cap-anndata 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cap_anndata/__init__.py +10 -10
- cap_anndata/backed_df.py +81 -69
- cap_anndata/backed_dict.py +34 -34
- cap_anndata/cap_anndata.py +625 -600
- cap_anndata/reader.py +57 -57
- {cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/LICENSE +28 -28
- {cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/METADATA +67 -54
- cap_anndata-0.4.0.dist-info/RECORD +10 -0
- {cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/WHEEL +1 -1
- cap_anndata-0.3.0.dist-info/RECORD +0 -10
- {cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/top_level.txt +0 -0
cap_anndata/reader.py
CHANGED
@@ -1,57 +1,57 @@
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import logging
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import h5py
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import warnings
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from cap_anndata import CapAnnData
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logger = logging.getLogger(__name__)
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def read_h5ad(file_path: str, edit: bool = False):
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"""
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This is the main read method for CapAnnData.
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Must be used in 'with' context.
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"""
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mode = "r+" if edit else "r"
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logger.debug(f"Read file {file_path} mode={mode} in context...")
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try:
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file = h5py.File(file_path, mode)
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cap_adata = CapAnnData(file)
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logger.debug(f"Successfully read anndata file path {file_path}")
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return cap_adata
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except Exception as error:
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logger.error(
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f"Error during read anndata file at path: {file_path}, error = {error}!"
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)
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raise error
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def deprecated(message):
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def deprecated_decorator(func):
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def deprecated_func(*args, **kwargs):
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warnings.warn(
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"{} is a deprecated function. {}".format(func.__name__, message),
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category=DeprecationWarning,
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stacklevel=2,
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)
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warnings.simplefilter("default", DeprecationWarning)
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return func(*args, **kwargs)
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return deprecated_func
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return deprecated_decorator
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# TODO: remove deprecated function
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@deprecated(
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"It will be removed in the next version of package. Please replace it with `read_h5ad`."
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)
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def read_directly(file_path: str, edit: bool = False) -> CapAnnData:
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"""
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Must be used only in specific cases.
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User is responsible to close the h5py file when the work with CapAnnData instance done.
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"""
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return read_h5ad(file_path, edit)
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import logging
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import h5py
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import warnings
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from cap_anndata import CapAnnData
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logger = logging.getLogger(__name__)
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def read_h5ad(file_path: str, edit: bool = False):
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"""
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This is the main read method for CapAnnData.
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Must be used in 'with' context.
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"""
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mode = "r+" if edit else "r"
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logger.debug(f"Read file {file_path} mode={mode} in context...")
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try:
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file = h5py.File(file_path, mode)
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cap_adata = CapAnnData(file)
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logger.debug(f"Successfully read anndata file path {file_path}")
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return cap_adata
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except Exception as error:
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logger.error(
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f"Error during read anndata file at path: {file_path}, error = {error}!"
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)
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raise error
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def deprecated(message):
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def deprecated_decorator(func):
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def deprecated_func(*args, **kwargs):
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warnings.warn(
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"{} is a deprecated function. {}".format(func.__name__, message),
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category=DeprecationWarning,
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stacklevel=2,
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)
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warnings.simplefilter("default", DeprecationWarning)
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return func(*args, **kwargs)
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return deprecated_func
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return deprecated_decorator
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# TODO: remove deprecated function
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@deprecated(
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"It will be removed in the next version of package. Please replace it with `read_h5ad`."
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)
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def read_directly(file_path: str, edit: bool = False) -> CapAnnData:
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"""
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Must be used only in specific cases.
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User is responsible to close the h5py file when the work with CapAnnData instance done.
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"""
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return read_h5ad(file_path, edit)
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@@ -1,28 +1,28 @@
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BSD 3-Clause License
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Copyright (c) 2024, R. Mukhin, A. Isaev, Cell-Annotation Platform
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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BSD 3-Clause License
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Copyright (c) 2024, R. Mukhin, A. Isaev, Cell-Annotation Platform
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Metadata-Version: 2.
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Name: cap_anndata
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Version: 0.
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Summary: Partial read/write of AnnData (h5ad) files for low-memory operations with large datasets.
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Home-page: https://github.com/cellannotation/cap-anndata
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Author: R. Mukhin, A. Isaev
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Author-email: roman@ebookapplications.com
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Project-URL: Bug Tracker, https://github.com/cellannotation/cap-anndata/issues
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Classifier:
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Metadata-Version: 2.2
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Name: cap_anndata
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Version: 0.4.0
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Summary: Partial read/write of AnnData (h5ad) files for low-memory operations with large datasets.
