def test_check_is_pair_4b():
read1 = Sequence(name='seq/1', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
try:
check_is_pair(read1, read2)
assert False # check_is_pair should fail here.
except ValueError:
pass
def test_check_is_pair_4b():
read1 = Sequence(name='seq/1', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
try:
check_is_pair(read1, read2)
assert False # check_is_pair should fail here.
except ValueError:
pass
def test_check_is_pair_7():
read1 = Sequence(name='seq/2', sequence='AAA')
read2 = Sequence(name='seq/1', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_3_fa():
read1 = Sequence(name='seq 1::', sequence='AAA')
read2 = Sequence(name='seq 2::', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_3_broken_fq_2():
read1 = Sequence(name='seq 1::', quality='###', sequence='AAA')
read2 = Sequence(name='seq', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_2():
read1 = Sequence(name='seq/1', quality='###', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
assert check_is_pair(read1, read2)
def broken_paired_reader(screed_iter,
min_length=None,
force_single=False,
require_paired=False):
"""Read pairs from a stream.
A generator that yields singletons and pairs from a stream of FASTA/FASTQ
records (yielded by 'screed_iter'). Yields (n, is_pair, r1, r2) where
'r2' is None if is_pair is False.
The input stream can be fully single-ended reads, interleaved paired-end
reads, or paired-end reads with orphans, a.k.a. "broken paired".
Usage::
for n, is_pair, read1, read2 in broken_paired_reader(...):
...
Note that 'n' behaves like enumerate() and starts at 0, but tracks
the number of records read from the input stream, so is
incremented by 2 for a pair of reads.
If 'min_length' is set, all reads under this length are ignored (even
if they are pairs).
If 'force_single' is True, all reads are returned as singletons.
"""
record = None
prev_record = None
num = 0
if force_single and require_paired:
raise ValueError("force_single and require_paired cannot both be set!")
# handle the majority of the stream.
for record in screed_iter:
if prev_record:
if check_is_pair(prev_record, record) and not force_single:
if min_length and (len(prev_record.sequence) < min_length
or len(record.sequence) < min_length):
if require_paired:
record = None
else:
yield num, True, prev_record, record # it's a pair!
num += 2
record = None
else: # orphan.
if require_paired:
err = UnpairedReadsError(
"Unpaired reads when require_paired is set!",
prev_record, record)
raise err
# ignore short reads
if min_length and len(prev_record.sequence) < min_length:
pass
else:
yield num, False, prev_record, None
num += 1
prev_record = record
record = None
# handle the last record, if it exists (i.e. last two records not a pair)
if prev_record:
if require_paired:
raise UnpairedReadsError(
"Unpaired reads when require_paired "
"is set!", prev_record, None)
if min_length and len(prev_record.sequence) < min_length:
pass
else:
yield num, False, prev_record, None
def test_check_is_pair_7():
read1 = Sequence(name='seq/2', sequence='AAA')
read2 = Sequence(name='seq/1', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_3_fa():
read1 = Sequence(name='seq 1::', sequence='AAA')
read2 = Sequence(name='seq 2::', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_3_broken_fq_2():
read1 = Sequence(name='seq 1::', quality='###', sequence='AAA')
read2 = Sequence(name='seq', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_2():
read1 = Sequence(name='seq/1', quality='###', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
assert check_is_pair(read1, read2)
def broken_paired_reader(screed_iter, min_length=None,
force_single=False, require_paired=False):
"""Read pairs from a stream.
A generator that yields singletons and pairs from a stream of FASTA/FASTQ
records (yielded by 'screed_iter'). Yields (n, is_pair, r1, r2) where
'r2' is None if is_pair is False.
The input stream can be fully single-ended reads, interleaved paired-end
reads, or paired-end reads with orphans, a.k.a. "broken paired".
Usage::
for n, is_pair, read1, read2 in broken_paired_reader(...):
...
Note that 'n' behaves like enumerate() and starts at 0, but tracks
the number of records read from the input stream, so is
incremented by 2 for a pair of reads.
If 'min_length' is set, all reads under this length are ignored (even
if they are pairs).
If 'force_single' is True, all reads are returned as singletons.
"""
record = None
prev_record = None
num = 0
if force_single and require_paired:
raise ValueError("force_single and require_paired cannot both be set!")
# handle the majority of the stream.
for record in screed_iter:
if prev_record:
if check_is_pair(prev_record, record) and not force_single:
if min_length and (len(prev_record.sequence) < min_length or
len(record.sequence) < min_length):
if require_paired:
record = None
else:
yield num, True, prev_record, record # it's a pair!
num += 2
record = None
else: # orphan.
if require_paired:
err = UnpairedReadsError(
"Unpaired reads when require_paired is set!",
prev_record, record)
raise err
# ignore short reads
if min_length and len(prev_record.sequence) < min_length:
pass
else:
yield num, False, prev_record, None
num += 1
prev_record = record
record = None
# handle the last record, if it exists (i.e. last two records not a pair)
if prev_record:
if require_paired:
raise UnpairedReadsError("Unpaired reads when require_paired "
"is set!", prev_record, None)
if min_length and len(prev_record.sequence) < min_length:
pass
else:
yield num, False, prev_record, None
