"""
Command line object for PSICOV contact prediction application
"""
__author__ = "Felix Simkovic"
__date__ = "04 Aug 2016"
__version__ = 0.1
from Bio.Application import _Argument
from Bio.Application import _Option
from Bio.Application import _Switch
from Bio.Application import AbstractCommandline
[docs]class PsicovCommandLine(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.
.. [#] 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 :func:`psicov_cline` or via
the Python subprocess module.
"""
def __init__(self, cmd='psicov', **kwargs):
self.parameters = [
_Switch(['-a', 'lasso'],
"use approximate Lasso algorithm"),
_Switch(['-n', 'noshrink'],
"don't pre-shrink the sample covariance matrix"),
_Switch(['-f', 'filter'],
"filer low-scoring contacts"),
_Switch(['-p', 'ppv_output'],
"output PPV estimates rather than raw scores"),
_Switch(['-l', 'noapc'],
"don't apply APC to Lasso output"),
_Option(['-r', 'rho'],
"set initial rho paramter",
equate=False),
_Option(['-d', 'sparsity'],
"set target precision matrix sparsity [default: 0; not specified]",
equate=False),
_Option(['-t', 'convergence_threshold'],
"set Lasso convergence threshold [default: 1e-4]",
equate=False),
_Option(['-i', 'blosum_weighting'],
"select BLOSUM-like weighting with given identity threshold "
"[default selects threshold automatically]",
equate=False),
_Option(['-c', 'pseudocount'],
"set pseudocount value [default: 1]",
equate=False),
_Option(['-j', 'sequence_separation'],
"set minimum sequence sparation [default: 5]",
equate=False),
_Option(['-g', 'gap_fraction'],
"set maximum fraction of gaps [default: 0.9]",
equate=False),
_Option(['-z', 'nr_threads'],
"set maximum number of threads",
equate=False),
_Option(['-b', 'rho_parameter_file'],
"read rho parameter file",
filename=True,
equate=False),
_Argument(['alnfile'],
"Input alignment file [JONES format]",
filename=True,
is_required=True),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
