Human__lung__20240329__v3.0.0/10vek_to_zarr.py b/data/10vek__10X__VisiumHD__Human__lung__20240329__v3.0.0/10vek_to_zarr.py index 99f1089..044a482 100644 --- a/data/10vek__10X__VisiumHD__Human__lung__20240329__v3.0.0/10vek_to_zarr.py +++ b/data/10vek__10X__VisiumHD__Human__lung__20240329__v3.0.0/10vek_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10vj2__10X__Visium__Human__breast__20191212__v1.0.0/10vj2_to_zarr.py b/data/10vj2__10X__Visium__Human__breast__20191212__v1.0.0/10vj2_to_zarr.py index 6b1ae0c..6224704 100644 --- a/data/10vj2__10X__Visium__Human__breast__20191212__v1.0.0/10vj2_to_zarr.py +++ b/data/10vj2__10X__Visium__Human__breast__20191212__v1.0.0/10vj2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10vj2_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_1", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10vtf__10X__Visium__Human__breast__20210511__v1.2.0/10vtf_to_zarr.py b/data/10vtf__10X__Visium__Human__breast__20210511__v1.2.0/10vtf_to_zarr.py index 520f943..043c0a5 100644 --- a/data/10vtf__10X__Visium__Human__breast__20210511__v1.2.0/10vtf_to_zarr.py +++ b/data/10vtf__10X__Visium__Human__breast__20210511__v1.2.0/10vtf_to_zarr.py @@ -1,10 +1,11 @@ uid = "10vtf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Invasive_Ductal_Carcinoma", counts_file=str(path_read / "V1_Human_Invasive_Ductal_Carcinoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10vyh__10X__Visium__Human__lymph_node__20191212__v1.0.0/10vyh_to_zarr.py b/data/10vyh__10X__Visium__Human__lymph_node__20191212__v1.0.0/10vyh_to_zarr.py index e5cc58c..649aeb2 100644 --- a/data/10vyh__10X__Visium__Human__lymph_node__20191212__v1.0.0/10vyh_to_zarr.py +++ b/data/10vyh__10X__Visium__Human__lymph_node__20191212__v1.0.0/10vyh_to_zarr.py @@ -1,10 +1,11 @@ uid = "10vyh_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Lymph_Node", counts_file=str(path_read / "V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10w2u__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10w2u_to_zarr.py b/data/10w2u__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10w2u_to_zarr.py index 99f1089..044a482 100644 --- a/data/10w2u__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10w2u_to_zarr.py +++ b/data/10w2u__10X__Xenium__Human__breast__20230122__v1.0.2__InputsSlide/10w2u_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10w6u__10X__Visium__Mouse__brain__20230525__v2.1.0/10w6u_to_zarr.py b/data/10w6u__10X__Visium__Mouse__brain__20230525__v2.1.0/10w6u_to_zarr.py index 0461a08..aa9d8c8 100644 --- a/data/10w6u__10X__Visium__Mouse__brain__20230525__v2.1.0/10w6u_to_zarr.py +++ b/data/10w6u__10X__Visium__Mouse__brain__20230525__v2.1.0/10w6u_to_zarr.py @@ -1,10 +1,11 @@ uid = "10w6u_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Fresh_Frozen_Adult_Mouse_Brain", counts_file=str(path_read / "Visium_Fresh_Frozen_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10w90__10X__Visium__Human__ovary__20201027__v1.2.0/10w90_to_zarr.py b/data/10w90__10X__Visium__Human__ovary__20201027__v1.2.0/10w90_to_zarr.py index 99f1089..044a482 100644 --- a/data/10w90__10X__Visium__Human__ovary__20201027__v1.2.0/10w90_to_zarr.py +++ b/data/10w90__10X__Visium__Human__ovary__20201027__v1.2.0/10w90_to_zarr.py @@ -1 +1 @@ -# todo \ No newline at end of file +# todo diff --git a/data/10wcj__10X__Visium__Human__brain__20201027__v1.2.0/10wcj_to_zarr.py b/data/10wcj__10X__Visium__Human__brain__20201027__v1.2.0/10wcj_to_zarr.py index 6b291fa..2f48e1f 100644 --- a/data/10wcj__10X__Visium__Human__brain__20201027__v1.2.0/10wcj_to_zarr.py +++ b/data/10wcj__10X__Visium__Human__brain__20201027__v1.2.0/10wcj_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wcj_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_Glioblastoma", counts_file=str(path_read / "Parent_Visium_Human_Glioblastoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wfn__10X__Visium__Mouse__brain__20200623__v1.1.0/10wfn_to_zarr.py b/data/10wfn__10X__Visium__Mouse__brain__20200623__v1.1.0/10wfn_to_zarr.py index be7463a..98ff798 100644 --- a/data/10wfn__10X__Visium__Mouse__brain__20200623__v1.1.0/10wfn_to_zarr.py +++ b/data/10wfn__10X__Visium__Mouse__brain__20200623__v1.1.0/10wfn_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wfn_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wkh__10X__Visium__Human__cerebellum__20220712__v2.0.0/10wkh_to_zarr.py b/data/10wkh__10X__Visium__Human__cerebellum__20220712__v2.0.0/10wkh_to_zarr.py index bff0d29..28f1add 100644 --- a/data/10wkh__10X__Visium__Human__cerebellum__20220712__v2.0.0/10wkh_to_zarr.py +++ b/data/10wkh__10X__Visium__Human__cerebellum__20220712__v2.0.0/10wkh_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wkh_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_Cerebellum_Neuroscience", counts_file=str(path_read / "Targeted_Visium_Human_Cerebellum_Neuroscience_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wmu__10X__Xenium__Human__heart__20240305__v1.9.0/10wmu_to_zarr.py b/data/10wmu__10X__Xenium__Human__heart__20240305__v1.9.0/10wmu_to_zarr.py index 0f8a75e..e7c70c5 100644 --- a/data/10wmu__10X__Xenium__Human__heart__20240305__v1.9.0/10wmu_to_zarr.py +++ b/data/10wmu__10X__Xenium__Human__heart__20240305__v1.9.0/10wmu_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wmu_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wsf__10X__Visium__Human__breast__20191212__v1.0.0/10wsf_to_zarr.py b/data/10wsf__10X__Visium__Human__breast__20191212__v1.0.0/10wsf_to_zarr.py index 3246222..e1bed56 100644 --- a/data/10wsf__10X__Visium__Human__breast__20191212__v1.0.0/10wsf_to_zarr.py +++ b/data/10wsf__10X__Visium__Human__breast__20191212__v1.0.0/10wsf_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wsf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Breast_Cancer_Block_A_Section_2", counts_file=str(path_read / "V1_Breast_Cancer_Block_A_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wth__10X__Visium__Human__spinal_cord__20201027__v1.2.0/10wth_to_zarr.py b/data/10wth__10X__Visium__Human__spinal_cord__20201027__v1.2.0/10wth_to_zarr.py index 5d6d2a8..7fc52e6 100644 --- a/data/10wth__10X__Visium__Human__spinal_cord__20201027__v1.2.0/10wth_to_zarr.py +++ b/data/10wth__10X__Visium__Human__spinal_cord__20201027__v1.2.0/10wth_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wth_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_SpinalCord_Neuroscience", counts_file=str(path_read / "Targeted_Visium_Human_SpinalCord_Neuroscience_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10wv1__10X__Visium__Human__brain__20200623__v1.1.0/10wv1_to_zarr.py b/data/10wv1__10X__Visium__Human__brain__20200623__v1.1.0/10wv1_to_zarr.py index a6e594b..eea2d91 100644 --- a/data/10wv1__10X__Visium__Human__brain__20200623__v1.1.0/10wv1_to_zarr.py +++ b/data/10wv1__10X__Visium__Human__brain__20200623__v1.1.0/10wv1_to_zarr.py @@ -1,10 +1,11 @@ uid = "10wv1_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Human_Brain_Section_1", counts_file=str(path_read / "V1_Human_Brain_Section_1_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10x88__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate1/10x88_to_zarr.py b/data/10x88__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate1/10x88_to_zarr.py index 9dc0b6c..779cf33 100644 --- a/data/10x88__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate1/10x88_to_zarr.py +++ b/data/10x88__10X__Xenium__Mouse__brain__20230122__v1.0.2__Replicate1/10x88_to_zarr.py @@ -1,10 +1,11 @@ uid = "10x88_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10xa2__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype2.5months/10xa2_to_zarr.py b/data/10xa2__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype2.5months/10xa2_to_zarr.py index bb16da4..10535a8 100644 --- a/data/10xa2__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype2.5months/10xa2_to_zarr.py +++ b/data/10xa2__10X__Xenium__Mouse__brain__20230713__v1.4.0__Wildtype2.5months/10xa2_to_zarr.py @@ -1,10 +1,11 @@ uid = "10xa2_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10xay__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate2/10xay_to_zarr.py b/data/10xay__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate2/10xay_to_zarr.py index 19dd4a2..2e451ed 100644 --- a/data/10xay__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate2/10xay_to_zarr.py +++ b/data/10xay__10X__Xenium__Human__breast__20230122__v1.0.2__Replicate2/10xay_to_zarr.py @@ -1,10 +1,11 @@ uid = "10xay_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10xtf__10X__Visium__Mouse__brain__20191202__v1.0.0/10xtf_to_zarr.py b/data/10xtf__10X__Visium__Mouse__brain__20191202__v1.0.0/10xtf_to_zarr.py index 9a6ac8f..721fc15 100644 --- a/data/10xtf__10X__Visium__Mouse__brain__20191202__v1.0.0/10xtf_to_zarr.py +++ b/data/10xtf__10X__Visium__Mouse__brain__20191202__v1.0.0/10xtf_to_zarr.py @@ -1,10 +1,11 @@ uid = "10xtf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Adult_Mouse_Brain", counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10y80__10X__Xenium__Mouse__brain__20230122__v1.0.2__Fullcoronalsection/10y80_to_zarr.py b/data/10y80__10X__Xenium__Mouse__brain__20230122__v1.0.2__Fullcoronalsection/10y80_to_zarr.py index d9790e4..d1dae0d 100644 --- a/data/10y80__10X__Xenium__Mouse__brain__20230122__v1.0.2__Fullcoronalsection/10y80_to_zarr.py +++ b/data/10y80__10X__Xenium__Mouse__brain__20230122__v1.0.2__Fullcoronalsection/10y80_to_zarr.py @@ -1,10 +1,11 @@ uid = "10y80_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10yhc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1/10yhc_to_zarr.py b/data/10yhc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1/10yhc_to_zarr.py index 3393a8c..3e24efe 100644 --- a/data/10yhc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1/10yhc_to_zarr.py +++ b/data/10yhc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1/10yhc_to_zarr.py @@ -1,10 +1,11 @@ uid = "10yhc_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_11mm_FFPE_Mouse_TMA_3x3_1mm", counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_TMA_3x3_1mm_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10yhv__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate3/10yhv_to_zarr.py b/data/10yhv__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate3/10yhv_to_zarr.py index 91b7b73..942567a 100644 --- a/data/10yhv__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate3/10yhv_to_zarr.py +++ b/data/10yhv__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate3/10yhv_to_zarr.py @@ -1,10 +1,11 @@ uid = "10yhv_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep3", counts_file=str(path_read / "CytAssist_FFPE_Mouse_TMA_3x3_2mm_Lung_Rep3_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10z77__10X__Visium__Mouse__brain__20220712__v2.0.0/10z77_to_zarr.py b/data/10z77__10X__Visium__Mouse__brain__20220712__v2.0.0/10z77_to_zarr.py index 9987a5b..330ebd3 100644 --- a/data/10z77__10X__Visium__Mouse__brain__20220712__v2.0.0/10z77_to_zarr.py +++ b/data/10z77__10X__Visium__Mouse__brain__20220712__v2.0.0/10z77_to_zarr.py @@ -1,10 +1,11 @@ uid = "10z77_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="V1_Mouse_Brain_Sagittal_Posterior_Section_2", counts_file=str(path_read / "V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10z91__10X__CytAssist__Human__brain__20230515__v2.1.0/10z91_to_zarr.py b/data/10z91__10X__CytAssist__Human__brain__20230515__v2.1.0/10z91_to_zarr.py index 8354357..1a9bc46 100644 --- a/data/10z91__10X__CytAssist__Human__brain__20230515__v2.1.0/10z91_to_zarr.py +++ b/data/10z91__10X__CytAssist__Human__brain__20230515__v2.1.0/10z91_to_zarr.py @@ -1,10 +1,11 @@ uid = "10z91_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="CytAssist_FFPE_Protein_Expression_Human_Glioblastoma", counts_file=str(path_read / "CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zad__10X__Visium__Human__large_intestine__20201027__v1.2.0/10zad_to_zarr.py b/data/10zad__10X__Visium__Human__large_intestine__20201027__v1.2.0/10zad_to_zarr.py index fd8688a..f99b0e1 100644 --- a/data/10zad__10X__Visium__Human__large_intestine__20201027__v1.2.0/10zad_to_zarr.py +++ b/data/10zad__10X__Visium__Human__large_intestine__20201027__v1.2.0/10zad_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zad_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Parent_Visium_Human_ColorectalCancer", counts_file=str(path_read / "Parent_Visium_Human_ColorectalCancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zj1__10X__Xenium__unknown__unknown__20230420__v1.3.0__Alzheimers/10zj1_to_zarr.py b/data/10zj1__10X__Xenium__unknown__unknown__20230420__v1.3.0__Alzheimers/10zj1_to_zarr.py index 0ce0813..50972e9 100644 --- a/data/10zj1__10X__Xenium__unknown__unknown__20230420__v1.3.0__Alzheimers/10zj1_to_zarr.py +++ b/data/10zj1__10X__Xenium__unknown__unknown__20230420__v1.3.0__Alzheimers/10zj1_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zj1_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zm9__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designed+add-onpanel/10zm9_to_zarr.py b/data/10zm9__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designed+add-onpanel/10zm9_to_zarr.py index 6215f48..787a502 100644 --- a/data/10zm9__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designed+add-onpanel/10zm9_to_zarr.py +++ b/data/10zm9__10X__Xenium__Human__intestine_colon__20230829__v1.6.0__Cancerpre-designed+add-onpanel/10zm9_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zm9_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zvc__10X__Visium__Mouse__brain__20220329__v1.3.0/10zvc_to_zarr.py b/data/10zvc__10X__Visium__Mouse__brain__20220329__v1.3.0/10zvc_to_zarr.py index b4b2131..0d95d1e 100644 --- a/data/10zvc__10X__Visium__Mouse__brain__20220329__v1.3.0/10zvc_to_zarr.py +++ b/data/10zvc__10X__Visium__Mouse__brain__20220329__v1.3.0/10zvc_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zvc_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Visium_Adult_Mouse_Brain", counts_file=str(path_read / "Visium_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zwi__10X__Xenium__Human__skin__20231207__v1.7.0/10zwi_to_zarr.py b/data/10zwi__10X__Xenium__Human__skin__20231207__v1.7.0/10zwi_to_zarr.py index cc1cc34..779a595 100644 --- a/data/10zwi__10X__Xenium__Human__skin__20231207__v1.7.0/10zwi_to_zarr.py +++ b/data/10zwi__10X__Xenium__Human__skin__20231207__v1.7.0/10zwi_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zwi_" # CONSTANT -from spatialdata_io import xenium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import xenium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -38,7 +39,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/10zyf__10X__Visium__Human__brain__20201027__v1.2.0/10zyf_to_zarr.py b/data/10zyf__10X__Visium__Human__brain__20201027__v1.2.0/10zyf_to_zarr.py index dab1c38..d324c6f 100644 --- a/data/10zyf__10X__Visium__Human__brain__20201027__v1.2.0/10zyf_to_zarr.py +++ b/data/10zyf__10X__Visium__Human__brain__20201027__v1.2.0/10zyf_to_zarr.py @@ -1,10 +1,11 @@ uid = "10zyf_" # CONSTANT -from spatialdata_io import visium -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import visium DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -23,7 +24,7 @@ path=str(path_read), dataset_id="Targeted_Visium_Human_Glioblastoma_Pan_Cancer", counts_file=str(path_read / "Targeted_Visium_Human_Glioblastoma_Pan_Cancer_filtered_feature_bc_matrix.h5"), - fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"), + fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"), tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"), scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"), ) @@ -39,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/cij6u__MERSCOPE__HumanColonCancerPatient1/cij6u_to_zarr.py b/data/cij6u__MERSCOPE__HumanColonCancerPatient1/cij6u_to_zarr.py index dd18f97..5afbd82 100644 --- a/data/cij6u__MERSCOPE__HumanColonCancerPatient1/cij6u_to_zarr.py +++ b/data/cij6u__MERSCOPE__HumanColonCancerPatient1/cij6u_to_zarr.py @@ -1,10 +1,11 @@ uid = "cij6u_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -21,7 +22,11 @@ print("parsing the data... ", end="") sdata = merscope( path=str(path_read), - vpt_outputs={"cell_by_gene": path_read, "cell_metadata": path_read, "cell_boundaries": path_read/"cell_boundaries"}, + vpt_outputs={ + "cell_by_gene": path_read, + "cell_metadata": path_read, + "cell_boundaries": path_read / "cell_boundaries", + }, ) print("done") @@ -35,7 +40,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/eex9l__MERSCOPE__HumanOvarianCancerPatient2Slice1/eex9l_to_zarr.py b/data/eex9l__MERSCOPE__HumanOvarianCancerPatient2Slice1/eex9l_to_zarr.py index d1c3ad3..28ddcd9 100644 --- a/data/eex9l__MERSCOPE__HumanOvarianCancerPatient2Slice1/eex9l_to_zarr.py +++ b/data/eex9l__MERSCOPE__HumanOvarianCancerPatient2Slice1/eex9l_to_zarr.py @@ -1,10 +1,11 @@ uid = "eex9l_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/eib0d__MERSCOPE__HumanColonCancerPatient2/eib0d_to_zarr.py b/data/eib0d__MERSCOPE__HumanColonCancerPatient2/eib0d_to_zarr.py index 586933f..74367ba 100644 --- a/data/eib0d__MERSCOPE__HumanColonCancerPatient2/eib0d_to_zarr.py +++ b/data/eib0d__MERSCOPE__HumanColonCancerPatient2/eib0d_to_zarr.py @@ -1,10 +1,11 @@ uid = "eib0d_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/gei4o__MERSCOPE__HumanOvarianCancerPatient1/gei4o_to_zarr.py b/data/gei4o__MERSCOPE__HumanOvarianCancerPatient1/gei4o_to_zarr.py index 971b325..b8e3888 100644 --- a/data/gei4o__MERSCOPE__HumanOvarianCancerPatient1/gei4o_to_zarr.py +++ b/data/gei4o__MERSCOPE__HumanOvarianCancerPatient1/gei4o_to_zarr.py @@ -1,10 +1,11 @@ uid = "gei4o_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/ich1o__MERSCOPE__HumanOvarianCancerPatient2Slice3/ich1o_to_zarr.py b/data/ich1o__MERSCOPE__HumanOvarianCancerPatient2Slice3/ich1o_to_zarr.py index 9d1636d..f893f6c 100644 --- a/data/ich1o__MERSCOPE__HumanOvarianCancerPatient2Slice3/ich1o_to_zarr.py +++ b/data/ich1o__MERSCOPE__HumanOvarianCancerPatient2Slice3/ich1o_to_zarr.py @@ -1,10 +1,11 @@ uid = "ich1o_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/ka3ja__MERSCOPE__HumanLungCancerPatient1/ka3ja_to_zarr.py b/data/ka3ja__MERSCOPE__HumanLungCancerPatient1/ka3ja_to_zarr.py index ebede2e..9e29fe7 100644 --- a/data/ka3ja__MERSCOPE__HumanLungCancerPatient1/ka3ja_to_zarr.py +++ b/data/ka3ja__MERSCOPE__HumanLungCancerPatient1/ka3ja_to_zarr.py @@ -1,10 +1,11 @@ uid = "ka3ja_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/kie2u__MERSCOPE__HumanProstateCancerPatient2/kie2u_to_zarr.py b/data/kie2u__MERSCOPE__HumanProstateCancerPatient2/kie2u_to_zarr.py index b83bc42..8908d82 100644 --- a/data/kie2u__MERSCOPE__HumanProstateCancerPatient2/kie2u_to_zarr.py +++ b/data/kie2u__MERSCOPE__HumanProstateCancerPatient2/kie2u_to_zarr.py @@ -1,10 +1,11 @@ uid = "kie2u_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/lu6ph__MERSCOPE__HumanMelanomaPatient2/lu6ph_to_zarr.py b/data/lu6ph__MERSCOPE__HumanMelanomaPatient2/lu6ph_to_zarr.py index 6b41f29..5306be3 100644 --- a/data/lu6ph__MERSCOPE__HumanMelanomaPatient2/lu6ph_to_zarr.py +++ b/data/lu6ph__MERSCOPE__HumanMelanomaPatient2/lu6ph_to_zarr.py @@ -1,10 +1,11 @@ uid = "lu6ph_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/ohgh2__MERSCOPE__HumanLungCancerPatient2/ohgh2_to_zarr.py b/data/ohgh2__MERSCOPE__HumanLungCancerPatient2/ohgh2_to_zarr.py index de3d944..6ee92e0 100644 --- a/data/ohgh2__MERSCOPE__HumanLungCancerPatient2/ohgh2_to_zarr.py +++ b/data/ohgh2__MERSCOPE__HumanLungCancerPatient2/ohgh2_to_zarr.py @@ -1,10 +1,11 @@ uid = "ohgh2_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/pee2u__MERSCOPE__HumanProstateCancerPatient1/pee2u_to_zarr.py b/data/pee2u__MERSCOPE__HumanProstateCancerPatient1/pee2u_to_zarr.py index 0b59798..3860ecf 100644 --- a/data/pee2u__MERSCOPE__HumanProstateCancerPatient1/pee2u_to_zarr.py +++ b/data/pee2u__MERSCOPE__HumanProstateCancerPatient1/pee2u_to_zarr.py @@ -1,10 +1,11 @@ uid = "pee2u_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/shoh6__MERSCOPE__HumanUterineCancerPatient2-ROCostain/shoh6_to_zarr.py b/data/shoh6__MERSCOPE__HumanUterineCancerPatient2-ROCostain/shoh6_to_zarr.py index 3ed2694..666dbe9 100644 --- a/data/shoh6__MERSCOPE__HumanUterineCancerPatient2-ROCostain/shoh6_to_zarr.py +++ b/data/shoh6__MERSCOPE__HumanUterineCancerPatient2-ROCostain/shoh6_to_zarr.py @@ -1,10 +1,11 @@ uid = "shoh6_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/sie0e__MERSCOPE__HumanLiverCancerPatient1/sie0e_to_zarr.py b/data/sie0e__MERSCOPE__HumanLiverCancerPatient1/sie0e_to_zarr.py index 0e1d40f..92bc504 100644 --- a/data/sie0e__MERSCOPE__HumanLiverCancerPatient1/sie0e_to_zarr.py +++ b/data/sie0e__MERSCOPE__HumanLiverCancerPatient1/sie0e_to_zarr.py @@ -1,10 +1,11 @@ uid = "sie0e_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/soo4t__MERSCOPE__HumanLiverCancerPatient2/soo4t_to_zarr.py b/data/soo4t__MERSCOPE__HumanLiverCancerPatient2/soo4t_to_zarr.py index b68b02e..1f1c16c 100644 --- a/data/soo4t__MERSCOPE__HumanLiverCancerPatient2/soo4t_to_zarr.py +++ b/data/soo4t__MERSCOPE__HumanLiverCancerPatient2/soo4t_to_zarr.py @@ -1,10 +1,11 @@ uid = "soo4t_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/ush6c__MERSCOPE__HumanUterineCancerPatient2-RACostain/ush6c_to_zarr.py b/data/ush6c__MERSCOPE__HumanUterineCancerPatient2-RACostain/ush6c_to_zarr.py index 8bc774e..022edcc 100644 --- a/data/ush6c__MERSCOPE__HumanUterineCancerPatient2-RACostain/ush6c_to_zarr.py +++ b/data/ush6c__MERSCOPE__HumanUterineCancerPatient2-RACostain/ush6c_to_zarr.py @@ -1,10 +1,11 @@ uid = "ush6c_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/va9qu__MERSCOPE__HumanOvarianCancerPatient2Slice2/va9qu_to_zarr.py b/data/va9qu__MERSCOPE__HumanOvarianCancerPatient2Slice2/va9qu_to_zarr.py index 1223753..e0d6bf6 100644 --- a/data/va9qu__MERSCOPE__HumanOvarianCancerPatient2Slice2/va9qu_to_zarr.py +++ b/data/va9qu__MERSCOPE__HumanOvarianCancerPatient2Slice2/va9qu_to_zarr.py @@ -1,10 +1,11 @@ uid = "va9qu_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/vak6a__MERSCOPE__HumanMelanomaPatient1/vak6a_to_zarr.py b/data/vak6a__MERSCOPE__HumanMelanomaPatient1/vak6a_to_zarr.py index 4cb09d6..5180c95 100644 --- a/data/vak6a__MERSCOPE__HumanMelanomaPatient1/vak6a_to_zarr.py +++ b/data/vak6a__MERSCOPE__HumanMelanomaPatient1/vak6a_to_zarr.py @@ -1,10 +1,11 @@ uid = "vak6a_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/data/weer2__MERSCOPE__HumanUterineCancerPatient1/weer2_to_zarr.py b/data/weer2__MERSCOPE__HumanUterineCancerPatient1/weer2_to_zarr.py index de9aa4d..bcca5bf 100644 --- a/data/weer2__MERSCOPE__HumanUterineCancerPatient1/weer2_to_zarr.py +++ b/data/weer2__MERSCOPE__HumanUterineCancerPatient1/weer2_to_zarr.py @@ -1,10 +1,11 @@ uid = "weer2_" # CONSTANT -from spatialdata_io import merscope -import spatialdata as sd -from pathlib import Path import shutil +from pathlib import Path + +import spatialdata as sd +from spatialdata_io import merscope DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)] @@ -34,7 +35,7 @@ ## sdata = sd.SpatialData.read(path_write) -with open(dataset_path / f"{dataset_name}.contents", 'w') as file: +with open(dataset_path / f"{dataset_name}.contents", "w") as file: print(sdata, file=file) print(sdata) diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index b8c8d47..7c13499 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -1,4 +1,4 @@ /* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */ div.cell_output table.dataframe { - font-size: 0.8em; + font-size: 0.8em; } diff --git a/docs/contributing.md b/docs/contributing.md index 89c8840..7db288e 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -155,11 +155,11 @@ This will automatically create a git tag and trigger a Github workflow that crea Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features: -- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text -- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension). -- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks)) -- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types -- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/) +- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text +- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension). +- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks)) +- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types +- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/) See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own. @@ -183,10 +183,10 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu #### Hints -- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. - Only if you do so can sphinx automatically create a link to the external documentation. -- If building the documentation fails because of a missing link that is outside your control, - you can add an entry to the `nitpick_ignore` list in `docs/conf.py` +- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. + Only if you do so can sphinx automatically create a link to the external documentation. +- If building the documentation fails because of a missing link that is outside your control, + you can add an entry to the `nitpick_ignore` list in `docs/conf.py` (docs-building)= diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py index 1135204..0fbffef 100644 --- a/docs/extensions/typed_returns.py +++ b/docs/extensions/typed_returns.py @@ -12,7 +12,7 @@ def _process_return(lines: Iterable[str]) -> Generator[str, None, None]: for line in lines: if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line): - yield f'-{m["param"]} (:class:`~{m["type"]}`)' + yield f"-{m['param']} (:class:`~{m['type']}`)" else: yield line diff --git a/docs/notebooks/download_dataset_from_lamin.ipynb b/docs/notebooks/download_dataset_from_lamin.ipynb index ef663f4..b4a6561 100644 --- a/docs/notebooks/download_dataset_from_lamin.ipynb +++ b/docs/notebooks/download_dataset_from_lamin.ipynb @@ -1087,7 +1087,7 @@ "metadata": {}, "outputs": [], "source": [ - "artifact = ln.Artifact.get('wlgPi3jjfVoYUWjA0000')" + "artifact = ln.Artifact.get(\"wlgPi3jjfVoYUWjA0000\")" ] }, { diff --git a/scripts/add_metadata_from_csv.ipynb b/scripts/add_metadata_from_csv.ipynb index 8dec23d..3f5f0f8 100644 --- a/scripts/add_metadata_from_csv.ipynb +++ b/scripts/add_metadata_from_csv.ipynb @@ -22,10 +22,10 @@ } ], "source": [ - "import spatialdata as sd\n", "import os\n", + "\n", "import pandas as pd\n", - "import spatialdata_db" + "import spatialdata as sd" ] }, { @@ -43,14 +43,14 @@ "metadata": {}, "outputs": [], "source": [ - "SDDB_KEY = 'sample'\n", + "SDDB_KEY = \"sample\"\n", "\n", - "DATA_PATH = '/lustre/groups/ml01/projects/2024_spatialdata_db/data'\n", - "CSV_FILE_PATH = './metadata_10x.csv'\n", + "DATA_PATH = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\"\n", + "CSV_FILE_PATH = \"./metadata_10x.csv\"\n", "\n", - "df = pd.read_csv(CSV_FILE_PATH, sep='\\t')\n", + "df = pd.read_csv(CSV_FILE_PATH, sep=\"\\t\")\n", "\n", - "df = df[df['uid'].isin(uids_to_add)]" + "df = df[df[\"uid\"].isin(uids_to_add)]" ] }, { @@ -127,8 +127,8 @@ ], "source": [ "for index, row in df.iterrows():\n", - " uid = row['uid'] \n", - " meta = row.drop('uid') \n", + " uid = row[\"uid\"]\n", + " meta = row.drop(\"uid\")\n", "\n", " folder_path = None\n", " for folder in os.listdir(DATA_PATH):\n", @@ -142,7 +142,7 @@ "\n", " zarr_file = None\n", " for file in os.listdir(folder_path):\n", - " if file.endswith('.zarr'):\n", + " if file.endswith(\".zarr\"):\n", " zarr_file = os.path.join(folder_path, file)\n", " break\n", "\n", @@ -161,12 +161,11 @@ " # }\n", " sdata.attrs[SDDB_KEY] = metadata\n", "\n", - " metadata_zarr_file = os.path.splitext(zarr_file)[0] + '_attrs.zarr'\n", + " metadata_zarr_file = os.path.splitext(zarr_file)[0] + \"_attrs.zarr\"\n", "\n", " sdata.write(metadata_zarr_file, overwrite=True)\n", "\n", - " print(f\"Processed UID {uid} and updated metadata.\")\n", - "\n" + " print(f\"Processed UID {uid} and updated metadata.\")" ] }, { diff --git a/scripts/cleanup.ipynb b/scripts/cleanup.ipynb index 214bc64..29360f0 100644 --- a/scripts/cleanup.ipynb +++ b/scripts/cleanup.ipynb @@ -15,6 +15,7 @@ ], "source": [ "import warnings\n", + "\n", "warnings.filterwarnings(\"ignore\")\n", "import lamindb as ln" ] diff --git a/scripts/convert_to_sdata.ipynb b/scripts/convert_to_sdata.ipynb index 578a1ec..d381c3c 100644 --- a/scripts/convert_to_sdata.ipynb +++ b/scripts/convert_to_sdata.ipynb @@ -8,10 +8,9 @@ "source": [ "import os\n", "import tarfile\n", - "import spatialdata as sd\n", + "\n", "import pandas as pd\n", - "import spatialdata_db\n", - "from spatialdata_io import xenium, visium, visium_hd" + "from spatialdata_io import visium, visium_hd, xenium" ] }, { @@ -44,8 +43,8 @@ "metadata": {}, "outputs": [], "source": [ - "# uids_to_add = [\"10vek\", \"1000j\", \"1005m\", \"1012t\", \n", - "# \"101cw\", \"101in\", \"1025z\", \"103sm\", \"103te\", \n", + "# uids_to_add = [\"10vek\", \"1000j\", \"1005m\", \"1012t\",\n", + "# \"101cw\", \"101in\", \"1025z\", \"103sm\", \"103te\",\n", "# \"103uy\", \"104dm\", \"104pe\", \"105tt\", \"10fna\"]" ] }, @@ -55,7 +54,7 @@ "metadata": {}, "outputs": [], "source": [ - "#TODO: go through problem files: 10vek, 10s7d\n", + "# TODO: go through problem files: 10vek, 10s7d\n", "uids_to_add = [\"10s7d\"]\n", "# uids_to_add = [\"10vek\"]" ] @@ -66,13 +65,13 @@ "metadata": {}, "outputs": [], "source": [ - "SDDB_KEY = 'sample'\n", - "DATA_PATH = '/lustre/groups/ml01/projects/2024_spatialdata_db/data'\n", - "CSV_FILE_PATH = './metadata_10x.csv'\n", + "SDDB_KEY = \"sample\"\n", + "DATA_PATH = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\"\n", + "CSV_FILE_PATH = \"./metadata_10x.csv\"\n", "\n", - "df = pd.read_csv(CSV_FILE_PATH, sep='\\t')\n", + "df = pd.read_csv(CSV_FILE_PATH, sep=\"\\t\")\n", "\n", - "df = df[df['uid'].isin(uids_to_add)]" + "df = df[df[\"uid\"].isin(uids_to_add)]" ] }, { @@ -107,10 +106,10 @@ } ], "source": [ - "for index, row in df.iterrows():\n", - " uid = row['uid']\n", - " assay = row['assay']\n", - " meta = row.drop('uid') \n", + "for _index, row in df.iterrows():\n", + " uid = row[\"uid\"]\n", + " assay = row[\"assay\"]\n", + " meta = row.drop(\"uid\")\n", "\n", " folder_path = None\n", " for folder in os.listdir(DATA_PATH):\n", @@ -123,11 +122,11 @@ " continue\n", "\n", " # Check if a .zarr file exists in the folder\n", - " if any(file.endswith('.zarr') for file in os.listdir(folder_path)):\n", + " if any(file.endswith(\".zarr\") for file in os.listdir(folder_path)):\n", " print(f\".zarr file already exists for UID {uid} in {folder_path}. Skipping...