def setUp(self):
self.seq = Seq("CCCAAAATGTACTCCACTATCTGCTGATTTGGG", generic_dna)
self.feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=1)
self.feature_seq = self.seq[3:-3]
self.match = FeatureMatch(self.feature, self.feature_seq, 1, 3)
def test__init(self):
"Test FeatureMatch object creation"
# forward strand
m = self.match
self.assertEqual(m.direction, "forward")
self.assertEqual(str(m.dna), "ATGTACTCCACTATCTGCTGA")
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna), str(self.feature_seq.transcribe()))
self.assertEqual(
str(m.aas),
str(self.feature.extract(self.seq).translate(to_stop=True)))
# reverse strand
inv_seq = self.seq.reverse_complement()
feature_seq = inv_seq[3:-3]
inv_feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=-1)
m = FeatureMatch(inv_feature, feature_seq, -1, 3)
self.assertEqual(m.direction, "reverse")
self.assertEqual(str(m.dna),
str(feature_seq[3:-3].reverse_complement()))
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna),
str(feature_seq.transcribe().reverse_complement()))
self.assertEqual(
str(m.aas),
str(inv_feature.extract(inv_seq).translate(to_stop=True)))
