"""Refine MSA application."""
from ..apptools import DevelApp
__all__ = ['evol_refine']
APP = DevelApp('refine', 'refine an MSA by removing gapped rows/colums')
APP.setExample(
"""Refines MSA by removing gapped columns (residue positions)
and rows (sequences).
In the following, columns that are gaps in sequence with label
GTHB2_ONCKE will be removed from MSA:
$ evol refine piwi.slx -l GTHB2_ONCKE""", [])
APP.addArgument('msa',
help='MSA filename to be refined')
APP.addGroup('refine', 'refinement options')
APP.addArgument('-l', '--label',
dest='label',
help='sequence label, UniProt ID code, or PDB and chain identifier',
type=str,
metavar='STR',
group='refine')
APP.addArgument('-s', '--seqid',
dest='seqid',
help='identity threshold for selecting unique sequences',
default=None,
type=float,
metavar='FLOAT',
group='refine')
APP.addArgument('-c', '--colocc',
dest='colocc',
help='column (residue position) occupancy',
default=None,
type=float,
metavar='FLOAT',
group='refine')
APP.addArgument('-r', '--rowocc',
dest='rowocc',
help='row (sequence) occupancy',
default=None,
type=float,
metavar='FLOAT',
group='refine')
APP.addArgument('-k', '--keep',
dest='pdbres',
help='keep columns corresponding to residues not resolved in PDB '
'structure, applies label argument is a PDB identifier',
default=False,
action='store_true',
group='refine')
APP.addGroup('output', 'output options')
APP.addArgument('-o', '--outname',
dest='outname',
help='output filename, default is msa filename with _refined suffix',
type=str,
metavar='STR',
group='output')
APP.addArgument('-f', '--format',
dest='format',
type=str,
metavar='STR',
help='output MSA file format, default is same as input',
group='output')
APP.addArgument('-z', '--compressed',
dest='compressed',
action='store_true',
help='gzip refined MSA output',
group='output')
[docs]def evol_refine(msa, **kwargs):
from prody import parseMSA, refineMSA, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_refined' + ext
writeMSA(outname, refineMSA(parseMSA(msa), **kwargs), **kwargs)
LOGGER.info('Refined MSA is written in file: ' + outname)
APP.setFunction(evol_refine)
