/usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | #!/usr/bin/env python
from cogent.util.transform import make_trans
from cogent.struct.rna2d import wuss_to_vienna, Pairs
from cogent.parse.rfam import RfamParser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
def CMfinderParser(lines):
"""Parser for CMfinder output format
Parser tested through RfamParser test
"""
for info, alignment, struct in RfamParser(lines,strict=False):
struct = wuss_to_vienna(struct)
pairs = struct.toPairs()
return [alignment, pairs]
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