def setUp(self): self.test_mrna0 = XRNA(identifier='bdor_foo', indices=[3734, 7436], strand='-', parent_id=1) self.test_mrna1 = XRNA(identifier='bdor_foo2', indices=[3734, 7436], parent_id=1, seq_name="sctg_0080_0020", source="maker") self.fake_exon = Mock() self.fake_cds = Mock() self.fake_start_codon = Mock() self.test_mrna1.exon = self.fake_exon self.test_mrna1.cds = self.fake_cds self.test_mrna1.add_other_feature(self.fake_start_codon)
def process_rna_line(self, line, rna_type): """Extracts arguments from a line and instantiates an XRNA object.""" kwargs = self.extract_mrna_args(line) if not kwargs: return kwargs["rna_type"] = rna_type mrna_id = kwargs['identifier'] self.mrnas[mrna_id] = XRNA(**kwargs)
def test_indices_intersect_mrna_true(self): mrna = XRNA(identifier=1, indices=[10, 20], parent_id='foo') self.assertTrue(mrna.indices_intersect_mrna([5, 10])) self.assertTrue(mrna.indices_intersect_mrna([20, 25])) self.assertTrue(mrna.indices_intersect_mrna([9, 21]))
def test_indices_intersect_mrna_false(self): mrna = XRNA(identifier=1, indices=[10, 20], parent_id='foo') self.assertFalse(mrna.indices_intersect_mrna([5, 9])) self.assertFalse(mrna.indices_intersect_mrna([21, 25]))