def test_make_position(self):
self.assertEqual(
ranges.make_position('chr1', 10),
position_pb2.Position(
reference_name='chr1', position=10, reverse_strand=False))
self.assertEqual(
ranges.make_position('chr2', 100, reverse_strand=True),
position_pb2.Position(
reference_name='chr2', position=100, reverse_strand=True))
def make_position(chrom, position, reverse_strand=False):
"""Returns a nucleus.genomics.v1.Position.
Args:
chrom: str. The chromosome name.
position: int. The start position (0-based, inclusive).
reverse_strand: bool. If True, indicates the position is on the negative
strand.
"""
return position_pb2.Position(
reference_name=chrom, position=position, reverse_strand=reverse_strand)
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_position(chrom, position, reverse_strand=False):
"""Makes a third_party.nucleus.protos.Position."""
return position_pb2.Position(reference_name=chrom,
position=position,
reverse_strand=reverse_strand)
def make_position(chrom, position, reverse_strand=False):
"""Makes a nucleus.genomics.v1.Position."""
return position_pb2.Position(reference_name=chrom,
position=position,
reverse_strand=reverse_strand)
