def test_group_in_packets(self):
'It groups an iterator in packets of items'
packets = [packet for packet in 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 = [packet for packet in 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 _read_seqrecord_packets(fhands, size=get_setting('PACKET_SIZE'),
file_format=GUESS_FORMAT):
'''It yields SeqRecords in packets of the given size.'''
seqs = _read_seqrecords(fhands, file_format=file_format)
return group_in_packets(seqs, size)
def read_seq_packets(fhands, size=get_setting('PACKET_SIZE'), out_format=None,
file_format=GUESS_FORMAT, prefered_seq_classes=None):
'''It yields SeqItems in packets of the given size.'''
seqs = read_seqs(fhands, file_format, out_format=out_format,
prefered_seq_classes=prefered_seq_classes)
return group_in_packets(seqs, size)
def _read_seqrecord_packets(fhands, size=get_setting('PACKET_SIZE')):
'''It yields SeqRecords in packets of the given size.'''
seqs = _read_seqrecords(fhands)
return group_in_packets(seqs, size)
def read_seq_packets(fhands, size=PACKET_SIZE, file_format=GUESS_FORMAT):
'''It yields SeqRecords in packets of the given size.'''
seqs = read_seqrecords(fhands, file_format=file_format)
return group_in_packets(seqs, size)
def group_in_filter_packets(items, items_per_packet):
for packet in group_in_packets(items, items_per_packet):
yield {PASSED: packet, FILTERED_OUT: []}
def _read_seqrecord_packets(fhands, size=get_setting('PACKET_SIZE')):
'''It yields SeqRecords in packets of the given size.'''
seqs = _read_seqrecords(fhands)
return group_in_packets(seqs, size)
def read_seq_packets(fhands, size=get_setting('PACKET_SIZE'), out_format=None,
prefered_seq_classes=None):
'''It yields SeqItems in packets of the given size.'''
seqs = read_seqs(fhands, out_format=out_format,
prefered_seq_classes=prefered_seq_classes)
return group_in_packets(seqs, size)
def _itemize_fastq(fhand):
'It returns the fhand divided in chunks, one per seq'
blobs = group_in_packets(filter(_line_is_not_empty, fhand), 4)
return (SeqItem(_get_name_from_lines(lines), lines) for lines in blobs)
def group_in_filter_packets(items, items_per_packet):
for packet in group_in_packets(items, items_per_packet):
yield {PASSED: packet, FILTERED_OUT: []}
def _read_seqrecord_packets(fhands,
size=get_setting('PACKET_SIZE'),
file_format=GUESS_FORMAT):
'''It yields SeqRecords in packets of the given size.'''
seqs = _read_seqrecords(fhands, file_format=file_format)
return group_in_packets(seqs, size)
