def test_bad_create_args(self):
with self.assertRaisesRegexp(ValueError,
'multiple ones were found on 1'):
fasta.InMemoryFastaReader([
('1', 10, 'AC'),
('1', 20, 'AC'),
])
def test_query_edge_cases(self):
reader = fasta.InMemoryFastaReader([('1', 0, 'ACGT')])
# Check that we can query the first base correctly.
self.assertEqual(reader.query(ranges.make_range('1', 0, 1)), 'A')
# Check that we can query the last base correctly.
self.assertEqual(reader.query(ranges.make_range('1', 3, 4)), 'T')
# Check that we can query the entire sequence correctly.
self.assertEqual(reader.query(ranges.make_range('1', 0, 4)), 'ACGT')
def test_select_windows_returns_empty_list_when_no_reads(self):
self.assertEqual([],
window_selector.select_windows(
self.config,
ref_reader=fasta.InMemoryFastaReader([('chr1', 0,
'A' * 500)]),
reads=[],
region=ranges.make_range('chr1', 1, 100)))
def setUpClass(cls):
cls.fasta_reader = fasta.IndexedFastaReader(
test_utils.genomics_core_testdata('test.fasta'))
cls.in_mem = fasta.InMemoryFastaReader(
[(contig.name, 0,
cls.fasta_reader.query(
ranges.make_range(contig.name, 0, contig.n_bases)))
for contig in cls.fasta_reader.header.contigs])
def test_non_zero_start_query(self):
bases = 'ACGTAACCGGTT'
for start in range(len(bases)):
reader = fasta.InMemoryFastaReader([('1', start, bases[start:])])
self.assertEqual(reader.header.contigs[0].name, '1')
self.assertEqual(reader.header.contigs[0].n_bases, len(bases))
# Check that our query operation works as expected with a start position.
for end in range(start, len(bases)):
self.assertEqual(reader.query(ranges.make_range('1', start, end)),
bases[start:end])
def test_select_windows(self):
# Simple end-to-end test of the high-level select_windows function. We give
# it a few reads with a single candidate at 100 and we expect a window back
# centered at 100.
reads = [
test_utils.make_read('AGA', start=99, cigar='3M', quals=[64] * 3),
test_utils.make_read('AGA', start=99, cigar='3M', quals=[63] * 3),
test_utils.make_read('AGA', start=99, cigar='3M', quals=[62] * 3),
]
chrom = reads[0].alignment.position.reference_name
ref_reader = fasta.InMemoryFastaReader([(chrom, 0, 'A' * 300)])
region = ranges.make_range(chrom, 0, 200)
self.assertEqual(
window_selector.select_windows(self.config, ref_reader, reads, region),
[ranges.make_range(chrom, 96, 104)])
def assertCandidatesFromReadsEquals(self,
reads,
expected,
start=None,
end=None,
ref=None):
chrom = reads[0].alignment.position.reference_name
start = 0 if start is None else start
end = 20 if end is None else end
region = ranges.make_range(chrom, start, end)
if ref is None:
ref = 'A' * (ranges.length(region) + 512)
ref_reader = fasta.InMemoryFastaReader([(chrom, 0, ref)])
if isinstance(expected, type) and issubclass(expected, Exception):
with self.assertRaises(expected):
window_selector._candidates_from_reads(self.config, ref_reader,
reads, region)
else:
actual = window_selector._candidates_from_reads(
self.config, ref_reader, reads, region)
self.assertEqual(actual, expected)
def dummy_reference_reader():
return fasta.InMemoryFastaReader(chromosomes=[
('1', 0, 'AACCGGTTACGTTCGATTTTAAAACCCCGGGG'),
('2', 0, 'GCAGTGACGTAGCGATGACGTAGACGCTTACG'),
])
def test_bad_query_with_start(self, start, end):
reader = fasta.InMemoryFastaReader([('1', 10, 'ACGT')])
with self.assertRaises(ValueError):
reader.query(ranges.make_range('1', start, end))
