def evol_merge(*msa, **kwargs):
import prody
from prody import parseMSA, mergeMSA, LOGGER, writeMSA, MSAFile
from prody.sequence.msafile import MSAEXTMAP
from os.path import splitext
if len(msa) < 2:
raise ValueError('multiple msa filenames must be specified')
msaobj = []
try:
msaobj = [parseMSA(fn) for fn in msa]
except:
raise IOError('failed to parse {0}'.format(fn))
msafile = MSAFile(msa[0])
format = kwargs.get('format') or msafile.format
outname = kwargs.get('outname') or (msafile.getTitle() + '_merged' +
MSAEXTMAP[msafile.format])
writeMSA(outname, mergeMSA(*msaobj), **kwargs)
LOGGER.info('Merged MSA is saved as: {0}'.format(outname))
def testMerge(self):
merged = mergeMSA(FASTA, FASTA)
length = FASTA.numResidues()
self.assertEqual(merged[:, :length], merged[:, length:])
def testMerge(self):
merged = mergeMSA(FASTA, FASTA)
length = FASTA.numResidues()
self.assertEqual(merged[:, :length], merged[:, length:])