<reponame>sauloal/cnidaria<filename>scripts/venv/lib/python2.7/site-packages/cogent/parse/cmfinder.py
#!/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__ = "<NAME>"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["<NAME>"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__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]
    
