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Utilities for the management of molecular polymorphism data.

Project description

oldowan.polymorphism is a small bioinformatic utility for the management of molecular polymorphism data.

Installation Instructions

This package is pure Python and has no dependencies outside of the standard library. The easist way to install is using easy_install from the setuptools package. This usually goes something like this:

$ easy_install oldowan.polymorphism

or on a unix-like system, assuming you are installing to the main Python site-packages directory as a non-privileged user, this:

$ sudo easy_install oldowan.polymorphism

You may also use the standard python distutils setup method. Download the current source archive from the file list towards the bottom of this page, unarchive it, and install. On Mac OS X and many other unix-like systems, having downloaded the archive and changed to the directory containing this archive in your shell, this might go something like:

$ tar xvzf oldowan.polymorphism*
$ cd oldowan.polymorphism*
$ python setup.py install

Quick Start

This package provides a single utility class, Polymorphism. Import this class from oldowan.polymorphism:

>>> from oldowan.polymorphism import Polymorphism

Create a new Polymorphism object:

>>> p1 = Polymorphism(16223,0,'A','T')

The Polymorphism constructor requires 3 arguments and accepts and optional fourth argument. These are (in order):

  1. position, integer.
  2. insert, 0 if polymorphism is exactly at that position, or 1,2,3,… if insertion after.
  3. value, character value of polymorphism
  4. reference, optional value of a reference sequence at that position

Release History

1.0.0 (March 25, 2009)
initial release of module.
1.0.1 (March 25, 2009)
minor update for correct version numbering
1.0.3 (August 4, 2015)
actually fixed the version numbering this time

Project details


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