/usr/lib/python2.7/dist-packages/cogent/parse/unafold.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #!/usr/bin/env python
from cogent.parse.ct import ct_parser
__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 unafold_parser(lines=None):
"""Parser for unafold output"""
result = ct_parser(lines)
return result
def order_structs(result):
"""Order structures according to energy value
Order the structures so that the structure with lowest energy is ranked
first and so on...
Unafold returns results in the same order as the input files
"""
for i in result:
i.reverse()
result.sort()
#result.reverse() #to test with the lowest negetiv value as the best struct
for i in result:
i.reverse()
return result
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