/usr/share/pyshared/cogent/parse/pfold.py is in python-cogent 1.5.3-2.
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 26 27 28 29 30 31 32 33 34 | #!/usr/bin/env python
from string import split,strip
from cogent.struct.rna2d import Pairs,ViennaStructure
from cogent.parse.column import column_parser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
def pfold_parser(lines):
"""Parser for Pfold output
"""
tree,lines = tree_struct_sep(lines)
result = column_parser(lines)
return result
def tree_struct_sep(lines):
"""Separates tree structure from rest of the data.
This is done to get an excepted format for the column_parser
"""
indx = None
for line in lines:
if line.startswith('; ********'):
indx = lines.index(line)+1
break
return lines[:indx],lines[indx:]
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