Command line object for PSICOV contact prediction application
PsicovCommandLine
(cmd='psicov', **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for PSICOV contact prediction application
http://bioinfadmin.cs.ucl.ac.uk/downloads/PSICOV/
The PSICOV program is a Accurate Contact Prediction from large protein alignments.
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). |