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. |
Notes
In order to use bbcontacts, head over to the GitHub repository, download the latest version and install it using python setup.py install.
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 Python subprocess module.
Attributes
| parameters |
Methods
__call__([stdin, stdout, stderr, cwd, env]) |
Executes the command, waits for it to finish, and returns output. |
set_parameter(name[, value]) |
Set a commandline option for a program (OBSOLETE). |