Add support for _to_hgvs for CNVs

[korikuzma]

We're either going to add support for _to_hgvs for the CnvTranslator. Or we can deprecate the translate_to methods. Up to @larrybabb

[korikuzma]

Initial copy/paste work from AlleleTranslator's _to_hgvs

    def _to_hgvs(self, vo, namespace="refseq"):
        if vo.type != "CopyNumberChange":
            raise ValueError("Must provide CopyNumberChange because it's lossy")

        if not isinstance(vo.location.sequenceReference, models.SequenceReference):
            raise TypeError(
                "`vo.location.sequenceReference` expects a `SequenceReference`"
            )

        sequence = f"ga4gh:{export_sequencelocation_sequence_id(vo.location.sequenceReference)}"
        aliases = self.data_proxy.translate_sequence_identifier(sequence, namespace)

        # infer type of sequence based on accession
        # TODO: move to bioutils
        stypes = list(set(t for t in (self._ir_stype(a) for a in aliases) if t))
        if len(stypes) != 1:
            raise ValueError(f"Couldn't infer sequence type for {sequence} ({stypes})")
        stype = stypes[0]

        start, end = vo.location.start, vo.location.end
        start += 1

        ival = hgvs.location.Interval(
            start=hgvs.location.SimplePosition(start),
            end=hgvs.location.SimplePosition(end)
        )

        copy_change = vo.copyChange
        if copy_change == models.CopyChange.EFO_0030067.value:
            edit = hgvs.edit.NARefAlt(ref="", alt=None, uncertain=False)
        elif copy_change == models.CopyChange.EFO_0030070.value:
            edit = hgvs.edit.Dup(ref="", uncertain=False)
        else:
            raise ValueError("")

        posedit = hgvs.posedit.PosEdit(pos=ival, edit=edit)
        var = hgvs.sequencevariant.SequenceVariant(
            ac=None,
            type=stype,
            posedit=posedit)

        hgvs_exprs = []
        for alias in aliases:
            ns, a = alias.split(":")
            # skip GRCh accessions unless specifically requested
            # because they are ambiguous without their namespace,
            # which can't be included in HGVS expressions
            # TODO: use default_assembly_name here
            if ns.startswith("GRC") and namespace is None:
                continue

            if not (any(a.startswith(pfx) for pfx in ("NM", "NP", "NC", "NG"))):
                continue

            var.ac = a

            try:
                if not namespace.startswith("GRC"):
                    # if the namespace is GRC, can't normalize, since hgvs can't deal with it
                    hgvs_tools = self._get_hgvs_tools()
                    parsed = hgvs_tools.parse(str(var))
                    var = hgvs_tools.normalize(parsed)

                hgvs_exprs += [str(var)]
            except hgvs.exceptions.HGVSDataNotAvailableError:
                _logger.warning(f"No data found for accession {a}")
        return list(set(hgvs_exprs))

[github-actions]

This issue was marked stale due to inactivity.

[sivangbagri]

@korikuzma Is this still open ? Can I work on this?

[korikuzma]

@sivangbagri I'm not sure the status of this. @larrybabb what are your thoughts?