Metadata-Version: 2.0
Name: pymip
Version: 0.2.0
Summary: Provides a Python API to manipulate MIP
Home-page: https://github.com/robinandeer/pymip
Author: Robin Andeer
Author-email: robin.andeer@gmail.com
License: MIT
Keywords: p,y,m,i,p, ,d,e,v,e,l,o,p,m,e,n,t
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Environment :: Console
Requires-Dist: click
Requires-Dist: path.py
Requires-Dist: ped-parser
Requires-Dist: pyyaml
Requires-Dist: setuptools

# PyMIP [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url]
Provides a Python API to manipulate the [MIP][mip] analysis pipeline: setup, starting, monitoring, and parsing output.


## Features

* TODO

### Archive analysis
After 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.

Assets that are kept:

- CRAM file as a source of the raw (aligned) reads
- BCF file as a source of all (unannotated) variants
- QC metrics as a source for quality metrics

Pymip 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`.


## Install for development

```bash
$ pip install --editable .
```


## Contributing
Anyone can help make this project better - read [CONTRIBUTING](CONTRIBUTING.md) to get started!


## License
MIT. See the [LICENSE](LICENSE) file for more details.


[fury-url]: http://badge.fury.io/py/pymip
[fury-image]: https://badge.fury.io/py/pymip.png

[travis-url]: https://travis-ci.org/Clinical-Genomics/pymip
[travis-image]: https://img.shields.io/travis/Clinical-Genomics/pymip.svg?style=flat

[mip]: http://mip-api.readthedocs.org/en/latest/


