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#!/usr/bin/env python
"""
Parser for RNAPlot postscript output.
"""
from cogent.parse.record_finder import LabeledRecordFinder
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def get_sequence(lines):
"""Returns sequence string.
"""
if lines:
seq_line = ''.join(lines)
seq = seq_line.split('(')[1].split(') def')[0].strip('\n\\')
else:
seq = ''
return seq
def get_coordinates(lines):
"""Returns list of coordinates.
"""
coords = []
for l in lines:
if l.startswith('] def'):
break
elif l.startswith('['):
coords.append(map(float,l.strip('\n[]').split()))
return coords
def get_pairs(lines):
"""Returns list of pairing indices.
- Changes indices to zero based rather than 1 based.
"""
pairs = []
for l in lines:
if l.startswith('] def'):
break
elif l.startswith('['):
first,second = l.strip('\n[]').split()
pairs.append([int(first)-1,int(second)-1])
return pairs
def RnaPlotParser(lines):
"""Returns sequence, coordinates, and pairing indices.
"""
sequence = ''
coordinates = []
pairs = []
if lines:
#Split on sequence block
sequence_finder = LabeledRecordFinder(is_label_line=\
lambda x: x.startswith('/sequence'))
prefix, seq_block = list(sequence_finder(lines))
#split on coordinate block
coordinate_finder = LabeledRecordFinder(is_label_line=\
lambda x: x.startswith('/coor'))
#sequence block is first item in list
sequence_block, coord_block = list(coordinate_finder(seq_block))
#split on pairs block
pairs_finder = LabeledRecordFinder(is_label_line=\
lambda x: x.startswith('/pairs'))
#coordinate block is first item in list
coordinate_block, pairs_block = list(pairs_finder(coord_block))
sequence = get_sequence(sequence_block)
coordinates = get_coordinates(coordinate_block)
pairs = get_pairs(pairs_block)
return sequence, coordinates, pairs
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