biopython
Link to section 'Introduction' of 'biopython' Introduction
Biopython is a set of freely available tools for biological computation written in Python.
For more information, please check its website: https://biocontainers.pro/tools/biopython and its home page: https://biopython.org.
Link to section 'Versions' of 'biopython' Versions
- 1.70-np112py27
- 1.70-np112py36
- 1.78
Link to section 'Commands' of 'biopython' Commands
- easy_install
- f2py
- f2py3
- idle3
- pip
- pip3
- pydoc
- pydoc3
- python
- python3
- python3-config
- python3.9
- python3.9-config
- wheel
Link to section 'Module' of 'biopython' Module
You can load the modules by:
module load biocontainers
module load biopython
Link to section 'Interactive job' of 'biopython' Interactive job
To run biopython interactively on our clusters:
(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers biopython
(base) UserID@bell-a008:~ $ python
Python 3.9.1 | packaged by conda-forge | (default, Jan 26 2021, 01:34:10)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import SeqIO
>>> with open("input.gb") as input_handle:
for record in SeqIO.parse(input_handle, "genbank"):
print(record)
Link to section 'Batch job' of 'biopython' Batch job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Biopython on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=biopython
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers biopython
python script.py