def test_create(self):
self.assertEquals(2, self.w.n_reads_per_frag)
self.assertEquals(0, len(self.w))
self.assertEquals(0, self.w.n_fragments)
w = rapi.read_batch(1)
self.assertEquals(1, w.n_reads_per_frag)
def test_iteration_completeness_single_end(self):
seqs = stuff.get_mini_ref_seqs()
batch = rapi.read_batch(1)
for pair in seqs:
batch.append(pair[0], pair[1], pair[2], rapi.QENC_SANGER)
batch.append(pair[0], pair[3], pair[4], rapi.QENC_SANGER)
# test whether we iterate over all the fragments
self.assertEquals(2 * len(seqs), sum(1 for frag in batch))
it = iter(batch)
fragment = next(it)
self.assertEquals(1, len(fragment))
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_n_reads_per_frag(self):
self.assertEquals(2, self.w.n_reads_per_frag)
w = rapi.read_batch(1)
self.assertEquals(1, w.n_reads_per_frag)
def setUp(self):
self.opts = rapi.opts()
rapi.init(self.opts)
self.w = rapi.read_batch(2)