{ "info": { "author": "Michael Yourshaw", "author_email": "myourshaw@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "gsalib: Python/pandas package of utility functions for GATK\n=============================================================\n\n``gsalib`` makes it easy for Python users to analyze metrics reports created by the Broad Institute's Genome Analysis Toolkit (GATK). The Broad provides an R library called gsalib that allows you to load GATKReport files into R for further analysis (https://gatkforums.broadinstitute.org/gatk/discussion/1244/what-is-the-gatkreport-file-format). Python ``gsalib`` is an adaptation of the R libray that allows you to load GATKReport files into Python/pandas DataFrames.\n\nNeither the R nor Python versions of ``gsalib`` support the samtools.metrics reports created by `Picard Tools `_. To analyze Picard reports with Python, consider using the ``picard.parse`` function in the `Crimson `_ module.\n\nFeatures\n--------\n\n- Enables analysis of GATK reports with powerful pandas DataFrames and plotting\n- Reads GATKReport versions 0.x and 1.x\n- Compatible with Python >=2.7 and >=3.4\n\nInstallation\n------------\n\nInstall ``gsalib`` by running ::\n\n pip install gsalib\n\nExample\n-------\n\nRead a report and get a table's DataFrame::\n\n from gsalib import GatkReport\n\n report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table')\n table = report.tables['ExampleTable']\n\nDocumentation\n-------------\n\nhttps://gsalib.readthedocs.io/en/latest/\n\nContribute\n----------\n\n- Issue Tracker: https://github.com/myourshaw/gsalib/issues\n- Source Code: https://github.com/myourshaw/gsalib\n\nLicense\n-------\n\nThe project is licensed under the MIT license.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/myourshaw/gsalib", "keywords": "gsalib GATK report table R pandas DataFrame", "license": "MIT License", "maintainer": "", "maintainer_email": "", "name": "gsalib", "package_url": "https://pypi.org/project/gsalib/", "platform": "", "project_url": "https://pypi.org/project/gsalib/", "project_urls": { "Bug Reports": "https://github.com/myourshaw/gsalib/issues", "Documentation": "https://gsalib.readthedocs.io/en/latest/", "Funding": "https://donate.pypi.org", "Homepage": "https://github.com/myourshaw/gsalib", "Say Thanks!": "https://cran.r-project.org/web/packages/gsalib/index.html", "Source": "https://github.com/myourshaw/gsalib/" }, "release_url": "https://pypi.org/project/gsalib/1.0.6/", "requires_dist": [ "pandas" ], "requires_python": "", "summary": "Python version of R gsalib to read GATK Report tables into pandas DataFrames", "version": "1.0.6" }, "last_serial": 3692949, "releases": { "1.0.6": [ { "comment_text": "", "digests": { "md5": "5701218d5183e93ed0cdd90c2a5d25b9", "sha256": "00e59671709beb8859686d584075fa4a1f19a0a23002094ccb5e6256c5d2237b" }, "downloads": -1, "filename": "gsalib-1.0.6-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "5701218d5183e93ed0cdd90c2a5d25b9", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 6955, "upload_time": "2018-03-21T19:19:14", "url": "https://files.pythonhosted.org/packages/b1/62/62883a6e4c8671a28a4bbc7b7119e11274c86e77a8dafa88d75fbeda2b41/gsalib-1.0.6-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3a9e54eab6450511b2118b5ed376788d", "sha256": "43ce95242625826f5b339f7e250a0a259e78af4a821300f75dfcf470e590a0e1" }, "downloads": -1, "filename": "gsalib-1.0.6.tar.gz", "has_sig": false, "md5_digest": "3a9e54eab6450511b2118b5ed376788d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 23051, "upload_time": "2018-03-21T19:19:15", "url": "https://files.pythonhosted.org/packages/2b/92/ee3f35c37df93752985c1fdb03579cbd18ffd2f356228ecf1d5fa4e8d989/gsalib-1.0.6.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "5701218d5183e93ed0cdd90c2a5d25b9", "sha256": "00e59671709beb8859686d584075fa4a1f19a0a23002094ccb5e6256c5d2237b" }, "downloads": -1, "filename": "gsalib-1.0.6-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "5701218d5183e93ed0cdd90c2a5d25b9", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 6955, "upload_time": "2018-03-21T19:19:14", "url": "https://files.pythonhosted.org/packages/b1/62/62883a6e4c8671a28a4bbc7b7119e11274c86e77a8dafa88d75fbeda2b41/gsalib-1.0.6-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3a9e54eab6450511b2118b5ed376788d", "sha256": "43ce95242625826f5b339f7e250a0a259e78af4a821300f75dfcf470e590a0e1" }, "downloads": -1, "filename": "gsalib-1.0.6.tar.gz", "has_sig": false, "md5_digest": "3a9e54eab6450511b2118b5ed376788d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 23051, "upload_time": "2018-03-21T19:19:15", "url": "https://files.pythonhosted.org/packages/2b/92/ee3f35c37df93752985c1fdb03579cbd18ffd2f356228ecf1d5fa4e8d989/gsalib-1.0.6.tar.gz" } ] }