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)
