def test_name_check(self):
seqs = _build_some_paired_seqs()
try:
list(group_pairs(seqs, n_seqs_in_pair=4))
self.fail('InterleaveError expected')
except InterleaveError:
pass
seqs = _build_some_paired_seqs()
paired_seqs = list(
group_pairs(seqs, n_seqs_in_pair=4, check_name_matches=False))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C', 'T', 'G']
def test_name_check(self):
seqs = _build_some_paired_seqs()
try:
list(group_pairs(seqs, n_seqs_in_pair=4))
self.fail('InterleaveError expected')
except InterleaveError:
pass
seqs = _build_some_paired_seqs()
paired_seqs = list(group_pairs(seqs, n_seqs_in_pair=4,
check_name_matches=False))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C', 'T', 'G']
def test_n_seqs_check(self):
seqs = _build_some_paired_seqs()
seqs = seqs[:-1]
try:
list(group_pairs(seqs, n_seqs_in_pair=2))
self.fail('InterleaveError expected')
except InterleaveError:
pass
paired_seqs = list(group_pairs(seqs, n_seqs_in_pair=2,
check_all_same_n_seqs=False))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
def test_pair_grouper(self):
seqs = _build_some_paired_seqs()
paired_seqs = list(group_pairs(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T', 'G']
assert len(paired_seqs) == 2
seqs = _build_some_paired_seqs()
paired_seqs = list(group_pairs(seqs, n_seqs_in_pair=1,
check_name_matches=True))
assert [get_str_seq(s) for pair in paired_seqs for s in pair] == ['A',
'C', 'T', 'G']
def test_n_seqs_check(self):
seqs = _build_some_paired_seqs()
seqs = seqs[:-1]
try:
list(group_pairs(seqs, n_seqs_in_pair=2))
self.fail('InterleaveError expected')
except InterleaveError:
pass
paired_seqs = list(
group_pairs(seqs, n_seqs_in_pair=2, check_all_same_n_seqs=False))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
def test_pair_grouper(self):
seqs = _build_some_paired_seqs()
paired_seqs = list(group_pairs(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T', 'G']
assert len(paired_seqs) == 2
seqs = _build_some_paired_seqs()
paired_seqs = list(
group_pairs(seqs, n_seqs_in_pair=1, check_name_matches=True))
assert [get_str_seq(s) for pair in paired_seqs
for s in pair] == ['A', 'C', 'T', 'G']
def _read_pairs(in_fhands, paired_reads):
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
if paired_reads:
pairs = group_pairs_by_name(seqs)
else:
pairs = group_pairs(seqs, n_seqs_in_pair=1)
return pairs
def _read_pairs(in_fhands, paired_reads):
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
if paired_reads:
pairs = group_pairs_by_name(seqs)
else:
pairs = group_pairs(seqs, n_seqs_in_pair=1)
return pairs
def seq_to_trim_packets(seq_packets, group_paired_reads=False):
"It yields packets suitable for the filters"
for packet in seq_packets:
if group_paired_reads:
packet = list(group_pairs_by_name(packet))
else:
packet = list(group_pairs(packet, n_seqs_in_pair=1))
yield {SEQS_PASSED: packet, ORPHAN_SEQS: []}
def seq_to_filterpackets(seq_packets, group_paired_reads=False):
'It yields packets suitable for the filters'
for packet in seq_packets:
if group_paired_reads:
packet = list(group_pairs_by_name(packet))
else:
packet = list(group_pairs(packet, n_seqs_in_pair=1))
yield {SEQS_PASSED: packet, SEQS_FILTERED_OUT: []}
def seq_to_trim_packets(seq_packets, group_paired_reads=False):
'It yields packets suitable for the filters'
for packet in seq_packets:
if group_paired_reads:
packet = list(group_pairs_by_name(packet))
else:
packet = list(group_pairs(packet, n_seqs_in_pair=1))
yield {SEQS_PASSED: packet, ORPHAN_SEQS: []}
def test_empty_iter():
paired_seqs = list(group_pairs([]))
assert not paired_seqs
def test_empty_iter():
paired_seqs = list(group_pairs([]))
assert not paired_seqs