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.
License
Biopython is free to use and open source. It is dual licensed under Biopython License or BSD 3-Clause License.
Available
- Puhti: Python 3.10.6 with Biopython 1.79
In Puhti, Biopython libraries, as well as many other bioinformatics related Python libraries are available.
module load biopythontools
When the module is loaded, you can launch a biopython program with command:
python my_biopython_code.py
#!/bin/env python
and execute the python program
./my_biopython_code.pm
New python libraries can be installed with pip install command.
For example, Python library called OBITools3 could be installed with command:
pip install --user OBITools3
Further instructions on how to set the installation location etc can be found in the general Python page.
Manual
More information about biopython can be found form the homepage of biopython.