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Biopython

Biopython

Description

Biopython is a collection of python modules that facilitate the development of python scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do. On the other hand, Biopython provides reusable python modules that facilitate writing scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs. Consequently, Biopython enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
 


Available

Version on CSC's Servers

Biopython versions 1.70 and 1.61 are available in Taito


Usage

To use Biopython in Taito, give command:

module load biopython-env/3.4.5

This takes in use python version 3.4.5 and biopython 1.70.

module load biopython-env/2.7.13

This takes in use python aversion 2.7.13 and biopython 1.70.

Alternatively you can run command:

module load biopython-env

This module load command loads older versions of python (2.7.3) and biopython (1.61). These biopython environments use user specific virtual python environment which allows users own pythoin library installations with pip.

After this you can launch a biopython program with command

python my_biopython_code.py

Alternatively you can change the python definition in the first line of your code to

#!/bin/env python

and execute the python program

./my_biopython_code.pm


Discipline

Biosciences

References


Support


Manual

More information about biopython can be found form the homepage of biopython.

    www.biopython.org