Ejemplos de prune_seqs_matching_alignment en Python

Ejemplo n.º 1

Archivo: test_align.py Proyecto: jharman25/augur

    def test_prune_seqs_matching_alignment(self):
        sequence = {
            "seq1": SeqRecord(Seq("GTAC"), name="seq1"),
            "seq2": SeqRecord(Seq("CGTT"), name="seq2"),
            "seq3": SeqRecord(Seq("TAGC"), name="seq3"),
        }
        alignment = MultipleSeqAlignment([
            SeqRecord(Seq("GTAC"), name="seq1"),
            SeqRecord(Seq("TAGC"), name="seq3"),
        ])

        result = align.prune_seqs_matching_alignment(sequence, alignment)
        assert list(result.keys()) == ["seq2"]
        assert result["seq2"].seq == sequence["seq2"].seq

Ejemplo n.º 2

    def test_prune_seqs_matching_alignment(self):
        sequence = {
            "seq1": SeqRecord(Seq("GTAC"), name="seq1"),
            "seq2": SeqRecord(Seq("CGTT"), name="seq2"),
            "seq3": SeqRecord(Seq("TAGC"), name="seq3"),
        }
        alignment = MultipleSeqAlignment([
            SeqRecord(Seq("GTAC"), name="seq1"),
            SeqRecord(Seq("TAGC"), name="seq3"),
        ])

        result = align.prune_seqs_matching_alignment(sequence.values(),
                                                     alignment)
        assert [r.name for r in result] == ["seq2"]
        for r in result:
            assert r.seq == sequence[r.name].seq