def test_getting_codon_positions_reading_frame_2(self): seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGACATTTGATTTACAAATGTGGTGGTATCGACAAGCGT' seq_record = SeqRecordExpanded(seq, reading_frame=2) expected = 'CGGTGATAAAGCTATATGGAGAC' self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position') expected = 'ATACGACCCCGATTAAGGGTAAG' self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position') expected = 'ACCCCCGCTCAATGTCATTTCCGT' self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')
def test_getting_codon_positions_reading_frame_3(self): seq = 'GTCGTGGGGGCCCACGTGGACGTGG' seq_record = SeqRecordExpanded(seq, reading_frame=3) expected = 'CGGCCGCG' self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position') expected = 'GGGGCGGGG' self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position') expected = 'TTGCATAT' self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')
def test_getting_codon_positions_reading_frame_1(self): seq = 'GAATGGAAGACAAAGTCTCGTCCA' seq_record = SeqRecordExpanded(seq, reading_frame=1) expected = 'GTAAATCC' self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position') expected = 'AGACACGC' self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position') expected = 'AGGAGTTA' self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')