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 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
