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:]
|
