Python SeqRecordExpanded.third_codon_position Examples

Example #1

File: test_seqrecord_expanded.py Project: carlosp420/seqrecord-expanded

    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')

Example #2

File: test_seqrecord_expanded.py Project: carlosp420/seqrecord-expanded

    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')

Example #3

File: test_seqrecord_expanded.py Project: carlosp420/seqrecord-expanded

    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')