/usr/share/pyshared/cogent/parse/nupack.py is in python-cogent 1.5.3-2.
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 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | #!/usr/bin/env python
from string import strip,split,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d import Pairs,ViennaStructure
from cogent.struct.knots import opt_single_random
__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 nupack_parser(lines=None,pseudo=True):
"""Parser for NUPACK output format
pseudo - If True pseudoknot will be keept if False it will be removed
"""
result = line_parser(lines,pseudo)
return result
curly_to_dots_table = make_trans('{}','..')
bracket_to_dots_table = make_trans('()','..')
curly_to_bracket_table = make_trans('{}','()')
def line_parser(lines=None,pseudo=True):
"""Parser for nupack output format
Returns list containing: sequence, paris and energy
ex: [[seq,[struct],energy]]
"""
record = False
result = []
SSEList = [] #Sequence,Structure,Energy
for line in lines:
if line.startswith('Error'):#Error no structure found
result = [Pairs([])] #return empty pairs list
return result
if line.startswith('Sequence and a Minimum Energy Structure'):
record = True
elif record:
line = line.strip('\n')
SSEList.append(line)
SSEList[1] = to_pairs(SSEList,pseudo) #pairs
SSEList = SSEList[:3]
SSEList[-1] = atof(SSEList[-1].split()[2]) #energy
result.append(SSEList)
return result
def to_pairs(list=None,pseudo=True):
"""
Converts nupack structure string into pairs object
pseudoknotted and not pseudoknotted.
"""
tmp = list[1]
pairs = []
if list.__contains__('pseudoknotted!'):
#since pseudoknotted is denoted by {} it divides into {} and () string
#they are then turned into pairs lists seperatly and then the lists are
#joined to form the complete set of pairs
first = second = tmp
first = ViennaStructure(first.translate(curly_to_dots_table))
second = second.translate(bracket_to_dots_table)
second = ViennaStructure(second.translate(curly_to_bracket_table))
pairs = first.toPairs()
pairs.extend(second.toPairs())
pairs.sort()
if not pseudo:
pairs = opt_single_random(pairs)
pairs.sort()
else:
structure = ViennaStructure(tmp.translate(curly_to_bracket_table))
pairs = structure.toPairs()
pairs.sort()
return pairs
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