def test_make_read_produces_unique_read_names(self):
start = 0
read1 = test_utils.make_read('A', start=start)
read2 = test_utils.make_read('A', start=start)
self.assertGreater(len(read1.fragment_name), 0)
self.assertGreater(len(read2.fragment_name), 0)
self.assertNotEqual(read1.fragment_name, read2.fragment_name)
def test_read_end(self, update_cached_read_end_first):
"""Tests reads have their ends calculated correctly."""
start = 10000001
read = test_utils.make_read(
'AAACAG',
chrom='chrX',
start=start,
cigar='2M1I3M',
quals=range(10, 16),
name='read1')
if update_cached_read_end_first:
# Explicitly update cached_end.
read.cached_end = utils.read_end(read, use_cached_read_end=False)
self.assertEqual(
start + 5, read.cached_end)
self.assertEqual(
start + 5, utils.read_end(read))
read = test_utils.make_read(
'AAACAG',
chrom='chrX',
start=start,
cigar='2M16D3M',
quals=range(10, 16),
name='read1')
if update_cached_read_end_first:
# Explicitly update cached_end.
read.cached_end = utils.read_end(read, use_cached_read_end=False)
self.assertEqual(
start + 5 + 16, read.cached_end)
self.assertEqual(
start + 5 + 16,
utils.read_end(read))
def test_make_read(self):
bases = 'ACG'
quals = [30, 40, 50]
cigar = '3M'
mapq = 42
chrom = 'chr10'
start = 123
name = 'myname'
read = test_utils.make_read(bases,
quals=quals,
cigar=cigar,
mapq=mapq,
chrom=chrom,
start=start,
name=name)
self.assertEqual(read.aligned_sequence, bases)
self.assertEqual(read.aligned_quality, quals)
self.assertEqual(list(read.alignment.cigar), [
cigar_pb2.CigarUnit(operation_length=3,
operation=cigar_pb2.CigarUnit.ALIGNMENT_MATCH)
])
self.assertEqual(read.alignment.mapping_quality, mapq)
self.assertEqual(read.alignment.position.reference_name, chrom)
self.assertEqual(read.alignment.position.position, start)
self.assertEqual(read.fragment_name, name)
def test_read_end(self):
"""Tests reads have their ends calculated correctly."""
start = 10000001
read = test_utils.make_read('AAACAG',
chrom='chrX',
start=start,
cigar='2M1I3M',
quals=range(10, 16),
name='read1')
self.assertEqual(start + 5, utils.read_end(read))
read = test_utils.make_read('AAACAG',
chrom='chrX',
start=start,
cigar='2M16D3M',
quals=range(10, 16),
name='read1')
self.assertEqual(start + 5 + 16, utils.read_end(read))
def check_overlaps(chr1, start1, end1, chr2, start2, end2, expected):
nbp = end1 - start1
read = test_utils.make_read(
'A' * nbp, chrom=chr1, start=start1, cigar='{}M'.format(nbp))
region = ranges.make_range(chr2, start2, end2)
self.assertEqual(utils.read_overlaps_region(read, region), expected)
# This check ensures we get the same result calling ranges.ranges_overlap.
self.assertEqual(
ranges.ranges_overlap(region, utils.read_range(read)), expected)
def setUp(self):
self.read1 = test_utils.make_read(bases='ACCGT',
chrom='chr1',
start=10,
cigar='5M',
mapq=50,
quals=range(30, 35),
name='read1')
self.read2 = test_utils.make_read(bases='AACCTT',
chrom='chr2',
start=15,
cigar='7M',
mapq=40,
quals=range(20, 26),
name='read2')
self.contigs = [
reference_pb2.ContigInfo(name='chr1'),
reference_pb2.ContigInfo(name='chr2'),
]
self.header = reads_pb2.SamHeader()
