"""MSA residue coevolution calculation application."""
__author__ = 'Anindita Dutta, Ahmet Bakan'
from ..apptools import DevelApp
__all__ = ['evol_coevol']
APP = DevelApp('coevol',
help='analyze co-evolution using mutual information')
APP.setExample(
"""Analyze coevolution by performing mutual information calculation between
MSA positions. A refined MSA without gaps should be used.
Following example will save coevolution data and plot using default options:
$ evol coevol piwi_refined.slx -S
Following example will save coevolution data and plot for all correction and \
normalizations:
$ evol coevol piwi_refined.slx -S -c apc -c asc -m sument -m minent \
-m maxent -m mincon -m maxcon -m joint""", [])
APP.addArgument('msa',
help='refined MSA file')
APP.addGroup('calc', 'calculation options')
APP.addArgument('-n', '--no-ambiguity',
dest='ambiguity',
help='treat amino acids characters B, Z, J, and X as non-ambiguous',
default=True,
action='store_false',
group='calc')
APP.addArgument('-c', '--correction',
dest='correction',
help='also save corrected mutual information matrix data and plot',
choices=['apc', 'asc'],
metavar='STR',
type=str,
action='append',
group='calc')
APP.addArgument('-m', '--normalization',
dest='normalization',
help='also save normalized mutual information matrix data and plot',
choices='sument minent maxent mincon maxcon joint'.split(),
metavar='STR',
type=str,
action='append',
group='calc')
APP.addGroup('output', 'output options')
APP.addArgument('-t', '--heatmap',
dest='heatmap',
help='save heatmap files for all mutual information matrices',
default=False,
action='store_true',
group='output')
APP.addArgument('-p', '--prefix',
dest='prefix',
help='output filename prefix, default is '
'msa filename with _coevol suffix',
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('-L', '--cmin',
dest='cmin',
help='apply lower limits for figure plot',
type=float,
metavar='FLOAT')
APP.addFigarg('-U', '--cmax',
dest='cmax',
help='apply upper limits for figure plot',
type=float,
metavar='FLOAT')
APP.addFigarg('-X', '--xlabel',
dest='xlabel',
help='specify xlabel, by default will be applied on 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='figcoevol',
action='store_true',
help='save coevolution plot')
[docs]def evol_coevol(msa, **kwargs):
from numpy import arange
import prody
from prody import parseMSA, buildMutinfoMatrix, showMutinfoMatrix
from prody import applyMutinfoCorr, calcShannonEntropy
from prody import writeArray, LOGGER, applyMutinfoNorm, writeHeatmap
from os.path import splitext
prefix = kwargs.get('prefix')
if prefix is None:
prefix, _ = splitext(msa)
if _.lower() == '.gz':
prefix, _ = splitext(prefix)
prefix += '_mutinfo'
msa = parseMSA(msa)
mutinfo = buildMutinfoMatrix(msa, **kwargs)
numformat = kwargs.get('numformat', '%12g')
heatmap = kwargs.get('heatmap', False)
#writeArray(prefix + '.txt', mutinfo, format=numformat)
if heatmap:
hmargs = {
'xlabel': 'Residue', 'ylabel': 'Residue',
'xorigin': 1, 'xstep': 1,
'residue': arange(msa.numResidues())}
todo = [(None, None)]
norm = kwargs.get('normalization', [])
corr = kwargs.get('correction', [])
if norm is not None:
if 'joint' in norm:
todo.append(('norm', 'joint'))
for which in norm:
if which == 'join': continue
todo.append(('norm', which))
if corr is not None:
for which in corr:
todo.append(('corr', which))
entropy = None
for what, which in todo:
if what is None:
matrix = mutinfo
suffix = ''
tuffix = ' Mutual Information'
elif which == 'joint':
LOGGER.info('Applying {0} normalization.'.format(repr(which)))
matrix = buildMutinfoMatrix(msa, norm=True, **kwargs)
suffix = '_norm_joint'
tuffix = ' MI - Normalization: ' + which
elif what == 'norm':
LOGGER.info('Applying {0} normalization.'.format(repr(which)))
if entropy is None:
entropy = calcShannonEntropy(msa, **kwargs)
matrix = applyMutinfoNorm(mutinfo, entropy, norm=which)
suffix = '_norm_' + which
tuffix = ' MI - Normalization: ' + which
else:
LOGGER.info('Applying {0} correction.'.format(repr(which)))
matrix = applyMutinfoCorr(mutinfo, which)
suffix = '_corr_' + which
tuffix = ' MI - Correction: ' + which
writeArray(prefix + suffix + '.txt',
matrix, format=kwargs.get('numformat', '%12g'))
if heatmap:
writeHeatmap(prefix + suffix + '.hm', matrix,
title = msa.getTitle() + tuffix, **hmargs)
if kwargs.get('figcoevol'):
try:
import matplotlib.pyplot as plt
except ImportError:
LOGGER.warn('Matplotlib could not be imported, '
'figures are not saved.')
else:
cmin = kwargs.get('cmin', matrix.min())
cmax = kwargs.get('cmax', matrix.max())
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))
show = showMutinfoMatrix(matrix, msa=msa, clim=(cmin, cmax),
xlabel=xlabel, title=title)
format = kwargs.get('figformat', 'pdf')
figure.savefig(prefix + suffix + '.' + format, format=format,
dpi=kwargs.get('figdpi', 300))
APP.setFunction(evol_coevol)
