conkit.applications.ccmpred module¶
Command line object for CCMpred contact prediction application
-
class
CCMpredCommandline
(cmd='ccmpred', **kwargs)[source]¶ Bases:
Bio.Application.AbstractCommandline
Command line object for CCMpred [1] contact prediction application
https://github.com/soedinglab/CCMpred
The CCMpred program is a very fast pseudo-likelihood maximisation implementation of covariance detection in a Multiple Sequence Alignment. This wrapper allows for easy-to-use Python implementation.
[1] Seemayer S, Gruber M, Söding J (2014). CCMpred–fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 30(21), 3128-3130. Examples
To predict a contact map using a Multiple Sequence Alignment in JONES format, use:
>>> from conkit.applications import CCMpredCommandline >>> ccmpred_cline = CCMpredCommandline( ... alnfile="test.aln", matfile="output.mat" ... ) >>> print(ccmpred_cline) ccmpred test.aln output.mat
You would typically run the command line with
ccmpred_cline()
or via thesubprocess
module.