Biopython

Software Category
Version
1.68

Biopython

Biopython is a set of tools written in Python to analyze and process bioinformatics datasets including genomes, genetic sequence reads and protiens. The program contains a myriad of analysis tools and algorithms to use on these types of biological data.

Using Biopython on HPC

In order to use BioPython on HPC, you will need to install BioPython in either a conda virtual environment or a Python venv virtual environment.  The basic process for a Python virtual environment is as follows:

python3 -m venv ~/MYENV  # You can rename MYENV to any name you want
source ~/MYENV/bin/activate
pip install biopython

Example Biopython Library Call

After importing the python module, load python with the command python. Below are some example commands and results from section 2.2 of the tutorial executed on the HPC.


>>> from Bio.Seq import Seq
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq('AGTACACTGGT', Alphabet())
>>> print(my_seq)
AGTACACTGGT
>>> my_seq.alphabet
Alphabet()