def setUp(self):
self.test_mrna0 = MRNA(identifier='bdor_foo',
indices=[3734, 7436],
strand='-',
parent_id=1)
self.test_mrna1 = MRNA(identifier=2, indices=[3734, 7436], parent_id=1)
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_mrna_line(self, line):
"""Extracts arguments from a line and instantiates an MRNA object."""
kwargs = self.extract_mrna_args(line)
if not kwargs:
return
mrna_id = kwargs['identifier']
self.mrnas[mrna_id] = MRNA(**kwargs)
def test_indices_intersect_mrna_true(self):
mrna = MRNA(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_constructor_takes_annotations(self):
self.assertTrue(
MRNA(identifier="foo",
indices=[1, 10],
parent_id="bar",
annotations=[["Dbxref", "pfam:foo"]]))
def test_indices_intersect_mrna_false(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id='foo')
self.assertFalse(mrna.indices_intersect_mrna([5, 9]))
self.assertFalse(mrna.indices_intersect_mrna([21, 25]))