"""MSA residue coevolution calculation application."""
__author__ = 'Anindita Dutta, Ahmet Bakan'
from ..apptools import DevelApp
__all__ = ['evol_occupancy']
APP = DevelApp('occupancy',
help='calculate occupancy of rows and columns in MSA')
APP.setExample(
"""Calculate occupancy of rows and columns of the msa. Any msa file in
supported formats 'FASTA', 'SELEX', 'Stockholm' can be given as input.
These plots can be used to identify whether MSA needs refinement to reduce
the number of gaps in order to avoid false positives in later analysis.
Following example will save row occupancy data and plot using default options:
$ evol occupancy piwi_refined.slx
Following example will save both row and column occupancy and plot using
specified figure parameters:
$ evol occupancy piwi_refined.slx -o both -X Residue -Y Occupancy""")
APP.addArgument('msa',
help='MSA file')
APP.addGroup('calc', 'calculation options')
APP.addArgument('-o', '--occ-axis',
dest='occaxis',
help='calculate row or column occupancy or both.',
choices=['row', 'col', 'both'],
metavar='STR',
type=str,
default='row',
group='calc')
APP.addGroup('output', 'output options')
APP.addArgument('-p', '--prefix',
dest='prefix',
help='output filename prefix, default is '
'msa filename with _occupancy suffix',
type=str,
metavar='STR',
group='output')
APP.addArgument('-l', '--label',
dest='label',
help='index for column based on msa label',
type=str,
metavar='STR',
group='output')
APP.addArgument('-f', '--number-format',
dest='numformat', type=str, default='%12g',
metavar='STR', help='number output format', group='output')
APP.addFigarg('-X', '--xlabel',
dest='xlabel',
help='specify xlabel',
type=str,
metavar='STR',
default=None)
APP.addFigarg('-Y', '--ylabel',
dest='ylabel',
help='specify ylabel',
type=str,
metavar='STR',
default=None)
APP.addFigarg('-T', '--title',
dest='title',
help='figure title',
type=str,
metavar='STR',
default=None)
APP.addFigure('-S', '--save-plot',
dest='figocc',
action='store_true',
help='save occupancy plot/s')
[docs]def evol_occupancy(msa, **kwargs):
from numpy import arange
import prody
from prody import parseMSA, calcMSAOccupancy, showMSAOccupancy, writeArray
from os.path import splitext
prefix = kwargs.get('prefix')
if prefix is None:
prefix, _ = splitext(msa)
if _.lower() == '.gz':
prefix, _ = splitext(prefix)
prefix += '_occupancy'
msa = parseMSA(msa)
numformat = kwargs.get('numformat', '%12g')
occupancy , suffix = [], []
occaxis = kwargs.get('occaxis', 'row')
if occaxis == 'both':
suffix = ['_row', '_col']
occupancy.append(calcMSAOccupancy(msa, occ='row'))
occupancy.append(calcMSAOccupancy(msa, occ='col'))
else:
suffix = '_' + occaxis
occupancy.append(calcMSAOccupancy(msa, occ=occaxis))
for i, occ in enumerate(occupancy):
writeArray((prefix + suffix[i] + '.txt'), occ, format=numformat)
for i, occ in enumerate(occupancy):
if kwargs.get('figocc'):
try:
import matplotlib.pyplot as plt
except ImportError:
LOGGER.warn('Matplotlib could not be imported, '
'figures are not saved.')
else:
prody.SETTINGS['auto_show'] = False
width = kwargs.get('figwidth', 8)
height = kwargs.get('figheight', 6)
xlabel = kwargs.get('xlabel')
title = kwargs.get('title')
figure = plt.figure(figsize=(width, height))
label = kwargs.get('label')
show = showMSAOccupancy(msa=msa, occ=occ, label=label,
xlabel=xlabel, title=title)
format = kwargs.get('figformat', 'pdf')
figure.savefig(prefix + suffix[i] + '.' + format, format=format,
dpi=kwargs.get('figdpi', 300))
APP.setFunction(evol_occupancy)
