PopGen dev

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Contents

Development page for the PopGen module.

Abstract

The PopGen module will contain modules to handle population genetics data.

Philosophy

Most of the existing Bio.PopGen features are of non-core population genetics functionality. This was seen as feature (and not as a bug) in order to start building a module with functionality where newbie crass errors would not have dramatic consequences. Currently, with the experience accumulated is is possible and desirable to concentrate on core population genetics functionality (i.e., statistics).

Also worth noticing is that we wrap existing functionality whenever possible. For instance we don't provide our own coalescent simulator, but we provide wrappers to an existing one which is established and widely used (SIMCOAL2).

Future Goals

The fundamental goal is to have support for "classic" population genetics operations (statistics). This should be provided in an extensible, easy to use and future-proof framework. Code exists (see below on how to find it), but will probably be refactored. Below there is also a with list where you can add your desired features.

In the pipeline

Currently (i.e., for the near term) the following new functionality can be expected

  • STRUCTURE support
  • LDNe support


Code

The official production code is available on CVS.

Some of the development code is informally hosted on github:

How to contribute

Your contribution is most welcome, please have a look at the General Biopython contribution guidelines. Join us on the biopython-devel mailing list and tell us about your ideas!

Informal development versions can be found, for now, on github where you can create a free account, and then click on the 'Fork' button (something like http://github.com/dalloliogm/biopython---popgen/fork) and then start working on your separated branch.


Wish list

  • support for a binary format - like HDF5 or this one: snpfile
  • support for database: it is frequent to carry analysis on a big scale, so it is not unfrequent to use databases to store data
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