Command line object for CCMpred contact prediction application
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
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). |