Ejemplo n.º 1
0
    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)
Ejemplo n.º 2
0
 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))
Ejemplo n.º 3
0
 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)
Ejemplo n.º 4
0
 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)
Ejemplo n.º 5
0
 def setUp(self):
     self.opts = rapi.opts()
     rapi.init(self.opts)
     self.w = rapi.read_batch(2)