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
|
#!/usr/bin/env python
"""Parses RNAfold dot plot output file.
"""
from string import strip
from cogent.parse.record_finder import LabeledRecordFinder
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def RnaFoldParser(lines):
"""Returns a tuple containing sequence and dot plot indices.
(sequence, (index1, index2, pair probability))
"""
sequence = ''
indices = []
#Make sure lines is not empty
if lines:
#Get the block of lines that starts with /sequence
sequence_block = LabeledRecordFinder(\
lambda x: x.startswith('/sequence'))
#only care about the second element in the result
seq_block = list(sequence_block(lines))[1]
#Get the sequence from the block
sequence = getSequence(seq_block)
#Get the indices and pair probabilites from the block
indices = getIndices(seq_block)
return (sequence, indices)
def getSequence(lines):
"""Returns sequence that RNAfold dot plot represents, given lines.
"""
sequence_pieces = []
#For each line after the first, containing /sequence
for line in map(strip, lines[1:]):
#If the line which denotes the end of a sequence is not reached
if line.startswith(')'):
break
else:
#Strip of whitespace and add to list
sequence_pieces.append(line.replace('\\',''))
return ''.join(sequence_pieces)
def getIndices(lines):
"""Returns list of tuples: (index1,index2,pair probability).
"""
index_list = []
#For each line that ends with 'ubox' (which denotes lines with indices)
for line in filter(lambda x: x.endswith('ubox'), lines):
#split on whitespace
up_index,down_index,probability,ubox = line.split()
#Build tuple with indices and pair probability
index_list.append((int(up_index), int(down_index), \
float(probability)))
return index_list
|
