conkit.applications.psicov module¶
Command line object for PSICOV contact prediction application
-
class
PsicovCommandline
(cmd='psicov', **kwargs)[source]¶ Bases:
Bio.Application.AbstractCommandline
Command line object for PSICOV [1] contact prediction application
http://bioinfadmin.cs.ucl.ac.uk/downloads/PSICOV/
The PSICOV program is a Accurate Contact Prediction from large protein alignments.
[1] Jones, D.T., Buchan, D.W., Cozzetto, D. & Pontil, M. (2012). PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 28, 184-190. Examples
To predict a contact map using a Multiple Sequence Alignment in JONES format, use:
>>> from conkit.applications import PsicovCommandline >>> psicov_cline = PsicovCommandline(alnfile="test.aln") >>> print(ccmpred_cline) psicov test.aln
You would typically run the command line with
psicov_cline()
or via thesubprocess
module.