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#!/usr/bin/env python
from cogent.struct.rna2d import Pairs
from cogent.struct.knots import opt_single_random
from cogent.struct.pairs_util import adjust_base
__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 ilm_parser(lines=None,pseudo=True):
"""Ilm format parser
Takes lines as input and returns a list with Pairs object.
Pseudo - if True returns pairs with possible pseudoknot
if False removes pseudoknots
"""
pairs = []
for line in lines:
if line.startswith('Final') or len(line)==1:#skip these lines
continue
line = line.strip('\n')
line = map(int,line.split(None,2))
if line[1] == 0:
continue #Skip this line, not a pair
else:
pairs.append(line)
pairs = adjust_base(pairs,-1)
tmp = Pairs(pairs).directed()
tmp.sort()
if not pseudo:
tmp = opt_single_random(tmp)
tmp.sort()
result = []
result.append(tmp)
return result
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