# Testing BioPython

2008-07-27

Following my previous posts on Bioinformatics with Mac OS X and Installation of Python scientifical packages, I just try the BioPython package.

BioPython is an open-source project, based on the same principle as the older BioPerl project.1

It aims at providing a unified interface to traditionnal methods for computational molecular biology. The question then arises as to whether it conflicts with the Bioconductor or BioPerl initiative.

In fact, the Bioconductor project provides a set of about 260 packages (as of July 2008) that enhance the core R software. Most of them are supposed to integrate a growing collection of statistical tools. It is a popular library for microarray analysis since it supports most formats and comes with many graphical tools. On the contrary, BioPerl or BioPython are thought to be used to manipulate data file, organize the information and be interfaced with other programming languages. Thus, they fulfill their role of “universal” scripting language and appear very complementary of R biobase. Whether to use Perl or Python is then a matter of taste.

The installation of BioPython is quite easy, provided you have easy_install working properly.2 Thus, just type

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