================================
Cell Maps for AI PPI Downloader
================================
.. image:: https://img.shields.io/pypi/v/cellmaps_ppidownloader.svg
:target: https://pypi.python.org/pypi/cellmaps_ppidownloader
.. image:: https://app.travis-ci.com/idekerlab/cellmaps_ppidownloader.svg?branch=main
:target: https://app.travis-ci.com/idekerlab/cellmaps_ppidownloader
.. image:: https://readthedocs.org/projects/cellmaps-ppidownloader/badge/?version=latest
:target: https://cellmaps-ppidownloader.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://zenodo.org/badge/636892648.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10607408
:alt: Zenodo DOI badge
Downloads protein-protein interaction data
* Free software: MIT license
* Documentation: https://cellmaps-ppidownloader.readthedocs.io.
Dependencies
------------
* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
* `requests <https://pypi.org/project/requests>`__
* `mygene <https://pypi.org/project/mygene>`__
* `tqdm <https://pypi.org/project/tqdm>`__
Compatibility
-------------
* Python 3.8+
Installation
------------
.. code-block::
git clone https://github.com/idekerlab/cellmaps_ppidownloader
cd cellmaps_ppidownloader
make dist
pip install dist/cellmaps_ppidownloader*whl
Run **make** command with no arguments to see other build/deploy options including creation of Docker image
.. code-block::
make
Output:
.. code-block::
clean remove all build, test, coverage and Python artifacts
clean-build remove build artifacts
clean-pyc remove Python file artifacts
clean-test remove test and coverage artifacts
lint check style with flake8
test run tests quickly with the default Python
test-all run tests on every Python version with tox
coverage check code coverage quickly with the default Python
docs generate Sphinx HTML documentation, including API docs
servedocs compile the docs watching for changes
testrelease package and upload a TEST release
release package and upload a release
dist builds source and wheel package
install install the package to the active Python's site-packages
dockerbuild build docker image and store in local repository
dockerpush push image to dockerhub
Before running tests, please install ``pip install -r requirements_dev``.
Needed files
------------
* bait list file: TSV file of baits used for AP-MS experiments
* edge list file: TSV file of edges for protein interaction network
* provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)
Usage
-----
For information invoke :code:`cellmaps_ppidownloadercmd.py -h`
**Example usage**
.. code-block::
cellmaps_ppidownloadercmd.py ./cellmaps_ppidownloader_outdir --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json
Via Docker
~~~~~~~~~~~~~~~~~~~~~~
**Example usage**
.. code-block::
Coming soon...
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org
=======
History
=======
0.1.2 (2024-09-12)
------------------
* Bug fix in adding gene node attributes.
0.1.1 (2024-08-26)
------------------
* Bug fix in adding gene node attributes. The bug was resulting in duplicate entries and
missing gene names, related to ambiguous antibodies.
0.1.0 (2024-01-01)
------------------
* First release on PyPI.
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"description": "================================\nCell Maps for AI PPI Downloader\n================================\n\n\n.. image:: https://img.shields.io/pypi/v/cellmaps_ppidownloader.svg\n :target: https://pypi.python.org/pypi/cellmaps_ppidownloader\n\n.. image:: https://app.travis-ci.com/idekerlab/cellmaps_ppidownloader.svg?branch=main\n :target: https://app.travis-ci.com/idekerlab/cellmaps_ppidownloader\n\n.. image:: https://readthedocs.org/projects/cellmaps-ppidownloader/badge/?version=latest\n :target: https://cellmaps-ppidownloader.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/636892648.svg\n :target: https://zenodo.org/doi/10.5281/zenodo.10607408\n :alt: Zenodo DOI badge\n\n\nDownloads protein-protein interaction data\n\n\n* Free software: MIT license\n* Documentation: https://cellmaps-ppidownloader.readthedocs.io.\n\nDependencies\n------------\n\n* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__\n* `requests <https://pypi.org/project/requests>`__\n* `mygene <https://pypi.org/project/mygene>`__\n* `tqdm <https://pypi.org/project/tqdm>`__\n\nCompatibility\n-------------\n\n* Python 3.8+\n\nInstallation\n------------\n\n.. code-block::\n\n git clone https://github.com/idekerlab/cellmaps_ppidownloader\n cd cellmaps_ppidownloader\n make dist\n pip install dist/cellmaps_ppidownloader*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image\n\n.. code-block::\n\n make\n\nOutput:\n\n.. code-block::\n\n clean remove all build, test, coverage and Python artifacts\n clean-build remove build artifacts\n clean-pyc remove Python file artifacts\n clean-test remove test and coverage artifacts\n lint check style with flake8\n test run tests quickly with the default Python\n test-all run tests on every Python version with tox\n coverage check code coverage quickly with the default Python\n docs generate Sphinx HTML documentation, including API docs\n servedocs compile the docs watching for changes\n testrelease package and upload a TEST release\n release package and upload a release\n dist builds source and wheel package\n install install the package to the active Python's site-packages\n dockerbuild build docker image and store in local repository\n dockerpush push image to dockerhub\n\nBefore running tests, please install ``pip install -r requirements_dev``.\n\n\nNeeded files\n------------\n\n* bait list file: TSV file of baits used for AP-MS experiments\n* edge list file: TSV file of edges for protein interaction network\n* provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)\n\n\nUsage\n-----\n\nFor information invoke :code:`cellmaps_ppidownloadercmd.py -h`\n\n**Example usage**\n\n.. code-block::\n\n cellmaps_ppidownloadercmd.py ./cellmaps_ppidownloader_outdir --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json\n\n\nVia Docker\n~~~~~~~~~~~~~~~~~~~~~~\n\n**Example usage**\n\n.. code-block::\n\n Coming soon...\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _NDEx: http://www.ndexbio.org\n\n\n=======\nHistory\n=======\n\n0.1.2 (2024-09-12)\n------------------\n\n* Bug fix in adding gene node attributes.\n\n0.1.1 (2024-08-26)\n------------------\n\n* Bug fix in adding gene node attributes. The bug was resulting in duplicate entries and\n missing gene names, related to ambiguous antibodies.\n\n0.1.0 (2024-01-01)\n------------------\n\n* First release on PyPI.\n",
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