def test_make_positive(self): seq_len = 8 mrna = Mrna(start=1, end=7, strand='-') cds = Mock() cds.start = 1 cds.end = 7 cds.strand = '-' exon = Mock() exon.start = 1 exon.end = 7 cds.strand = '-' mrna.children = {'cds':[cds], 'exon':[exon]} mrna.make_positive(seq_len) self.assertEqual(mrna.start, 2) self.assertEqual(mrna.end, 8) self.assertEqual(mrna.strand, '+') self.assertEqual(cds.start, 2) self.assertEqual(cds.end, 8) self.assertEqual(cds.strand, '+') self.assertEqual(exon.start, 2) self.assertEqual(exon.end, 8) self.assertEqual(exon.strand, '+')
def test_create_starts_and_stops_creates_a_start_reverse_complement(self): mrna = Mrna() cds = Mock() cds.start = 1 cds.end = 6 cds.strand = '-' mrna.children = {'cds':[cds]} mrna.attributes = {'ID':'m.1234'} mrna.create_starts_and_stops('NNNCAT') self.assertTrue('start_codon' in mrna)
def test_create_starts_and_stops_creates_a_stop(self): mrna = Mrna() cds = Mock() cds.start = 1 cds.end = 6 cds.strand = '+' mrna.children = {'cds':[cds]} mrna.attributes = {'ID':'m.1234'} mrna.create_starts_and_stops('NNNTAG') self.assertTrue('stop_codon' in mrna)