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.
In Puhti, Biopython libraries, as well as many other bioinformatics related Python libraries are available
in the Python installations that are used by the bioconda environments. These environment also include
python virtual environments that allow users to create their own project specific Python environment with
pip installation tool.
These virtual environments use the PROJAPPL directory for installing the user specific libraries. Because of that, you must first set PROJAPPL environment variable to point to the PROJAPPL directory of the project you want to use.
module load bioconda biopython-env
module load bioconda/2 biopython-env
When the virtual environment is activated, you can launch a biopython program with command:
New python libraries can be installed with
pip install command.
For example, Python library called OBITools3 could be installed with command:
pip install OBITools3
More information about biopython can be found form the homepage of biopython.
Last edited Thu Apr 28 2022