def test_to_cigar_units(self, to_convert, expected):
# We can convert the raw form.
to_convert = list(to_convert)
expected = list(expected)
actual = cigar.to_cigar_units(to_convert)
self.assertEqual(actual, expected)
# We can also convert the string form by formatting actual.
self.assertEqual(
cigar.to_cigar_units(cigar.format_cigar_units(actual)), expected)
def test_to_cigar_units(self, to_convert, expected):
# We can convert the raw form.
to_convert = list(to_convert)
expected = list(expected)
actual = cigar.to_cigar_units(to_convert)
self.assertEqual(actual, expected)
# We can also convert the string form by formatting actual.
self.assertEqual(
cigar.to_cigar_units(cigar.format_cigar_units(actual)), expected)
def test_align_reads_simple(self, read_seq, expected_align_pos,
expected_cigar, comment):
"""Test Aligner.align_reads(). Simple tests.
Targets consist of
- original reference sequence.
- a sequence with 'AA' insertion at position 14 and
- 'T' deletion at position 19.
Args:
read_seq: str, read sequence.
expected_align_pos: int, expected aligned position
expected_cigar: [(int, str)], expected cigar information.
comment: str, test comment.
"""
ref_seq = 'AAAAAAAAAAAAATGCATGGGGGATTTTTTTTTTT'
region = ranges.make_range('ref', 10, 10 + len(ref_seq))
align_reads = self.make_test_aligner(ref_seq, region)
# redacted
# implemented. For local alignment, it ensures that there are enough exact
# matches between the reference and target for end-to-end alignment.
targets = [ref_seq, 'AAAAAAAAAAAAATAAGCAGGGGGATTTTTTTTTTT']
read = test_utils.make_read(
read_seq,
chrom='ref',
start=0,
cigar=[(len(read_seq), 'M')],
quals=[64] * len(read_seq),
name='read')
aligned_reads = align_reads.align_reads(targets, [read])
self.assertEqual(expected_align_pos,
aligned_reads[0].alignment.position.position, comment)
self.assertEqual(
_cigar.to_cigar_units(expected_cigar),
list(aligned_reads[0].alignment.cigar), comment)
read = test_utils.make_read(
read_seq,
chrom='ref',
start=0,
cigar=[(2, 'H'), (len(read_seq), 'M'), (1, 'H')],
quals=[64] * len(read_seq),
name='read')
aligned_reads = align_reads.align_reads(targets, [read])
expected_cigar_w_hard_clip = [(2, 'H')] + expected_cigar + [(1, 'H')]
self.assertEqual(
_cigar.to_cigar_units(expected_cigar_w_hard_clip),
list(aligned_reads[0].alignment.cigar), comment)
def test_align_reads_simple(self, read_seq, expected_align_pos,
expected_cigar, comment):
"""Test Aligner.align_reads(). Simple tests.
Targets consist of
- original reference sequence.
- a sequence with 'AA' insertion at position 14 and
- 'T' deletion at position 19.
Args:
read_seq: str, read sequence.
expected_align_pos: int, expected aligned position
expected_cigar: [(int, str)], expected cigar information.
comment: str, test comment.
"""
ref_seq = 'AAAAAAAAAAAAATGCATGGGGGATTTTTTTTTTT'
region = ranges.make_range('ref', 10, 10 + len(ref_seq))
align_reads = self.make_test_aligner(ref_seq, region)
# redacted
# implemented. For local alignment, it ensures that there are enough exact
# matches between the reference and target for end-to-end alignment.
targets = [ref_seq, 'AAAAAAAAAAAAATAAGCAGGGGGATTTTTTTTTTT']
read = test_utils.make_read(
read_seq,
chrom='ref',
start=0,
cigar=[(len(read_seq), 'M')],
quals=[64] * len(read_seq),
name='read')
aligned_reads = align_reads.align_reads(targets, [read])
self.assertEqual(expected_align_pos,
aligned_reads[0].alignment.position.position, comment)
self.assertEqual(
_cigar.to_cigar_units(expected_cigar),
list(aligned_reads[0].alignment.cigar), comment)
read = test_utils.make_read(
read_seq,
chrom='ref',
start=0,
cigar=[(2, 'H'), (len(read_seq), 'M'), (1, 'H')],
quals=[64] * len(read_seq),
name='read')
aligned_reads = align_reads.align_reads(targets, [read])
expected_cigar_w_hard_clip = [(2, 'H')] + expected_cigar + [(1, 'H')]
self.assertEqual(
_cigar.to_cigar_units(expected_cigar_w_hard_clip),
list(aligned_reads[0].alignment.cigar), comment)
def make_read(bases,
quals=None,
cigar=None,
mapq=50,
chrom='chr1',
start=1,
name='read'):
"""Makes a third_party.nucleus.protos.Read for testing."""
if quals and len(bases) != len(quals):
raise ValueError('Incompatable bases and quals', bases, quals)
read = reads_pb2.Read(
fragment_name=name,
proper_placement=True,
read_number=1,
number_reads=2,
aligned_sequence=bases,
aligned_quality=quals,
alignment=reads_pb2.LinearAlignment(
position=position_pb2.Position(reference_name=chrom, position=start),
mapping_quality=mapq,
cigar=_cigar.to_cigar_units(cigar) if cigar else []))
return read
def make_read(bases,
start,
quals=None,
cigar=None,
mapq=50,
chrom='chr1',
name=None):
"""Makes a nucleus.genomics.v1.Read for testing."""
if quals and len(bases) != len(quals):
raise ValueError('Incompatable bases and quals', bases, quals)
read = reads_pb2.Read(
fragment_name=name if name else 'read_' + str(make_read.counter),
proper_placement=True,
read_number=1,
number_reads=2,
aligned_sequence=bases,
aligned_quality=quals,
alignment=reads_pb2.LinearAlignment(
position=position_pb2.Position(reference_name=chrom, position=start),
mapping_quality=mapq,
cigar=_cigar.to_cigar_units(cigar) if cigar else []))
make_read.counter += 1
return read
def make_read(bases,
quals=None,
cigar=None,
mapq=50,
chrom='chr1',
start=1,
name='read'):
"""Makes a third_party.nucleus.protos.Read for testing."""
if quals and len(bases) != len(quals):
raise ValueError('Incompatable bases and quals', bases, quals)
read = reads_pb2.Read(
fragment_name=name,
proper_placement=True,
read_number=1,
number_reads=2,
aligned_sequence=bases,
aligned_quality=quals,
alignment=reads_pb2.LinearAlignment(
position=position_pb2.Position(reference_name=chrom,
position=start),
mapping_quality=mapq,
cigar=_cigar.to_cigar_units(cigar) if cigar else []))
return read