"""Calculate conservation in an MSA using Shannon entropy."""
from ..apptools import DevelApp
from prody import LOGGER
__all__ = ['evol_conserv']
APP = DevelApp('conserv',
help='analyze conservation using Shannon entropy')
APP.setExample(
"""This application calculates conservation using Shannon entropy for a \
refined multiple sequence alignment. Following example will save entropy \
data and plot using default options:
$ evol conserv piwi_refined.slx -S""", [])
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('-g', '--gaps',
dest='omitgaps',
help='do not omit gap characters',
default=True,
action='store_false',
group='calc')
APP.addGroup('output', 'output options')
APP.addArgument('-p', '--prefix',
dest='prefix',
help='output filename prefix, default is '
'msa filename with _conserv 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.addFigure('-S', '--save-plot',
dest='figent',
action='store_true',
help='save conservation plot')
[docs]def evol_conserv(msa, **kwargs):
import prody
from prody import parseMSA, calcShannonEntropy, showShannonEntropy
from prody import writeArray
from os.path import splitext
prefix = kwargs.get('prefix')
if prefix is None:
prefix, _ = splitext(msa)
if _.lower() == '.gz':
prefix, _ = splitext(prefix)
prefix += '_conserv'
msa = parseMSA(msa)
entropy = calcShannonEntropy(msa, **kwargs)
writeArray(prefix + '.txt',
entropy, format=kwargs.get('numformat', '%12g'))
if kwargs.get('figent'):
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)
figargs = kwargs.get('figargs', ())
figure = plt.figure(figsize=(width, height))
show = showShannonEntropy(entropy, msa=msa, *figargs)
format = kwargs.get('figformat', 'pdf')
figure.savefig(prefix + '.' + format, format=format,
dpi=kwargs.get('figdpi', 300))
APP.setFunction(evol_conserv)
