Introduction

Welcome to interPopula.

interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relavant human population datasets (e.g. Ensembl and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided.

In concrete, what is interPopula?

  1. First, and foremost, it is a Python library to access the HapMap project.
  2. It also supports access to gene annotation information from both UCSC Genome Browser and Ensembl. Gene annotation information is useful to process HapMap data.
  3. It is a set of scripts demonstrating the integration of the databases above with existing tools (and other databases) relevant to population genetics.
  4. It is a set of guidelines to deal with inconsistencies across databases

Download

interPopula is available for download (GPL v3 licensed).


Citation

If you use interPopula please cite: interPopula: a Python API to access the HapMap Project dataset, T. Antao, BMC Bioinformatics.

User Guide

An introductory user guide, cookbook style, is made available. For advanced usage scenarios see database and tool integration below.

The automatically generated documentation serves as reference for the library.

We also recommend inspecting the scripts as they are fully commented and an effort was made to make them as readable as possible.

We also have a Q&A forum.


Database and tool integration

Integration of different databases and tools can be complex. Issues like code complexity are minor but inconsistencies between databases might produce erroneous results. Several integration guidelines and examples, involving tools and databases, are presented.

Screenshot gallery

Have a look at the screenshot gallery.


Development

Interested in the development of interPopula? Check our development site in launchpad!


Contact

Questions, ideas? Do not hesitate to email!