{ "info": { "author": "Robin Andeer", "author_email": "robin.andeer@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Topic :: Software Development" ], "description": "# PyMIP [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url]\nProvides a Python API to manipulate the [MIP][mip] analysis pipeline: setup, starting, monitoring, and parsing output.\n\n\n## Features\n\n* TODO\n\n### Archive analysis\nAfter a case has been solved or abandoned it is necessary to wrap up the analysis and archive the results. Pymip will handle this task by bundling the most vital assets from the output and deleting the rest.\n\nAssets that are kept:\n\n- CRAM file as a source of the raw (aligned) reads\n- BCF file as a source of all (unannotated) variants\n- QC metrics as a source for quality metrics\n\nPymip will not touch any of the files under \"exomes/genomes\" only \"analysis\". Physically the files will be collected in a folder under \"exomes/genomes\" names \"archive\". The script will also update the `AnalysisRunStatus` in the QC sample info file to `Archived`.\n\n\n## Install for development\n\n```bash\n$ pip install --editable .\n```\n\n\n## Contributing\nAnyone can help make this project better - read [CONTRIBUTING](CONTRIBUTING.md) to get started!\n\n\n## License\nMIT. See the [LICENSE](LICENSE) file for more details.\n\n\n[fury-url]: http://badge.fury.io/py/pymip\n[fury-image]: https://badge.fury.io/py/pymip.png\n\n[travis-url]: https://travis-ci.org/Clinical-Genomics/pymip\n[travis-image]: https://img.shields.io/travis/Clinical-Genomics/pymip.svg?style=flat\n\n[mip]: http://mip-api.readthedocs.org/en/latest/", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/robinandeer/pymip", "keywords": "pymip development", "license": "MIT", "maintainer": null, "maintainer_email": null, "name": "pymip", "package_url": "https://pypi.org/project/pymip/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/pymip/", "project_urls": { "Download": "UNKNOWN", "Homepage": "https://github.com/robinandeer/pymip" }, "release_url": "https://pypi.org/project/pymip/0.2.0/", "requires_dist": null, "requires_python": null, "summary": 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