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Biopython

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

In Puhti, Biopythoin libraries, as well as many outher bioinformatics related Python libraries are available in the Pyhtion installations that are used by the bioconda environments. These environment also include python virtual environments that allow users to create theiy own project specific Python environment with pip installation tool.

These virtual environments use the PROJAPPL directory for installing the user specific libraties. Because of that, you must first set PROJAPPL environment variable to point to the PROJAPPL directory of the project you want to use.

export PROJAPPL=/projappl/project_your_proj_num

After that, a virtual Python environment using Python 3.7.3 and biopython can be set up with commands:

module load bioconda
biopython-env

If you want to use old Python 2.7.5 with biopython in stead, use setup commands:

module load bioconda/2
biopython-env

However, we strongly recommend using Python 3 versions in stead of Python 2.

When the virtual enviroinment is activated, 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

New python libraries can be installed with pip install commad. For example, Python library called OBITools3 could be installed with command:

pip install OBITools3

Manual

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