"""Pfam MSA download application."""
__author__ = 'Ahmet Bakan, Anindita Dutta'
from ..apptools import DevelApp
__all__ = ['evol_fetch']
APP = DevelApp('fetch', help='fetch MSA files from Pfam')
APP.setExample(
"""Fetch MSA files from Pfam database for given Pfam ID code or
accession.
Fetch PFAM ID Cys_knot:
$ evol fetch Cys_knot
Fetch PFAM accession with specific parameters:
$ evol fetch PF00007 --compressed --format fasta --outname mymsa""", [])
APP.addArgument('acc',
help='Pfam accession or ID',
type=str)
APP.addGroup('download', 'download options')
APP.addArgument('-a', '--alignment',
dest='alignment',
type=str,
default='full',
metavar='STR',
help='alignment type',
choices='full seed ncbi metagenomics'.split(),
group='download')
APP.addArgument('-f', '--format',
dest='format',
type=str,
default='stockholm',
metavar='STR',
help='Pfam supported MSA format',
choices='selex fasta stockholm'.split(),
group='download')
APP.addArgument('-o', '--order',
dest='order',
type=str,
default='tree',
metavar='STR',
help='ordering of sequences',
choices='tree alphabetical'.split(),
group='download')
APP.addArgument('-i', '--inserts',
dest='inserts',
type=str,
default='upper',
metavar='STR',
help='letter case for inserts',
choices='upper lower'.split(),
group='download')
APP.addArgument('-g', '--gaps',
dest='gaps',
type=str,
default='dashes',
metavar='STR',
help='gap character',
choices='dashes dots mixed'.split(),
group='download')
APP.addArgument('-t', '--timeout',
dest='timeout',
type=int,
default=60,
metavar='INT',
help='timeout for blocking connection attempts',
group='download')
APP.addGroup('output', 'output options')
APP.addArgument('-d', '--outdir',
dest='folder',
type=str,
default='.',
metavar='PATH',
help='output directory',
group='output')
APP.addArgument('-p', '--outname',
dest='outname',
type=str,
default=None,
metavar='STR',
help='output filename, default is accession and alignment type',
group='output')
APP.addArgument('-z', '--compressed',
dest='compressed',
action='store_true',
help='gzip downloaded MSA file',
group='output')
[docs]def evol_fetch(acc, **kwargs):
import prody
prody.fetchPfamMSA(acc, **kwargs)
APP.setFunction(evol_fetch)
