def _match_pairs_from_sorted_reads(sorted_reads):
prev_reads = []
prev_reads_name = None
prev_reads_directions = []
#{'read': None, 'name': None, 'direction': None}
for read in sorted_reads:
title = get_title(read)
try:
name, direction = _parse_pair_direction_and_name_from_title(title)
except PairDirectionError:
name, direction = None, None
if direction is not None and prev_reads_name is None:
prev_reads = [read]
prev_reads_name = name
prev_reads_directions = [direction]
continue
elif direction is None:
if prev_reads:
yield prev_reads
prev_reads = []
prev_reads_name = None
prev_reads_directions = []
yield [read]
elif name == prev_reads_name:
if direction == REV:
prev_reads.append(read)
prev_reads_directions.append(direction)
else:
prev_reads.insert(0, read)
prev_reads_directions.insert(0, direction)
else:
if prev_reads:
yield prev_reads
prev_reads = [read]
prev_reads_name = name
prev_reads_directions = [direction]
if prev_reads:
yield prev_reads
def _key(seq):
return get_title(seq)
def _parse_pair_direction_and_name(seq):
'It parses the description field to get the name and the pair direction'
return _parse_pair_direction_and_name_from_title(get_title(seq))
def _parse_pair_direction_and_name(seq):
'It parses the description field to get the name and the pair direction'
return _parse_pair_direction_and_name_from_title(get_title(seq))
def _key(seq):
return get_title(seq)