def test_bad_create_args(self):
with self.assertRaisesRegexp(ValueError,
'multiple ones were found on 1'):
fasta.InMemoryRefReader([
('1', 10, 'AC'),
('1', 20, 'AC'),
])
def test_query_edge_cases(self):
reader = fasta.InMemoryRefReader([('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 setUpClass(cls):
cls.fasta_reader = fasta.RefFastaReader(
test_utils.genomics_core_testdata('test.fasta'))
cls.in_mem = fasta.InMemoryRefReader(
[(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.InMemoryRefReader([('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_bad_query_with_start(self, start, end):
reader = fasta.InMemoryRefReader([('1', 10, 'ACGT')])
with self.assertRaises(ValueError):
reader.query(ranges.make_range('1', start, end))