\")\n", " continue\n", - " \n", - " raw_output = os.path.join(folder_path, 'raw_output')\n", + "\n", + " raw_output = os.path.join(folder_path, \"raw_output\")\n", " print(f\"Processing {uid}\")\n", " print(f\"Path {raw_output}\")\n", "\n", @@ -137,18 +136,18 @@ " decrompress_if_not_done(raw_output, file_name)\n", "\n", " sdata = None\n", - " if assay == 'Xenium':\n", + " if assay == \"Xenium\":\n", " sdata = xenium(raw_output)\n", - " elif assay == 'Visium':\n", + " elif assay == \"Visium\":\n", " sdata = visium(raw_output)\n", - " elif assay == 'VisiumHD':\n", + " elif assay == \"VisiumHD\":\n", " sdata = visium_hd(raw_output)\n", "\n", " if sdata is None:\n", " print(f\"Assay {assay} not supported.\")\n", " continue\n", "\n", - " zarr_filename = folder_path.split('/')[-1] + '.zarr'\n", + " zarr_filename = folder_path.split(\"/\")[-1] + \".zarr\"\n", " print(f\"Writing to {zarr_filename}\")\n", " sdata.write(os.path.join(folder_path, zarr_filename))" ] diff --git a/scripts/create_uids.ipynb b/scripts/create_uids.ipynb index 1058706..9a6bb07 100644 --- a/scripts/create_uids.ipynb +++ b/scripts/create_uids.ipynb @@ -13,10 +13,11 @@ "metadata": {}, "outputs": [], "source": [ - "import pandas as pd\n", - "import string\n", "import itertools\n", - "import numpy as np" + "import string\n", + "\n", + "import numpy as np\n", + "import pandas as pd" ] }, { @@ -160,7 +161,7 @@ ], "source": [ "def generate_all_possible_ids(\n", - " size: int = 5, chars=string.ascii_lowercase + string.digits, exclude: str = \"lbogq\", prefix: str = \"\" \n", + " size: int = 5, chars=string.ascii_lowercase + string.digits, exclude: str = \"lbogq\", prefix: str = \"\"\n", "):\n", " \"\"\"Generate all possible permutations of IDs.\"\"\"\n", " excluded_chars = set(exclude)\n", @@ -168,6 +169,7 @@ "\n", " return [prefix + \"\".join(p) for p in itertools.product(filtered_chars, repeat=size)]\n", "\n", + "\n", "uids_for_10x = pd.DataFrame({\"uid\": generate_all_possible_ids(size=3, prefix=\"10\")})\n", "uids_for_vizgen = pd.DataFrame({\"uid\": generate_all_possible_ids(size=3, prefix=\"vg\")})\n", "uids_for_nanostring = pd.DataFrame({\"uid\": generate_all_possible_ids(size=3, prefix=\"ns\")})\n", @@ -183,10 +185,8 @@ " (\"xx\", \"misc\"),\n", "]\n", "\n", - "conditions_choices = [\n", - " (uids[\"uid\"].str.startswith(prefix), source) for prefix, source in prefix_source_map\n", - "]\n", - "conditions, choices = zip(*conditions_choices)\n", + "conditions_choices = [(uids[\"uid\"].str.startswith(prefix), source) for prefix, source in prefix_source_map]\n", + "conditions, choices = zip(*conditions_choices, strict=False)\n", "uids[\"source\"] = np.select(conditions, choices, default=\"unknown\")\n", "\n", "uids[\"id\"] = None\n", diff --git a/scripts/download_10X_data.ipynb b/scripts/download_10X_data.ipynb index f5915c9..250456c 100644 --- a/scripts/download_10X_data.ipynb +++ b/scripts/download_10X_data.ipynb @@ -13,15 +13,15 @@ "metadata": {}, "outputs": [], "source": [ - "import pathlib as pl\n", - "import pandas as pd\n", "import json\n", + "import pathlib as pl\n", "import subprocess\n", "from concurrent.futures import ThreadPoolExecutor, as_completed\n", - "from tqdm.auto import tqdm\n", - "from urllib.parse import urlparse\n", "from datetime import datetime\n", + "from urllib.parse import urlparse\n", "\n", + "import pandas as pd\n", + "from tqdm.auto import tqdm\n", "\n", "OUTPUT_DIR = pl.Path(\"/lustre/groups/ml01/projects/2024_spatialdata_db/data\")" ] @@ -243,44 +243,38 @@ "source": [ "download_jobs = []\n", "\n", + "\n", "def create_directory(path: pl.Path):\n", " if not path.exists():\n", " path.mkdir()\n", " print(f\"Created directory: {path}\")\n", "\n", + "\n", "def sanitize_key(key: str):\n", - " return (\n", - " key\n", - " .replace(\" \", \"_\")\n", - " .replace(\"(\", \"\")\n", - " .replace(\")\", \"\")\n", - " .replace(\":\", \"\")\n", - " .replace(\"&\", \"n\")\n", - " )\n", + " return key.replace(\" \", \"_\").replace(\"(\", \"\").replace(\")\", \"\").replace(\":\", \"\").replace(\"&\", \"n\")\n", + "\n", "\n", "download_jobs = []\n", "\n", "for idx, row in data.iterrows():\n", " dataset_path = OUTPUT_DIR / row[\"id\"]\n", - " create_directory(dataset_path) \n", + " create_directory(dataset_path)\n", "\n", " raw_input_path = dataset_path / \"raw_input\"\n", - " create_directory(raw_input_path) \n", + " create_directory(raw_input_path)\n", " raw_output_path = dataset_path / \"raw_output\"\n", - " create_directory(raw_output_path) \n", + " create_directory(raw_output_path)\n", "\n", - " for idx, field in enumerate(['input_links', 'output_links']):\n", - " if row.get(field): \n", + " for idx, field in enumerate([\"input_links\", \"output_links\"]):\n", + " if row.get(field):\n", " links = json.loads(row[field])\n", - " links_dict = {sanitize_key(link['name']): link['url'] for link in links}\n", + " links_dict = {sanitize_key(link[\"name\"]): link[\"url\"] for link in links}\n", " for name, url in links_dict.items():\n", " # filter out links to the support page and subsets\n", " if \"https\" in url and \"subset\" not in name:\n", - " download_jobs.append({\n", - " \"name\": name,\n", - " \"url\": url,\n", - " \"output_folder\": [raw_input_path, raw_output_path][idx]\n", - " })\n", + " download_jobs.append(\n", + " {\"name\": name, \"url\": url, \"output_folder\": [raw_input_path, raw_output_path][idx]}\n", + " )\n", "\n", "download_jobs" ] @@ -316,25 +310,23 @@ "def download_file(job):\n", " \"\"\"Download a file using curl and save it to a specified path.\"\"\"\n", " # Parse the file name from the URL\n", - " parsed_url = urlparse(job['url'])\n", + " parsed_url = urlparse(job[\"url\"])\n", " file_name = pl.Path(parsed_url.path).name\n", - " output_path = job['output_folder'] / file_name\n", + " output_path = job[\"output_folder\"] / file_name\n", "\n", - " curl_command = [\n", - " 'curl', '-o', str(output_path), \n", - " '-L', job['url']\n", - " ]\n", + " curl_command = [\"curl\", \"-o\", str(output_path), \"-L\", job[\"url\"]]\n", "\n", " try:\n", - " subprocess.run(curl_command, check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n", + " subprocess.run(curl_command, check=True, capture_output=True)\n", " return job, None\n", " except subprocess.CalledProcessError as e:\n", " return job, e\n", "\n", + "\n", "def main(download_jobs):\n", " timestamp = datetime.now().strftime(\"%Y%m%d_%H%M%S\")\n", - " log_file = f'failed_downloads_{timestamp}.log'\n", - " with open(log_file, 'w') as log:\n", + " log_file = f\"failed_downloads_{timestamp}.log\"\n", + " with open(log_file, \"w\") as log:\n", " with ThreadPoolExecutor() as executor:\n", " futures = [executor.submit(download_file, job) for job in download_jobs]\n", " for future in tqdm(as_completed(futures), total=len(download_jobs), desc=\"Downloading files\"):\n", @@ -344,6 +336,7 @@ " log.write(error_message)\n", " print(error_message)\n", "\n", + "\n", "if __name__ == \"__main__\":\n", " main(download_jobs)" ] diff --git a/scripts/download_10X_data.py b/scripts/download_10X_data.py index 5a258b7..5f7b3eb 100644 --- a/scripts/download_10X_data.py +++ b/scripts/download_10X_data.py @@ -1,20 +1,19 @@ #!/usr/bin/env python -# coding: utf-8 -# # Download 10X data +# # Download 10X data # In[1]: -import pathlib as pl -import pandas as pd import json +import pathlib as pl import subprocess from concurrent.futures import ThreadPoolExecutor, as_completed -from tqdm.auto import tqdm -from urllib.parse import urlparse from datetime import datetime +from urllib.parse import urlparse +import pandas as pd +from tqdm.auto import tqdm OUTPUT_DIR = pl.Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data") @@ -33,44 +32,38 @@ download_jobs = [] + def create_directory(path: pl.Path): if not path.exists(): path.mkdir() print(f"Created directory: {path}") + def sanitize_key(key: str): - return ( - key - .replace(" ", "_") - .replace("(", "") - .replace(")", "") - .replace(":", "") - .replace("&", "n") - ) + return key.replace(" ", "_").replace("(", "").replace(")", "").replace(":", "").replace("&", "n") + download_jobs = [] for idx, row in data.iterrows(): dataset_path = OUTPUT_DIR / row["id"] - create_directory(dataset_path) + create_directory(dataset_path) raw_input_path = dataset_path / "raw_input" - create_directory(raw_input_path) + create_directory(raw_input_path) raw_output_path = dataset_path / "raw_output" - create_directory(raw_output_path) + create_directory(raw_output_path) - for idx, field in enumerate(['input_links', 'output_links']): - if row.get(field): + for idx, field in enumerate(["input_links", "output_links"]): + if row.get(field): links = json.loads(row[field]) - links_dict = {sanitize_key(link['name']): link['url'] for link in links} + links_dict = {sanitize_key(link["name"]): link["url"] for link in links} for name, url in links_dict.items(): # filter out links to the support page and subsets if "https" in url and "subset" not in name: - download_jobs.append({ - "name": name, - "url": url, - "output_folder": [raw_input_path, raw_output_path][idx] - }) + download_jobs.append( + {"name": name, "url": url, "output_folder": [raw_input_path, raw_output_path][idx]} + ) download_jobs @@ -83,25 +76,23 @@ def sanitize_key(key: str): def download_file(job): """Download a file using curl and save it to a specified path.""" # Parse the file name from the URL - parsed_url = urlparse(job['url']) + parsed_url = urlparse(job["url"]) file_name = pl.Path(parsed_url.path).name - output_path = job['output_folder'] / file_name + output_path = job["output_folder"] / file_name - curl_command = [ - 'curl', '-o', str(output_path), - '-L', job['url'] - ] + curl_command = ["curl", "-o", str(output_path), "-L", job["url"]] try: - subprocess.run(curl_command, check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + subprocess.run(curl_command, check=True, capture_output=True) return job, None except subprocess.CalledProcessError as e: return job, e + def main(download_jobs): timestamp = datetime.now().strftime("%Y%m%d_%H%M%S") - log_file = f'failed_downloads_{timestamp}.log' - with open(log_file, 'w') as log: + log_file = f"failed_downloads_{timestamp}.log" + with open(log_file, "w") as log: with ThreadPoolExecutor() as executor: futures = [executor.submit(download_file, job) for job in download_jobs] for future in tqdm(as_completed(futures), total=len(download_jobs), desc="Downloading files"): @@ -111,6 +102,6 @@ def main(download_jobs): log.write(error_message) print(error_message) + if __name__ == "__main__": main(download_jobs) - diff --git a/scripts/parse_10X_ST_table.ipynb b/scripts/parse_10X_ST_table.ipynb index e4dff41..03e30de 100644 --- a/scripts/parse_10X_ST_table.ipynb +++ b/scripts/parse_10X_ST_table.ipynb @@ -16,20 +16,19 @@ "metadata": {}, "outputs": [], "source": [ - "from selenium import webdriver\n", - "from selenium.webdriver.firefox.service import Service\n", - "from selenium.webdriver.firefox.options import Options\n", - "from selenium.webdriver.common.by import By\n", - "from selenium.webdriver.common.keys import Keys\n", - "from selenium.webdriver.support.ui import WebDriverWait\n", - "from selenium.webdriver.support import expected_conditions as EC\n", - "from bs4 import BeautifulSoup\n", - "import time\n", - "import pandas as pd\n", - "import re\n", "import json\n", "import random\n", "import string\n", + "import time\n", + "\n", + "import pandas as pd\n", + "from bs4 import BeautifulSoup\n", + "from selenium import webdriver\n", + "from selenium.webdriver.common.by import By\n", + "from selenium.webdriver.firefox.options import Options\n", + "from selenium.webdriver.firefox.service import Service\n", + "from selenium.webdriver.support import expected_conditions as EC\n", + "from selenium.webdriver.support.ui import WebDriverWait\n", "\n", "random.seed(8)" ] @@ -45,11 +44,11 @@ "\n", "# Use my user-profile so I'm already logged in\n", "firefox_options.add_argument(\"-profile\")\n", - "firefox_options.add_argument(\"/Users/tim.treis/Library/Application Support/Firefox/Profiles/9qiwq385.default-release-1697557194190\")\n", - "s = Service(\"./geckodriver\") \n", - "driver = webdriver.Firefox(\n", - " service=s, options=firefox_options\n", + "firefox_options.add_argument(\n", + " \"/Users/tim.treis/Library/Application Support/Firefox/Profiles/9qiwq385.default-release-1697557194190\"\n", ")\n", + "s = Service(\"./geckodriver\")\n", + "driver = webdriver.Firefox(service=s, options=firefox_options)\n", "\n", "# only 4 datasets for testing\n", "# url = \"https://www.10xgenomics.com/datasets?query=&page=1&configure%5Bfacets%5D%5B0%5D=chemistryVersionAndThroughput&configure%5Bfacets%5D%5B1%5D=pipeline.version&configure%5BhitsPerPage%5D=50&configure%5BmaxValuesPerFacet%5D=1000&menu%5Bproducts.name%5D=Spatial%20Gene%20Expression&refinementList%5Bproduct.name%5D%5B0%5D=HD%20Spatial%20Gene%20Expression\"\n", @@ -60,16 +59,14 @@ "time.sleep(10)\n", "\n", "# Scroll because it's dynamically loaded\n", - "scroll_increment = 500 \n", + "scroll_increment = 500\n", "while True:\n", " driver.execute_script(f\"window.scrollBy(0, {scroll_increment});\")\n", - " time.sleep(10) \n", + " time.sleep(10)\n", "\n", " # Check if we've reached the bottom\n", " scroll_height = driver.execute_script(\"return document.body.scrollHeight;\")\n", - " current_position = driver.execute_script(\n", - " \"return window.pageYOffset + window.innerHeight;\"\n", - " )\n", + " current_position = driver.execute_script(\"return window.pageYOffset + window.innerHeight;\")\n", " if current_position >= scroll_height:\n", " break\n", "html = driver.page_source\n", @@ -79,7 +76,7 @@ "table = soup.find(\"table\", class_=\"css-118cv4k\")\n", "headers = [th.get_text() for th in table.find_all(\"th\")]\n", "\n", - "rows = driver.find_elements(By.CSS_SELECTOR, \"tr.css-1mz91s4\") # might have to adjust when they change it\n", + "rows = driver.find_elements(By.CSS_SELECTOR, \"tr.css-1mz91s4\") # might have to adjust when they change it\n", "dataset_information = []\n", "for row in rows:\n", " tds = row.find_elements(By.CSS_SELECTOR, \"td\")\n", @@ -88,11 +85,11 @@ " for td in tds:\n", " # Check if the 'td' element contains an 'a' tag (link)\n", " try:\n", - " link = td.find_element(By.TAG_NAME, 'a').get_attribute('href')\n", + " link = td.find_element(By.TAG_NAME, \"a\").get_attribute(\"href\")\n", " # Get the full URL if the href attribute is a relative path\n", - " if link.startswith('/'):\n", - " link = driver.current_url.rsplit('/', 1)[0] + link\n", - " except Exception as e:\n", + " if link.startswith(\"/\"):\n", + " link = driver.current_url.rsplit(\"/\", 1)[0] + link\n", + " except Exception:\n", " # If there is no 'a' tag, just extract the text\n", " pass\n", " row_data.append(link)\n", @@ -534,7 +531,6 @@ "rows_for_df = []\n", "for row in dataset_information:\n", " if len(row) != 0 and not (len(row) == 1 and row[0] is None):\n", - "\n", " # weirdly, sometimes the 2nd element is empty\n", " if len(row) == len(extended_headers) + 1 and len(row[1]) == 0:\n", " row.pop(1)\n", @@ -580,7 +576,7 @@ "source": [ "def has_replicates(html_content):\n", " soup = BeautifulSoup(html_content, \"html.parser\")\n", - " files_box = soup.find('div', text='Files')\n", + " files_box = soup.find(\"div\", text=\"Files\")\n", " return files_box is not None\n", "\n", "\n", @@ -612,12 +608,11 @@ "\n", " return replicate_data\n", "\n", + "\n", "driver = webdriver.Firefox(service=s, options=firefox_options)\n", - "link_df = pd.DataFrame(\n", - " columns=[\"Datasets\", \"Replicate\", \"HTML\"]\n", - ")\n", + "link_df = pd.DataFrame(columns=[\"Datasets\", \"Replicate\", \"HTML\"])\n", "\n", - "for idx, row in df.iterrows():\n", + "for _idx, row in df.iterrows():\n", " driver.get(row[\"dataset_link\"])\n", " time.sleep(10)\n", " html_content = driver.page_source\n", @@ -657,18 +652,12 @@ " input_files_html = str(table)\n", " input_soup = BeautifulSoup(input_files_html, \"html.parser\")\n", " input_links = input_soup.select(\"table a\")\n", - " input_files = [\n", - " {\"name\": link.get_text(strip=True), \"url\": link[\"href\"]}\n", - " for link in input_links\n", - " ]\n", + " input_files = [{\"name\": link.get_text(strip=True), \"url\": link[\"href\"]} for link in input_links]\n", " elif \"Output Files\" in table.text:\n", " output_files_html = str(table)\n", " output_soup = BeautifulSoup(output_files_html, \"html.parser\")\n", " output_links = output_soup.select(\"table a\")\n", - " output_files = [\n", - " {\"name\": link.get_text(strip=True), \"url\": link[\"href\"]}\n", - " for link in output_links\n", - " ]\n", + " output_files = [{\"name\": link.get_text(strip=True), \"url\": link[\"href\"]} for link in output_links]\n", "\n", " # Convert input_files and output_files to JSON strings\n", " input_files_json = json.dumps(input_files) if input_files else None\n", @@ -940,9 +929,7 @@ "metadata": {}, "outputs": [], "source": [ - "def generate_unique_ids(\n", - " n: int, size: int = 5, chars=string.ascii_lowercase + string.digits\n", - "):\n", + "def generate_unique_ids(n: int, size: int = 5, chars=string.ascii_lowercase + string.digits):\n", " \"\"\"Generate a list of n unique pseudo-random IDs.\"\"\"\n", " unique_ids = set()\n", " while len(unique_ids) < n:\n", diff --git a/scripts/query_artifacts.ipynb b/scripts/query_artifacts.ipynb index 0fb1a18..cb06fa7 100644 --- a/scripts/query_artifacts.ipynb +++ b/scripts/query_artifacts.ipynb @@ -6,8 +6,8 @@ "metadata": {}, "outputs": [], "source": [ - "import lamindb as ln\n", - "import bionty as bt" + "import bionty as bt\n", + "import lamindb as ln" ] }, { diff --git a/scripts/rename_on_lustre.ipynb b/scripts/rename_on_lustre.ipynb index 7898776..eca1e10 100644 --- a/scripts/rename_on_lustre.ipynb +++ b/scripts/rename_on_lustre.ipynb @@ -13,11 +13,12 @@ "metadata": {}, "outputs": [], "source": [ - "import pandas as pd\n", - "from tqdm import tqdm\n", "import os\n", "from concurrent.futures import ProcessPoolExecutor, as_completed\n", "\n", + "import pandas as pd\n", + "from tqdm import tqdm\n", + "\n", "tenx = pd.read_csv(\"data/datasets_10x.csv\", sep=\";\")" ] }, @@ -249,7 +250,7 @@ } ], "source": [ - "uid_mapping = dict(zip(tenx['uid_old'], tenx['uid']))\n", + "uid_mapping = dict(zip(tenx[\"uid_old\"], tenx[\"uid\"], strict=False))\n", "uid_mapping" ] }, @@ -259,21 +260,22 @@ "metadata": {}, "outputs": [], "source": [ - "\n", "def gather_files(target_dir, extensions=None):\n", " \"\"\"\n", " Gather all file paths in the target directory (recursively) that match the specified extensions.\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " target_dir (str): Path to the target directory.\n", " extensions (list, optional): List of file extensions to include (e.g., ['.txt', '.md']).\n", " If None, all files are included.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " list: List of file paths to process.