Command line object for bbcontacts contact filtering application
BbcontactsCommandline
(cmd=’bbcontacts’, **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for bbcontacts [1] contact filtering application
https://github.com/soedinglab/bbcontacts
The bbcontacts program is a Python program predicting residue-level contacts between beta-strands by detecting patterns in matrices of predicted couplings. bbcontacts can make use of a secondary structure assignment or a secondary structure prediction.
[1] | Andreani J., Söding J. (2015). bbcontacts: prediction of beta-strand pairing from direct coupling patterns. Bioinformatics 31(11), 1729-1737. |
Examples
To filter a contact map using a Multiple Sequence Alignment in CCMpred format, use:
>>> from conkit.applications import BbcontactsCommandline
>>> bbcontacts_cline = BbcontactsCommandline(
... matfile='test.mat', diversity_score=0.482, prefix='test'
... )
>>> print(bbcontacts_cline)
bbcontacts
You would typically run the command line with bbcontacts_cline()
or via
the subprocess
module.
Note
Installation instructions are available via the GitHub repository.