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"""
Command line object for PSICOV contact prediction application
"""
__author__ = "Felix Simkovic"
__date__ = "04 Aug 2016"
__version__ = "0.13.3"
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 :mod:`~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)
