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 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).