test_hgvs_variantmapper_cp_altseqbuilder.py 文件源码

def _run_comparison(self, hgvsc, expected_sequence):

        # test replicates the internal class of p_to_c
        @attr.s(slots=True)
        class RefTranscriptData(object):
            transcript_sequence = attr.ib()
            aa_sequence = attr.ib()
            cds_start = attr.ib()
            cds_stop = attr.ib()
            protein_accession = attr.ib()

            @classmethod
            def setup_transcript_data(cls, ac, ac_p, db, ref="GRCh37.p10"):
                """helper for generating RefTranscriptData from for c_to_p"""
                tx_info = db.get_tx_info(ac)
                tx_seq = db.get_tx_seq(ac)

                if tx_info is None or tx_seq is None:
                    raise hgvs.exceptions.HGVSError("Missing transcript data for accession: {}".format(ac))

                # use 1-based hgvs coords
                cds_start = tx_info["cds_start_i"] + 1
                cds_stop = tx_info["cds_end_i"]

                # padding list so biopython won't complain during the conversion
                tx_seq_to_translate = tx_seq[cds_start - 1:cds_stop]
                if len(tx_seq_to_translate) % 3 != 0:
                    "".join(list(tx_seq_to_translate).extend(["N"] * ((3 - len(tx_seq_to_translate) % 3) % 3)))

                tx_seq_cds = Seq(tx_seq_to_translate)
                protein_seq = str(tx_seq_cds.translate())

                transcript_data = RefTranscriptData(tx_seq, protein_seq, cds_start, cds_stop, ac_p)

                return transcript_data

        ac_p = "DUMMY"
        var = self._parser.parse_hgvs_variant(hgvsc)
        transcript_data = RefTranscriptData.setup_transcript_data(var.ac, ac_p, self._datasource)

        builder = altseqbuilder.AltSeqBuilder(var, transcript_data)
        insert_result = builder.build_altseq()
        actual_sequence = insert_result[0].transcript_sequence
        msg = "expected: {}\nactual  : {}".format(expected_sequence, actual_sequence)
        self.assertEqual(expected_sequence, actual_sequence, msg)