\n", " \"\"\"\n", " files_to_process = []\n", - " for root, dirs, files in os.walk(target_dir):\n", + " for root, _dirs, files in os.walk(target_dir):\n", " for name in files:\n", " if extensions:\n", " if not any(name.lower().endswith(ext) for ext in extensions):\n", @@ -282,18 +284,21 @@ " files_to_process.append(file_path)\n", " return files_to_process\n", "\n", + "\n", "def gather_directories(target_dir):\n", " \"\"\"\n", " Gather all directory paths in the target directory (recursively).\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " target_dir (str): Path to the target directory.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " list: List of directory paths to process.\n", " \"\"\"\n", " directories_to_process = []\n", - " for root, dirs, files in os.walk(target_dir):\n", + " for root, dirs, _files in os.walk(target_dir):\n", " for name in dirs:\n", " dir_path = os.path.join(root, name)\n", " directories_to_process.append(dir_path)\n", @@ -304,18 +309,20 @@ " \"\"\"\n", " Rename a single file by replacing occurrences of uid_old with uid in the filename.\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " file_path (str): Path to the file to be renamed.\n", " mapping (dict): Dictionary mapping 'uid_old' to 'uid'.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " bool: True if renamed successfully, False otherwise.\n", " \"\"\"\n", " directory, filename = os.path.split(file_path)\n", " new_filename = filename\n", " for uid_old, uid in mapping.items():\n", " new_filename = new_filename.replace(uid_old, uid)\n", - " \n", + "\n", " if new_filename != filename:\n", " new_file_path = os.path.join(directory, new_filename)\n", " try:\n", @@ -331,22 +338,25 @@ " return False\n", " return False # No renaming needed\n", "\n", + "\n", "def rename_directory(dir_path, mapping):\n", " \"\"\"\n", " Rename a single directory by replacing occurrences of uid_old with uid in the directory name.\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " dir_path (str): Path to the directory to be renamed.\n", " mapping (dict): Dictionary mapping 'uid_old' to 'uid'.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " bool: True if renamed successfully, False otherwise.\n", " \"\"\"\n", " parent_dir, dir_name = os.path.split(dir_path)\n", " new_dir_name = dir_name\n", " for uid_old, uid in mapping.items():\n", " new_dir_name = new_dir_name.replace(uid_old, uid)\n", - " \n", + "\n", " if new_dir_name != dir_name:\n", " new_dir_path = os.path.join(parent_dir, new_dir_name)\n", " try:\n", @@ -362,22 +372,25 @@ " return False\n", " return False # No renaming needed\n", "\n", + "\n", "def rename_files_parallel(files, mapping):\n", " \"\"\"\n", " Rename files in parallel by replacing uid_old with uid in filenames.\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " files (list): List of file paths to rename.\n", " mapping (dict): Dictionary mapping 'uid_old' to 'uid'.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " int: Number of files successfully renamed.\n", " \"\"\"\n", " renamed_count = 0\n", " with ProcessPoolExecutor() as executor:\n", " # Submit all rename tasks\n", " future_to_file = {executor.submit(rename_file, file, mapping): file for file in files}\n", - " \n", + "\n", " for future in tqdm(as_completed(future_to_file), total=len(future_to_file), desc=\"Renaming files\"):\n", " file = future_to_file[future]\n", " try:\n", @@ -388,22 +401,25 @@ " print(f\"Error processing file {file}: {e}\")\n", " return renamed_count\n", "\n", + "\n", "def rename_directories_parallel(directories, mapping):\n", " \"\"\"\n", " Rename directories in parallel by replacing uid_old with uid in directory names.\n", "\n", - " Parameters:\n", + " Parameters\n", + " ----------\n", " directories (list): List of directory paths to rename.\n", " mapping (dict): Dictionary mapping 'uid_old' to 'uid'.\n", "\n", - " Returns:\n", + " Returns\n", + " -------\n", " int: Number of directories successfully renamed.\n", " \"\"\"\n", " renamed_count = 0\n", " with ProcessPoolExecutor() as executor:\n", " # Submit all rename tasks\n", " future_to_dir = {executor.submit(rename_directory, dir_path, mapping): dir_path for dir_path in directories}\n", - " \n", + "\n", " for future in tqdm(as_completed(future_to_dir), total=len(future_to_dir), desc=\"Renaming directories\"):\n", " dir_path = future_to_dir[future]\n", " try:\n", @@ -412,8 +428,7 @@ " renamed_count += 1\n", " except Exception as e:\n", " print(f\"Error processing directory {dir_path}: {e}\")\n", - " return renamed_count\n", - "\n" + " return renamed_count" ] }, { @@ -422,7 +437,7 @@ "metadata": {}, "outputs": [], "source": [ - "target_directory = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\" " + "target_directory = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\"" ] }, { diff --git a/scripts/spatial_data_curator.ipynb b/scripts/spatial_data_curator.ipynb index 5b61350..52625d5 100644 --- a/scripts/spatial_data_curator.ipynb +++ b/scripts/spatial_data_curator.ipynb @@ -32,19 +32,13 @@ ], "source": [ "import os\n", - "\n", "import warnings\n", - "warnings.filterwarnings(\"ignore\")\n", "\n", - "import spatialdata as sd\n", - "import pandas as pd\n", - "from lamin_spatial import SpatialDataCurator\n", - "\n", - "import lamindb as ln\n", + "warnings.filterwarnings(\"ignore\")\n", "\n", "import bionty as bt\n", - "\n", - "from lnschema_core import ULabel\n", + "import lamindb as ln\n", + "import spatialdata as sd\n", "\n", "from spatialdata_db import SpatialDataDBCurator" ] @@ -55,7 +49,7 @@ "metadata": {}, "outputs": [], "source": [ - "DATA_PATH = '/lustre/groups/ml01/projects/2024_spatialdata_db/data'" + "DATA_PATH = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\"" ] }, { @@ -77,19 +71,17 @@ "\n", " for filename in os.listdir(folder_path):\n", " if \"attrs\" in filename:\n", - " file_path = os.path.join(folder_path, filename) \n", + " file_path = os.path.join(folder_path, filename)\n", "\n", " sdata = sd.read_zarr(file_path)\n", "\n", " for table in sdata.tables.keys():\n", - " sdata.tables[table].var['gene_symbols'] = sdata.tables[table].var.index\n", - " sdata.tables[table].var.index = sdata.tables[table].var['gene_ids'].values\n", + " sdata.tables[table].var[\"gene_symbols\"] = sdata.tables[table].var.index\n", + " sdata.tables[table].var.index = sdata.tables[table].var[\"gene_ids\"].values\n", "\n", " tables = {table_key: bt.Gene.ensembl_gene_id for table_key in sdata.tables.keys()}\n", "\n", - " sdc = SpatialDataDBCurator(sdata, \n", - " var_index=tables,\n", - " organism=sdata.attrs['sample']['organism'].lower())\n", + " sdc = SpatialDataDBCurator(sdata, var_index=tables, organism=sdata.attrs[\"sample\"][\"organism\"].lower())\n", "\n", " return sdc, sdata" ] @@ -118,10 +110,7 @@ "metadata": {}, "outputs": [], "source": [ - "sdc = SpatialDataDBCurator(\n", - " sdata, \n", - " var_index=tables,\n", - " organism='human')" + "sdc = SpatialDataDBCurator(sdata, var_index=tables, organism=\"human\")" ] }, { @@ -185,7 +174,7 @@ } ], "source": [ - "sdc.standardize(\"organism\", accessor='sample')" + "sdc.standardize(\"organism\", accessor=\"sample\")" ] }, { @@ -270,7 +259,7 @@ "metadata": {}, "outputs": [], "source": [ - "sdc, sdata = get_curator('10nsr')" + "sdc, sdata = get_curator(\"10nsr\")" ] }, { @@ -279,7 +268,7 @@ "metadata": {}, "outputs": [], "source": [ - "sdc = SpatialDataDBCurator(sdata, var_index=tables, organism='human')" + "sdc = SpatialDataDBCurator(sdata, var_index=tables, organism=\"human\")" ] }, { @@ -345,9 +334,9 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", - "sdc.standardize(\"disease\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", + "sdc.standardize(\"disease\", accessor=\"sample\")" ] }, { @@ -394,7 +383,18 @@ "metadata": {}, "outputs": [], "source": [ - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]" + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")" ] }, { @@ -484,7 +484,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10u63')\n", + "sdc, sdata = get_curator(\"10u63\")\n", "sdc.validate()" ] }, @@ -503,8 +503,8 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")" ] }, { @@ -554,7 +554,18 @@ ], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -600,7 +611,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10wmu')\n", + "sdc, sdata = get_curator(\"10wmu\")\n", "sdc.validate()" ] }, @@ -619,8 +630,8 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")" ] }, { @@ -671,7 +682,18 @@ ], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -719,7 +741,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10tsy')\n", + "sdc, sdata = get_curator(\"10tsy\")\n", "sdc.validate()" ] }, @@ -739,9 +761,9 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", - "sdc.add_new_from(\"tissue\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", + "sdc.add_new_from(\"tissue\", accessor=\"sample\")" ] }, { @@ -793,7 +815,18 @@ ], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -838,7 +871,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10k5p')\n", + "sdc, sdata = get_curator(\"10k5p\")\n", "sdc.validate()" ] }, @@ -857,8 +890,8 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")" ] }, { @@ -909,7 +942,18 @@ ], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -957,7 +1001,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10f2z')\n", + "sdc, sdata = get_curator(\"10f2z\")\n", "sdc.validate()" ] }, @@ -977,9 +1021,9 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", - "sdc.standardize(\"tissue\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", + "sdc.standardize(\"tissue\", accessor=\"sample\")" ] }, { @@ -1030,7 +1074,18 @@ ], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -1077,7 +1132,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10zvc')\n", + "sdc, sdata = get_curator(\"10zvc\")\n", "sdc.validate()" ] }, @@ -1096,8 +1151,8 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", "# sdc.add_new_from_var_index(table='table')" ] }, @@ -1177,7 +1232,18 @@ } ], "source": [ - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -1188,7 +1254,18 @@ "outputs": [], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -1237,7 +1314,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10fn9')\n", + "sdc, sdata = get_curator(\"10fn9\")\n", "sdc.validate()" ] }, @@ -1287,9 +1364,9 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", - "sdc.add_new_from_var_index(table='table')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", + "sdc.add_new_from_var_index(table=\"table\")" ] }, { @@ -1299,7 +1376,18 @@ "outputs": [], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, @@ -1348,7 +1436,7 @@ } ], "source": [ - "sdc, sdata = get_curator('10jff')\n", + "sdc, sdata = get_curator(\"10jff\")\n", "sdc.validate()" ] }, @@ -1358,8 +1446,8 @@ "metadata": {}, "outputs": [], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")" ] }, { @@ -1369,7 +1457,18 @@ "outputs": [], "source": [ "sdc.validate()\n", - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] } diff --git a/scripts/update_uid_master.py b/scripts/update_uid_master.py index b841e5e..164923f 100644 --- a/scripts/update_uid_master.py +++ b/scripts/update_uid_master.py @@ -1,4 +1,5 @@ import os + import pandas as pd @@ -17,9 +18,7 @@ def update_master_with_ids(uid_master_csv_path, file_paths): ) print(uid_master_df) - master_df = uid_master_df.merge( - df[["uid", "id"]], on="uid", how="left", suffixes=("", "_new") - ) + master_df = uid_master_df.merge(df[["uid", "id"]], on="uid", how="left", suffixes=("", "_new")) master_df["id"] = master_df["id"].combine_first(master_df["id_new"]) print(master_df) @@ -30,7 +29,7 @@ def update_master_with_ids(uid_master_csv_path, file_paths): if __name__ == "__main__": - master_csv_path = "data/uid_master.csv" + master_csv_path = "data/uid_master.csv" dataset_paths = [ "data/datasets_10x.csv", # tbd diff --git a/scripts/upload_1000j_visium.ipynb b/scripts/upload_1000j_visium.ipynb index 67ff796..2f656a7 100644 --- a/scripts/upload_1000j_visium.ipynb +++ b/scripts/upload_1000j_visium.ipynb @@ -25,16 +25,15 @@ ], "source": [ "import os\n", - "\n", "import warnings\n", + "\n", "warnings.filterwarnings(\"ignore\")\n", "\n", - "import spatialdata as sd\n", + "import lamindb as ln\n", "import pandas as pd\n", - "from spatialdata_db import SpatialDataDBCurator\n", - "import spatialdata_db\n", + "import spatialdata as sd\n", "\n", - "import lamindb as ln" + "from spatialdata_db import SpatialDataDBCurator" ] }, { @@ -46,8 +45,8 @@ "def replace_var_index(sdata):\n", " for table_name, table in sdata.tables.items():\n", " if isinstance(table.var, pd.DataFrame):\n", - " table.var['gene_names'] = table.var.index\n", - " table.var.set_index('gene_ids', inplace=True)\n", + " table.var[\"gene_names\"] = table.var.index\n", + " table.var.set_index(\"gene_ids\", inplace=True)\n", " sdata.tables[table_name] = table" ] }, @@ -82,7 +81,7 @@ "metadata": {}, "outputs": [], "source": [ - "DATA_PATH = '/lustre/groups/ml01/projects/2024_spatialdata_db/data'\n", + "DATA_PATH = \"/lustre/groups/ml01/projects/2024_spatialdata_db/data\"\n", "uid = \"1000j\"" ] }, @@ -110,7 +109,7 @@ "source": [ "file = None\n", "for file in os.listdir(folder_path):\n", - " if file.endswith('.zarr'):\n", + " if file.endswith(\".zarr\"):\n", " break\n", "\n", "if file is None:\n", @@ -176,7 +175,7 @@ } ], "source": [ - "sdc = SpatialDataDBCurator(sdata, organism='human')\n", + "sdc = SpatialDataDBCurator(sdata, organism=\"human\")\n", "sdc.validate()" ] }, @@ -198,11 +197,11 @@ } ], "source": [ - "sdc.standardize(\"assay\", accessor='sample')\n", - "sdc.add_new_from(\"chemistry_version\", accessor='sample')\n", - "sdc.standardize(\"organism\", accessor='sample')\n", - "sdc.add_new_from(\"tissue\", accessor='sample')\n", - "sdc.add_new_from(\"disease\", accessor='sample')" + "sdc.standardize(\"assay\", accessor=\"sample\")\n", + "sdc.add_new_from(\"chemistry_version\", accessor=\"sample\")\n", + "sdc.standardize(\"organism\", accessor=\"sample\")\n", + "sdc.add_new_from(\"tissue\", accessor=\"sample\")\n", + "sdc.add_new_from(\"disease\", accessor=\"sample\")" ] }, { @@ -278,7 +277,18 @@ } ], "source": [ - "description = '10X, '+ sdata.attrs['sample']['assay']+ ', '+ sdata.attrs['sample']['organism']+ ', '+sdata.attrs['sample']['disease']+', '+ sdata.attrs['sample']['tissue']+ ', '+ sdata.attrs['sample']['date'][:4]\n", + "description = (\n", + " \"10X, \"\n", + " + sdata.attrs[\"sample\"][\"assay\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"organism\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"disease\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"tissue\"]\n", + " + \", \"\n", + " + sdata.attrs[\"sample\"][\"date\"][:4]\n", + ")\n", "sdc.save_artifact(description=description)" ] }, diff --git a/scripts/validator_demo.ipynb b/scripts/validator_demo.ipynb index a0e2432..6d60bae 100644 --- a/scripts/validator_demo.ipynb +++ b/scripts/validator_demo.ipynb @@ -29,12 +29,12 @@ ], "source": [ "import warnings\n", + "\n", "warnings.filterwarnings(\"ignore\")\n", "\n", "import lamindb as ln\n", - "import bionty as bt\n", - "import pandas as pd\n", "import spatialdata as sd\n", + "\n", "from spatialdata_db import SpatialDataValidator" ] }, diff --git a/src/spatialdata_db/__init__.py b/src/spatialdata_db/__init__.py index 2a4c6b4..5598c4d 100644 --- a/src/spatialdata_db/__init__.py +++ b/src/spatialdata_db/__init__.py @@ -1,7 +1,10 @@ from importlib.metadata import version -from spatialdata_db.parsing import load_10x_metadata + from django.core.exceptions import ImproperlyConfigured from lamin_utils import logger + +from spatialdata_db.parsing import load_10x_metadata + try: from spatialdata_db.lamin_spatialdatadb_curator import SpatialDataDBCurator except ImproperlyConfigured: diff --git a/src/spatialdata_db/parsing.py b/src/spatialdata_db/parsing.py index f20c867..a70dbfd 100644 --- a/src/spatialdata_db/parsing.py +++ b/src/spatialdata_db/parsing.py @@ -1,4 +1,5 @@ from importlib import resources + import pandas as pd From 87962d9e5f21e2a377b1686771580a3330a99851 Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 14:04:01 +0100 Subject: [PATCH 13/19] chore: update required numba version to 0.61.0 --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 78bcb44..1786cfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ authors = [ { name = "Lea Zimmermann" }, { name = "Lukas Heumos" }, ] -requires-python = ">=3.10, <3.13" +requires-python = ">=3.10,<3.13" classifiers = [ "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: 3.10", @@ -27,11 +27,12 @@ classifiers = [ ] dependencies = [ "lamindb[aws,bionty,jupyter]>=1.0.4", + "numba>=0.61", + "session-info2", "spatialdata", "spatialdata-io", "spatialdata-plot", "vitessce", - "session-info2" ] optional-dependencies.dev = [ "pre-commit", From f3d5b57822d823e2d50ab17f465d4a71051475bf Mon Sep 17 00:00:00 2001 From: zimea Date: Mon, 17 Feb 2025 18:08:30 +0100 Subject: [PATCH 14/19] fix: setup lamin instance before test session --- tests/conftest.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 tests/conftest.py diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..3e5d7bd --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,12 @@ +import pytest +import lamindb_setup as ln_setup + +@pytest.fixture(scope="session") +def setup_instance(): + """ + Initialize a LamindB test instance before all tests start. + Cleans up after the test session ends. + """ + ln_setup.init(storage="tests", name="tests", schema="bionty") + yield # Run tests using this instance + ln_setup.delete("tests", force=True, require_empty=False) From b221adec68790dade925547adcc06069e5e239ad Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 17 Feb 2025 17:08:51 +0000 Subject: [PATCH 15/19] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/conftest.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/conftest.py b/tests/conftest.py index 3e5d7bd..0023030 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,6 @@ -import pytest import lamindb_setup as ln_setup +import pytest + @pytest.fixture(scope="session") def setup_instance(): From f9636f8aa415e2bf56d3ba3329cd8ba0e39174e4 Mon Sep 17 00:00:00 2001 From: zimea Date: Tue, 18 Feb 2025 09:46:01 +0100 Subject: [PATCH 16/19] fix: setup temp lamin test instance to run pytest --- tests/conftest.py | 26 ++++++++++---------- tests/integrations/test_lamin_wrappers.py | 30 ++++++++++------------- 2 files changed, 26 insertions(+), 30 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 0023030..a517b7f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,13 +1,13 @@ -import lamindb_setup as ln_setup -import pytest - - -@pytest.fixture(scope="session") -def setup_instance(): - """ - Initialize a LamindB test instance before all tests start. - Cleans up after the test session ends. - """ - ln_setup.init(storage="tests", name="tests", schema="bionty") - yield # Run tests using this instance - ln_setup.delete("tests", force=True, require_empty=False) +import lamindb.setup as ln_setup + + +def pytest_sessionstart(session): + """Initialize LamindB before any test runs (ensures it's available for imports).""" + print("\n🔹 Setting up LamindB test instance...") + ln_setup.init(storage="lamin_test_instance", name="lamin_test_instance", schema="bionty") + + +def pytest_sessionfinish(session): + """Clean up LamindB after all tests are completed.""" + print("\n🔹 Cleaning up LamindB test instance after all tests are done...") + ln_setup.delete("lamin_test_instance", force=True, require_empty=False) diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py index 38264cd..547f7ed 100644 --- a/tests/integrations/test_lamin_wrappers.py +++ b/tests/integrations/test_lamin_wrappers.py @@ -10,13 +10,9 @@ DEFAULT_FILE_NAME = "test_data.zarr" -# Only initialize a test instance in GitHub Actions -if os.getenv("GITHUB_ACTIONS") == "true": - ln.setup.init(storage="./test_lamindb") - @pytest.fixture(scope="function") -def fake_artifact(tmp_path): +def mock_artifact(tmp_path): artifact = MagicMock(spec=ln.Artifact) # Mock with ln.Artifact attributes zarr_path = tmp_path / DEFAULT_FILE_NAME zarr_path.mkdir() @@ -25,9 +21,9 @@ def fake_artifact(tmp_path): return artifact -def test_store_artifact_custom_path(fake_artifact, tmp_path): +def test_store_artifact_custom_path(mock_artifact, tmp_path): """Test storing artifact in a provided directory.""" - artifact = fake_artifact + artifact = mock_artifact target_path = tmp_path / "custom_dir" target_path.mkdir() @@ -37,9 +33,9 @@ def test_store_artifact_custom_path(fake_artifact, tmp_path): assert Path(result_path).parent == target_path -def test_store_artifact_rename(fake_artifact, tmp_path): +def test_store_artifact_rename(mock_artifact, tmp_path): """Test storing artifact with a custom name.""" - artifact = fake_artifact + artifact = mock_artifact target_path = tmp_path / "custom_dir" target_path.mkdir() @@ -64,9 +60,9 @@ def test_store_artifact_file_not_found(tmp_path): store_dataset(artifact, path=target_path) -def test_store_artifact_permission_error(fake_artifact, tmp_path): +def test_store_artifact_permission_error(mock_artifact, tmp_path): """Test that PermissionError is raised if the target directory is not writable.""" - artifact = fake_artifact + artifact = mock_artifact locked_dir = tmp_path / "locked" locked_dir.mkdir() os.chmod(locked_dir, 0o400) # Read-only directory @@ -77,9 +73,9 @@ def test_store_artifact_permission_error(fake_artifact, tmp_path): os.chmod(locked_dir, 0o700) # Restore permissions -def test_store_artifact_os_error(fake_artifact, monkeypatch, tmp_path): +def test_store_artifact_os_error(mock_artifact, monkeypatch, tmp_path): """Test that OSError is raised if a simulated system error occurs.""" - artifact = fake_artifact + artifact = mock_artifact def mock_move(*args, **kwargs): raise OSError("Mocked OS error") @@ -91,9 +87,9 @@ def mock_move(*args, **kwargs): store_dataset(artifact, path=target_path) -def test_store_artifact_overwrite_false(fake_artifact, tmp_path): +def test_store_artifact_overwrite_false(mock_artifact, tmp_path): """Test that FileExistsError is raised if overwrite=False and file exists.""" - artifact = fake_artifact + artifact = mock_artifact target_path = tmp_path / "existing_dir" target_path.mkdir() existing_file = target_path / DEFAULT_FILE_NAME @@ -103,9 +99,9 @@ def test_store_artifact_overwrite_false(fake_artifact, tmp_path): store_dataset(artifact, path=target_path, overwrite=False) -def test_store_artifact_overwrite_true(fake_artifact, tmp_path): +def test_store_artifact_overwrite_true(mock_artifact, tmp_path): """Test that artifact is stored correctly when overwrite=True.""" - artifact = fake_artifact + artifact = mock_artifact target_path = tmp_path / "existing_dir" target_path.mkdir() existing_file = target_path / DEFAULT_FILE_NAME From 44ace65fb09956f691fc5f2efc53892cc9af4506 Mon Sep 17 00:00:00 2001 From: zimea Date: Tue, 18 Feb 2025 10:48:38 +0100 Subject: [PATCH 17/19] chore: ignore coverage output --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index fa757a6..3e65b03 100644 --- a/.gitignore +++ b/.gitignore @@ -21,6 +21,7 @@ __pycache__/ /data/ /scripts/data/ /node_modules/ +.coverage # docs /docs/generated/ From 3922998a44889f46e2ada083b3926dd58434105c Mon Sep 17 00:00:00 2001 From: zimea Date: Tue, 18 Feb 2025 10:50:05 +0100 Subject: [PATCH 18/19] test: cover different potential permission errors --- .../integrations/lamindb_wrappers.py | 13 ++++++-- tests/integrations/test_lamin_wrappers.py | 33 +++++++++++++++++-- 2 files changed, 41 insertions(+), 5 deletions(-) diff --git a/src/spatialdata_db/integrations/lamindb_wrappers.py b/src/spatialdata_db/integrations/lamindb_wrappers.py index 4357050..d40a0bc 100644 --- a/src/spatialdata_db/integrations/lamindb_wrappers.py +++ b/src/spatialdata_db/integrations/lamindb_wrappers.py @@ -29,15 +29,22 @@ def store_dataset( - FileExistsError: If the target file already exists and overwrite=False. """ target_dir = Path(path).resolve() - target_dir.mkdir(parents=True, exist_ok=True) + + try: + target_dir.mkdir(parents=True, exist_ok=True) + except PermissionError as e: + raise PermissionError(f"Failed to create the target directory due to insufficient permissions: {e}") from e cached_path = artifact.cache() cached_path = Path(cached_path).resolve() final_path = target_dir / (name if name else cached_path.name) - if final_path.exists() and not overwrite: - raise FileExistsError(f"Target file already exists: {final_path}. Use overwrite=True to replace it.") + try: + if final_path.exists() and not overwrite: + raise FileExistsError(f"Target file already exists: {final_path}. Use overwrite=True to replace it.") + except PermissionError as e: + raise PermissionError(f"Insufficient permissions: {e}") from e if cached_path != final_path: try: diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py index 547f7ed..50d074f 100644 --- a/tests/integrations/test_lamin_wrappers.py +++ b/tests/integrations/test_lamin_wrappers.py @@ -60,19 +60,48 @@ def test_store_artifact_file_not_found(tmp_path): store_dataset(artifact, path=target_path) -def test_store_artifact_permission_error(mock_artifact, tmp_path): +def test_store_artifact_reading_permission_error(mock_artifact, tmp_path): """Test that PermissionError is raised if the target directory is not writable.""" artifact = mock_artifact locked_dir = tmp_path / "locked" locked_dir.mkdir() os.chmod(locked_dir, 0o400) # Read-only directory - with pytest.raises(PermissionError): + with pytest.raises(PermissionError, match="Insufficient permissions"): store_dataset(artifact, path=locked_dir) os.chmod(locked_dir, 0o700) # Restore permissions +def test_store_artifact_directory_creation_permission_error(mock_artifact, tmp_path): + """Test that PermissionError is raised if creating the target directory fails due to insufficient permissions.""" + locked_parent = tmp_path / "locked_parent" + locked_parent.mkdir() + os.chmod(locked_parent, 0o400) # Read-only directory + + locked_dir = locked_parent / "subdir" + + with pytest.raises(PermissionError, match="Failed to create the target directory"): + store_dataset(mock_artifact, path=locked_dir) + + os.chmod(locked_parent, 0o700) # Restore permissions + + +def test_store_artifact_move_permission_error(mock_artifact, monkeypatch, tmp_path): + """Test that PermissionError is raised if moving the artifact fails due to insufficient permissions.""" + artifact = mock_artifact + target_path = tmp_path / "custom_dir" + target_path.mkdir() + + def mock_move(*args, **kwargs): + raise PermissionError("Mocked permission error") + + monkeypatch.setattr(shutil, "move", mock_move) # Mock shutil.move to always raise PermissionError + + with pytest.raises(PermissionError, match="Failed to move artifact due to insufficient permissions"): + store_dataset(artifact, path=target_path) + + def test_store_artifact_os_error(mock_artifact, monkeypatch, tmp_path): """Test that OSError is raised if a simulated system error occurs.""" artifact = mock_artifact From aa4fb2f476ed4820544eee4bd1108e121037a52a Mon Sep 17 00:00:00 2001 From: zimea Date: Tue, 18 Feb 2025 10:58:03 +0100 Subject: [PATCH 19/19] refactor: clean-up variable names and docstrings --- tests/conftest.py | 2 +- tests/integrations/test_lamin_wrappers.py | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index a517b7f..2556551 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,7 @@ def pytest_sessionstart(session): - """Initialize LamindB before any test runs (ensures it's available for imports).""" + """Initialize LamindB before any test runs.""" print("\n🔹 Setting up LamindB test instance...") ln_setup.init(storage="lamin_test_instance", name="lamin_test_instance", schema="bionty") diff --git a/tests/integrations/test_lamin_wrappers.py b/tests/integrations/test_lamin_wrappers.py index 50d074f..f9438d2 100644 --- a/tests/integrations/test_lamin_wrappers.py +++ b/tests/integrations/test_lamin_wrappers.py @@ -24,7 +24,7 @@ def mock_artifact(tmp_path): def test_store_artifact_custom_path(mock_artifact, tmp_path): """Test storing artifact in a provided directory.""" artifact = mock_artifact - target_path = tmp_path / "custom_dir" + target_path = tmp_path / "target_dir" target_path.mkdir() result_path = store_dataset(artifact, path=target_path) @@ -36,7 +36,7 @@ def test_store_artifact_custom_path(mock_artifact, tmp_path): def test_store_artifact_rename(mock_artifact, tmp_path): """Test storing artifact with a custom name.""" artifact = mock_artifact - target_path = tmp_path / "custom_dir" + target_path = tmp_path / "target_dir" target_path.mkdir() new_name = "renamed_data.zarr" @@ -55,13 +55,13 @@ def test_store_artifact_file_not_found(tmp_path): # Explicitly add the `cache` method artifact.cache = MagicMock(return_value=str(zarr_path)) - target_path = tmp_path / "custom_dir" + target_path = tmp_path / "target_dir" with pytest.raises(FileNotFoundError): store_dataset(artifact, path=target_path) def test_store_artifact_reading_permission_error(mock_artifact, tmp_path): - """Test that PermissionError is raised if the target directory is not writable.""" + """Test that PermissionError is raised if the user has insufficient permissions for the target directory.""" artifact = mock_artifact locked_dir = tmp_path / "locked" locked_dir.mkdir() @@ -90,7 +90,7 @@ def test_store_artifact_directory_creation_permission_error(mock_artifact, tmp_p def test_store_artifact_move_permission_error(mock_artifact, monkeypatch, tmp_path): """Test that PermissionError is raised if moving the artifact fails due to insufficient permissions.""" artifact = mock_artifact - target_path = tmp_path / "custom_dir" + target_path = tmp_path / "target_dir" target_path.mkdir() def mock_move(*args, **kwargs): @@ -111,7 +111,7 @@ def mock_move(*args, **kwargs): monkeypatch.setattr(shutil, "move", mock_move) - target_path = tmp_path / "custom_dir" + target_path = tmp_path / "target_dir" with pytest.raises(OSError, match="Mocked OS error"): store_dataset(artifact, path=target_path)