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A new secret project :P

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# Puzzle [![Build Status][travis-image]][travis-url] [![Test Coverage][coveralls-img]][coveralls-url]

Variant Caller GUI and genetic disease analysis tool.

`bash $ git clone https://github.com/robinandeer/puzzle.git $ cd puzzle $ pip install --editable . $ puzzle view tests/fixtures/ # open webbrowser on port 5000 $ open http://localhost:5000 `

## Using Puzzle Puzzle will look for variant calling resources such as VCF files and [GEMINI][gemini] databases and visualize their content. It lets you inspect, annotate, and analyze variant calls.

Puzzle is not primarily meant to be run as a persistant server but think of it more as an webinterface to quickly spin to visualize your variant calls.

We set out to make Puzzle both very simple to install as well as intuitive to use. You can be up and running in minutes with minimal prerequisites.

## Developing Puzzle Puzzle is a Python Flask app with a command line interface. It can work with multiple backends using plugins; raw VCFs, GEMINI, MongoDB.

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

### Install for development I decided to try out [Otto][otto] for this project so make sure you have it installed :smile:

`bash $ git clone https://github.com/robinandeer/puzzle.git $ cd puzzle $ otto dev $ otto dev ssh > npm install > sudo apt-get install vim python-pip git > pip install --user --editable . > puzzle /vagrant/tests/ # open webbrowser on port 5000 `

## Testing Puzzle To run the tests, you need [pytest](pytest) installed in your system. You can install pytest together with the other development libraries by running pip install -r requirements-dev.txt.

You will also need to download the database used for testing, which you can do by executing this command:

` wget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapFew.db -O tests/fixtures/HapMapFew.db `

Then, just run py.test tests/

## Use a gemini database ##

Make sure you have gemini installed in your local environment

` puzzle --mode gemini view -i path/to/gemini_database.db `

## Use ped info ##

Puzzle uses the ped file to show more information in family view and in variant calls:

` puzzle view -i tests/fixtures/hapmap.vcf --family_file/-f tests/fixtures/hapmap.vcf `

## Credits Puzzle Piece by Creative Stall from the Noun Project

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

[travis-url]: https://travis-ci.org/robinandeer/puzzle?branch=master [travis-image]: https://img.shields.io/travis/robinandeer/puzzle/master.svg?style=flat-square [coveralls-url]: https://coveralls.io/github/robinandeer/puzzle [coveralls-img]: https://img.shields.io/coveralls/robinandeer/puzzle.svg?style=flat-square [otto]: https://ottoproject.io/ [gemini]: https://github.com/arq5x/gemini [pytest]: http://pytest.org/latest/

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