def setUp(self):
self.opts = rapi.opts()
self.opts.share_ref_mem = False # for Travis
rapi.init(self.opts)
self.ref = rapi.ref(stuff.MiniRef)
aligner = rapi.aligner(self.opts)
self.batch = rapi.read_batch(2)
reads = stuff.get_mini_ref_seqs()
for row in reads:
self.batch.append(row[0], row[1], row[2], rapi.QENC_SANGER)
self.batch.append(row[0], row[3], row[4], rapi.QENC_SANGER)
aligner.align_reads(self.ref, self.batch)
def test_ref_contigs(self):
r = rapi.ref(MiniRef)
try:
contigs = [ c for c in r ]
self.assertEquals(1, len(contigs))
self.assertEquals(len(r), len(contigs))
c0 = contigs[0]
self.assertEquals('chr1', c0.name)
self.assertEquals(60000, c0.len)
for v in (c0.assembly_identifier, c0.species, c0.uri, c0.md5):
self.assertIsNone(v)
finally:
r.unload()
def test_ref_load_unload(self):
r = rapi.ref(MiniRef)
self.assertEqual(MiniRef, r.path)
self.assertEqual(1, len(r))
r.unload()
def setUp(self):
self.opts = rapi.opts()
self.opts.share_ref_mem = False # for Travis
rapi.init(self.opts)
self.ref = rapi.ref(stuff.MiniRef)
