def group_pairs(seqs, n_seqs_in_pair=None, check_all_same_n_seqs=True,
check_name_matches=True):
seqs = iter(seqs)
if n_seqs_in_pair is None:
first_pair, next_read = _get_first_pair_by_name(seqs)
if first_pair is None:
n_seqs_in_pair = None
else:
yield first_pair
n_seqs_in_pair = len(first_pair)
seqs = chain([next_read], seqs)
if n_seqs_in_pair == 1:
# No need to check anything, a pair cannot have less than one read
# or more than one name
check_all_same_n_seqs = False
check_name_matches = False
if n_seqs_in_pair:
pairs = group_in_packets_fill_last(seqs, packet_size=n_seqs_in_pair)
for pair in pairs:
pair = filter(lambda seq: seq is not None, pair)
if check_all_same_n_seqs and n_seqs_in_pair != len(pair):
msg = 'The last pair has fewer reads'
raise InterleaveError(msg)
if check_name_matches:
_check_name_and_direction_match(*pair)
yield pair
def group_pairs(seqs,
n_seqs_in_pair=None,
check_all_same_n_seqs=True,
check_name_matches=True):
seqs = iter(seqs)
if n_seqs_in_pair is None:
first_pair, next_read = _get_first_pair_by_name(seqs)
if first_pair is None:
n_seqs_in_pair = None
else:
yield first_pair
n_seqs_in_pair = len(first_pair)
seqs = chain([next_read], seqs)
if n_seqs_in_pair == 1:
# No need to check anything, a pair cannot have less than one read
# or more than one name
check_all_same_n_seqs = False
check_name_matches = False
if n_seqs_in_pair:
pairs = group_in_packets_fill_last(seqs, packet_size=n_seqs_in_pair)
for pair in pairs:
pair = filter(lambda seq: seq is not None, pair)
if check_all_same_n_seqs and n_seqs_in_pair != len(pair):
msg = 'The last pair has fewer reads'
raise InterleaveError(msg)
if check_name_matches:
_check_name_and_direction_match(*pair)
yield pair
def test_group_in_packets(self):
'It groups an iterator in packets of items'
packets = list(group_in_packets(range(4), 2))
assert packets == [(0, 1), (2, 3)]
packets = [packet for packet in group_in_packets(range(5), 2)]
assert packets == [(0, 1), (2, 3), (4,)]
packets = list(group_in_packets_fill_last(range(5), 2))
assert packets == [(0, 1), (2, 3), (4, None)]
packets = list(group_in_packets([], 2))
assert packets == []
def test_group_in_packets(self):
'It groups an iterator in packets of items'
packets = list(group_in_packets(range(4), 2))
assert packets == [(0, 1), (2, 3)]
packets = [packet for packet in group_in_packets(range(5), 2)]
assert packets == [(0, 1), (2, 3), (4,)]
packets = list(group_in_packets_fill_last(range(5), 2))
assert packets == [(0, 1), (2, 3), (4, None)]
packets = list(group_in_packets([], 2))
assert packets == []
def _itemize_fastq(fhand):
'It returns the fhand divided in chunks, one per seq'
# group_in_packets_fill_last is faster than group_in_packets
blobs = group_in_packets_fill_last(ifilter(_line_is_not_empty, fhand), 4)
return (SeqItem(_get_name_from_lines(lines), lines) for lines in blobs)
def _itemize_fastq_singleline(fhand):
'It returns the fhand divided in chunks, one per seq'
# group_in_packets_fill_last is faster than group_in_packets
blobs = group_in_packets_fill_last(ifilter(_line_is_not_empty, fhand), 4)
return (SeqItem(_get_name_from_lines(lines), lines) for lines in blobs)