/usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.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 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 85 86 87 88 89 90 91 92 | #!/usr/bin/env python
#file: rnashapes_parser.py
"""
Author: Shandy Wikman (ens01svn@cs.umu.se)
Status: Development. According to future requirements behavior will be changed
Parser to parse RNAshapes output and returns list of lists [Seq,Pairs,Ene]
Revision History:
2006 Shandy Wikman created file
"""
from string import split,strip,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d import Pairs,ViennaStructure
__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 RNAshapes_parser(lines=None,order=True):
"""
Returns a list containing tuples of (sequence,pairs object,energy) for
every sequence
[[Seq,Pairs,Ene],[Seq,Pairs,Ene],...]
Structures will be ordered by the structure energy by default, of ordered
isnt desired set order to False
"""
result = lineParser(lines)
if order:
result = order_structs(result)
return result
def lineParser(list=None):
"""
Parses Lines from output and returns a list of tuples
"""
result = []
s = False
seq = ''
energy = 0.0
pairs = ''
for line in list:
if len(seq)>1 and energy != 0.0 and len(pairs)>1:
result.append([seq,pairs,energy])
seq = energy = pairs = ''
if line.startswith('>'):
name = line.strip('>\n')
s = True #signals that sequence is next line
elif s:
seq = line.strip()
s = False
elif line.startswith('-'):
struct = line.split(None,2)[1].strip('\n')
energy = atof(line.split(None,2)[0].strip('\n'))
pairs = to_Pairs(struct)
return result
def to_Pairs(struct=None):
"""
Converts a vienna structure into a pairs object
Returns pairs object
"""
struct = ViennaStructure(struct)
pairs = struct.toPairs()
return pairs
def order_structs(result):
"""
order structure so that the structure whit highetst MFE(most negative)
will be placed first and so on to the lowest MFE structure.
"""
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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