/usr/share/pyshared/cogent/parse/pknotsrg.py is in python-cogent 1.5.3-2.
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"""Parser for NUPACK output format
If pseudoknotted first steam will be denoted by [] brackets and second steam
with {} brackets
"""
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 pknotsrg_parser(lines=None,pseudo=True):
"""Parser for pknotsrg output format
Returns a list containing: sequence, structure and energy
ex: [[seq,[structure],energy]]
pseudo - If True pairs will be returned with pseudoknots
If False pairs will be returned without pseudoknots
"""
result = []
struct = str(lines[1]).strip('\n')
seq = lines[0].strip()
tmp_pairs,energy = to_pairs(struct)
tmp_pairs.sort()
if not pseudo:
tmp_pairs = opt_single_random(tmp_pairs)
tmp_pairs.sort()
result.append([seq,tmp_pairs,energy])
return result
primary_table = make_trans('{[]}','....')
first_table = make_trans('({[]})','..()..')
second_table = make_trans('([{}])','..()..')
def to_pairs(struct=None):
"""
Converts structure string in to a pairs object.
Starts by checking for pseudoknots if pseudoknotted it translates each
steam in to vienna notation and from there makes a pairs object.
Each pairs object is then joined to form the final pairs object of
the entire structure
Returns a tuple of the pairs object and the energy
"""
primary = first = second = struct.split(None,2)[0]
energy = atof(struct.split(None,2)[1].strip('()'))
if struct.__contains__('['): #Checks for first pseudoknot steam
primary = ViennaStructure(primary.translate(primary_table))
first = ViennaStructure(first.translate(first_table))
pairs = primary.toPairs()
pairs.extend(first.toPairs()) #Adds the first steam to pairs object
if struct.__contains__('{'): #Checks for second pseudo steam
second = ViennaStructure(second.translate(second_table))
pairs.extend(second.toPairs())
else:
primary = ViennaStructure(primary.translate(primary_table))
pairs = primary.toPairs()
return pairs,energy
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