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Home-page: https://github.com/cellannotation/cap-anndata
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Author: R. Mukhin, A. Isaev
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Author-email: roman@ebookapplications.com
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Project-URL: Bug Tracker, https://github.com/cellannotation/cap-anndata/issues
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Project-URL: Changelog, https://github.com/cellannotation/cap-anndata/blob/main/CHANGELOG.md
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Project-URL: Documentation, https://github.com/cellannotation/cap-anndata/blob/main/HOWTO.md
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Classifier: Programming Language :: Python :: 3.9
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Classifier: License :: OSI Approved :: BSD License
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy>=1.23.5
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Requires-Dist: pandas>=2.2.0
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Requires-Dist: anndata>=0.10.0
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Provides-Extra: dev
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Requires-Dist: pytest>=8.0.0; extra == "dev"
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Requires-Dist: setuptools~=69.1.1; extra == "dev"
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Dynamic: author
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Dynamic: author-email
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Dynamic: classifier
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Dynamic: description
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Dynamic: home-page
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Dynamic: summary
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# CAP-AnnData: Partial I/O for AnnData (.h5ad) Files
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## Overview
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CAP-AnnData offering functionalities for selective reading and writing of [AnnData](https://pypi.org/project/anndata/)
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file fields without the need for loading entire dataset (or even entire field) into memory.
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For example, it allows to read and modify the single `obs` column taking nothing into memory except the column itself.
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Package eager to replicate the original AnnData API as much as possible,
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while providing additional features for efficient data manipulation for heavy datasets.
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## Installation
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Install CAP-AnnData via pip:
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```commandline
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pip install -U cap-anndata
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```
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## Basic Example
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The example below displayes how to read a single `obs` column, create new obs column and propagate it to the `.h5ad` file.
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```python
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from cap_anndata import read_h5ad
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file_path = "your_data.h5ad"
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with read_h5ad(file_path=file_path, edit=True) as cap_adata:
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print(cap_adata.obs_keys()) # ['a', 'b', 'c']
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print(cap_adata.obs) # Empty DataFrame
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cap_adata.read_obs(columns=['a'])
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print(cap_adata.obs.columns) # ['a']
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cap_adata.obs['new_col'] = cap_adata.obs['a']
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cap_adata.overwrite(fields=['obs'])
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```
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More example can be found in the [How-TO](https://github.com/cellannotation/cap-anndata/blob/main/HOWTO.md) file.
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cap_anndata/__init__.py,sha256=WRAQEDsWTvLbJWVUA5FmKCVrD2GN4oRd5I3c8jc9ajo,197
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cap_anndata/backed_df.py,sha256=2OVomvTY51V05sYwEXg-4JYBgd9iJCA2-Lt7nEAL1Ug,3255
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cap_anndata/backed_dict.py,sha256=Hb1SjnKuQ13mBUitQ5sL3kmcQ1j3GgB19r3yXkC0oIo,1019
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cap_anndata/cap_anndata.py,sha256=-Lp6wxPncVcl_TaECnE6uHTfD9j_Ow_rScvpAWKK_fs,21081
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cap_anndata/reader.py,sha256=UpZBCjaS4-K2w_9m6IuYetO9LwmEEJ5KvAw9aAoMRno,1609
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cap_anndata-0.4.0.dist-info/LICENSE,sha256=XXTH6JikkxH7Gqy9VEj4crSizuwxzv04ROzkQ-ZS6o4,1532
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cap_anndata-0.4.0.dist-info/METADATA,sha256=IXvItMAdXH-CunN3fNlyHPNFmxfoF9dOrU58tl17eLQ,2539
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cap_anndata-0.4.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
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cap_anndata-0.4.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
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cap_anndata-0.4.0.dist-info/RECORD,,
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cap_anndata/__init__.py,sha256=m-iyYXl6oIgczQMXr_rqhoObblRAs37YYxMoWidm7i4,207
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cap_anndata/backed_df.py,sha256=06wZwEjszFQ8lkvy6-GgD_SD14idu9857RtlfMQiBjE,2691
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cap_anndata/backed_dict.py,sha256=jPJl7RxPxV7s5ywD23ZxkInWPrgValyKHmlKZplDuTE,1053
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cap_anndata/cap_anndata.py,sha256=RDozLa-RZoNq_-CWNbrEoLbrNfaD8GkIU8vmAkxFuoQ,21197
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cap_anndata/reader.py,sha256=yiY8kButhg5TDc_OcXNOZkJv5Bbdht3XOzswjgDogdQ,1666
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cap_anndata-0.3.0.dist-info/LICENSE,sha256=JAV0w7TBl6wQe9iFcCKjAWgpurym0f-Q0B75zm2PrKw,1560
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cap_anndata-0.3.0.dist-info/METADATA,sha256=Fj4jPwlPbFr_u-e8-cW2KX5H0bUyhiZ5wcNACGrwK9w,2172
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cap_anndata-0.3.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
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cap_anndata-0.3.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
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cap_anndata-0.3.0.dist-info/RECORD,,
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