This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description
<p align="center">
<a href="http://chanjo.co">
<img height="235" <br=""> width="244"
src="docs/assets/logo.png"/>
</a>
</p>

# Chanjo [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url] [![bioconda-badge][bioconda-img]][bioconda-url]

Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to [UNIX pipeline philosophy][unix].

## Installation
Chanjo is distributed through `pip`. Install the latest stable release by running:

```bash
$ pip install chanjo
```

... or locally for development:

```bash
$ git clone https://github.com/robinandeer/chanjo.git && cd chanjo
$ ansible-galaxy install -r provision/requirements.yml
$ vagrant up
$ vagrant ssh
```

## Usage
Chanjo exposes a decomposable command line interface with a nifty config file implementation.

```bash
$ chanjo init --setup
$ chanjo load /path/to/sambamba.output.bed
$ chanjo calculate mean
{"metrics": {"completeness_10": 90.92, "mean_coverage": 193.85}, "sample_id": "sample1"}
```

## Documentation
Read the Docs is hosting the [official documentation][docs].

If you are looking to learn more about handling sequence coverage data in clinical sequencing, feel free to download and skim through my own [Master's thesis][thesis] and article references.

## Features

### What Chanjo does
Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. The database also works 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))
- John Kern ([kern3020](https://github.com/kern3020))
- Måns Magnusson ([moonso](https://github.com/moonso))

## 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/
[thesis]: https://s3.amazonaws.com/tudo/chanjo/RobinAndeerMastersThesisFinal_2013.pdf
[report]: https://github.com/robinandeer/chanjo-report
[sambamba]: http://lomereiter.github.io/sambamba/

[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://img.shields.io/travis/robinandeer/chanjo.svg?style=flat-square

[coveralls-url]: https://coveralls.io/r/robinandeer/chanjo
[coveralls-image]: https://img.shields.io/coveralls/robinandeer/chanjo.svg?style=flat-square

[bioconda-url]: http://bioconda.github.io
[bioconda-img]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
Release History

Release History

4.0.0b4

This version

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4.0.0b0

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3.4.1

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3.4.0

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3.3.1

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3.3.0

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3.2.1

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3.2.0

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3.1.1

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3.1.0

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3.0.2

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3.0.1

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3.0.0

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3.0.0b2

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3.0.0b0

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2.3.2

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2.3.1

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2.3.0

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2.2.1

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2.2.0

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2.1.3

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2.1.2

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2.1.1

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2.1.0

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2.0.2

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2.0.1

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2.0.0

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2.0.0-beta6

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2.0.0-beta5

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2.0.0-beta4

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2.0.0-beta3

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2.0.0-beta2

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2.0.0-beta

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1.1.1

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1.1.0

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1.0.2

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1.0.2-beta

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1.0.1-beta

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1.0.0-beta

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0.5.4

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0.5.3

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0.5.1

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0.5.0

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0.4.0

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0.3.2

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0.3.1

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0.3.0

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0.2.1

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0.2.0

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0.1.0

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v0.0.4

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0.0.3

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Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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v0.0.3-beta

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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v0.0.2-beta

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.0.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
chanjo-4.0.0b4-py2.py3-none-any.whl (75.4 kB) Copy SHA256 Checksum SHA256 2.7 Wheel Sep 2, 2016
chanjo-4.0.0b4.tar.gz (397.5 kB) Copy SHA256 Checksum SHA256 Source Sep 2, 2016

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