Metadata-Version: 1.1
Name: chanjo
Version: 2.0.0
Summary: Coverage analysis tool for clinical sequencing
Home-page: http://www.chanjo.co/
Author: Robin Andeer
Author-email: robin.andeer@gmail.com
License: MIT
Description: <p align="center">
          <a href="http://chanjo.co">
            <img height="235"
                 width="244"
                 src="artwork/logo.png"/>
          </a>
        </p>
        
        # Chanjo [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]
        
        # Chanjo
        Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to [UNIX pipeline philisophy][unix].
        
        ## Installation
        Chanjo is distruibuted through "pip". Install the latest release by running:
        
        ```bash
        $ pip install chanjo
        ```
        
        ... or locally for development:
        
        ```bash
        $ git clone https://github.com/robinandeer/chanjo.git && cd chanjo
        $ pip install --editable .
        ```
        
        Do note that Chanjo is built on some of kind-of tricky dependencies. If you are experiencing any issues, help is just a click away in the [documentation][docs].
        
        ## Usage
        Chanjo exposes a composable command line interface. You can always save intermediary files at any stage and customize every option. However, using a ``chanjo.toml`` config and UNIX pipes you can end up with something like:
        
        ```bash
        $ chanjo convert CCDS.sorted.txt | chanjo annotate alignment.bam > coverage.bed
        ```
        
        ## Documentation
        Read the Docs is hosting the [official documentation][docs].
        
        I can specifically recommend the fully [interactive demo](http://www.chanjo.co/en/latest/introduction.html#demo), complete with sample data to get you started right away.
        
        ## Features
        
        ### What Chanjo does
        Chanjo works on BAM alignment files and extracts interesting coverage related statistics. You use a BED-file to define which regions of the genome that you particularly care about. The output takes the shape of an extended BED-file.
        
        An optional final step is to load data into a SQL database. This will aggregate data from exons to transcripts and genes. The database will later work as an API to downstream tools like the Chanjo Coverage Report generator.
        
        ### What Chanjo doesn't
        Chanjo is not the right choice if you care about coverage for every base across the entire genome. Detailed histograms is something [BEDTools][bedtools] already handles with confidence.
        
        ## Contributors
        Robin Andeer
        
        Luca Beltrame ([lbeltrame](https://github.com/lbeltrame))
        
        ## License
        MIT. See the [LICENSE](LICENSE) file for more details.
        
        ## Contributing
        Anyone can help make this project better - read [CONTRIBUTION](CONTRIBUTION.md) to get started!
        
        
        [unix]: http://en.wikipedia.org/wiki/Unix_philosophy
        [docs]: http://www.chanjo.co/en/latest/
        [bedtools]: http://bedtools.readthedocs.org/en/latest/
        
        [coveralls-url]: https://coveralls.io/r/robinandeer/chanjo
        [coveralls-image]: https://img.shields.io/coveralls/robinandeer/chanjo.svg
        
        [fury-url]: http://badge.fury.io/py/chanjo
        [fury-image]: https://badge.fury.io/py/chanjo.png
        
        [travis-url]: https://travis-ci.org/robinandeer/chanjo
        [travis-image]: https://travis-ci.org/robinandeer/chanjo.png?branch=master
        
Keywords: coverage sequencing clinical exome completeness diagnostics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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
