Introduction

The name comes from genome python tools. Originally, this package was called genometools, but was renamed to avoid confusion as another popular project uses that name.

The fundamental goal of gepyto is to provide bioinformaticians with a set of tools to make developing scripts faster. This means that most features are included in gepyto because they provide a clear and eloquent way of expressing common genomics tasks through Python code. As an example, fetching gene or variant information from public databases is abstracted away through extensible Python objects letting users focus on data manipulation rather than losing time writing code to handle HTTP requests and database queries.

Demos

This project will use IPython notebooks for feature demonstrations. They are available both in the demos directory or through nbviewer:

• Sequence analysis

We didn't write demos yet, but we have the nice gepyto.formats module which adds functionality to parse both Impute2 and SeqXML files.

Installation

For users

The easiest way to install is to simply use pip:

pip install gepyto

If you want the most recent version, you should install from the Github repo.

git clone https://github.com/legaultmarc/gepyto.git
cd gepyto
python setup.py install

You can run the tests from a Python interactive session using:

import gepyto
gepyto.test()

If you want a more detailed output, use:

import gepyto
gepyto.test(2)

Note that the test coverage is fairly low for now. Don't hesitate to contact us to report problems with the installation.

See also: Instructions for contributors.

You could use the "For users" instructions, but if you will be changing things it will be easier to simply add the package to your python path. To do this, fork the repository, clone it and add it to your PYTHONPATH.

1. git clone git@github.com:your_user/gepyto.git
2. Find the absolute path to the gepyto root directory and add it to your path by using export PYTHONPATH="${PYTHONPATH}:your_absolute_path".

You can either use the export command in every terminal you use to work on gepyto or you can add the line from step 2. to your ~/.bash_profile or equivalent.

It is also still a good idea to run python setup.py test to make sure the tests pass.

A script automating the previously described steps would look like this:

git clone git@github.com:your_user/gepyto.git
gtpath=$(find $PWD -maxdepth 1 -name gepyto)
echo 'export PYTHONPATH="${PYTHONPATH}:'${gtpath}'"' >> ~/.bash_profile

Don't forget to change your_user with your Github username.

Note that this will work on most Linux and Mac OS versions.

About

This project was intitated by a bioinformatician at the Beaulieu-Saucier Pharmacogenomics Center and a student of the StatGen lab.

Both are located at the Montreal Heart Institute in Canada.