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 the subprocess module.