vrs_map.py

"""Map transcripts to VRS objects."""

import logging
import os
from collections.abc import Iterable
from itertools import cycle

from Bio.Seq import Seq
from bioutils.accessions import infer_namespace
from cool_seq_tool.schemas import AnnotationLayer, Strand
from ga4gh.core import ga4gh_identify, sha512t24u
from ga4gh.vrs._internal.models import (
    Allele,
    Haplotype,
    LiteralSequenceExpression,
    ReferenceLengthExpression,
    SequenceLocation,
    SequenceString,
)
from ga4gh.vrs.normalize import normalize
from mavehgvs.util import parse_variant_strings
from mavehgvs.variant import Variant

from dcd_mapping.exceptions import (
    MissingSequenceIdError,
    UnsupportedReferenceSequenceNameSpaceError,
    UnsupportedReferenceSequencePrefixError,
)
from dcd_mapping.lookup import (
    cdot_rest,
    get_chromosome_identifier,
    get_seqrepo,
    translate_hgvs_to_vrs,
)
from dcd_mapping.resource_utils import is_missing_value, request_with_backoff
from dcd_mapping.schemas import (
    AlignmentResult,
    MappedScore,
    ScoreRow,
    TargetGene,
    TargetSequenceType,
    TargetType,
    TxSelectResult,
)
from dcd_mapping.transcripts import TxSelectError

__all__ = ["vrs_map"]


_logger = logging.getLogger(__name__)

CLINGEN_API_URL = os.environ.get("CLINGEN_API_URL", "https://reg.genome.network/allele")


def _hgvs_variant_is_valid(hgvs_string: str) -> bool:
    return not hgvs_string.endswith((".=", ")", "X"))


def _process_any_aa_code(hgvs_pro_string: str) -> str:
    """Substitute "Xaa" for "?" in variation expression.

    Some expressions seem to use the single-character "?" wildcard in the context of
    three-letter amino acid codes. This is weird, and the proper replacement is "Xaa".

    Note that we currently do NOT make any alterations to nucleotide strings that use
    weird apparently-wildcard characters like "X" -- we just treat them as invalid (see
    _hgvs_variant_is_valid()).

    :param hgvs_string: MAVE HGVS expression
    :return: processed variation (equivalent to input if no wildcard code found)
    """
    if "?" in hgvs_pro_string:
        _logger.debug("Substituting Xaa for ? in %s", hgvs_pro_string)
        hgvs_pro_string = hgvs_pro_string.replace("?", "Xaa")
    return hgvs_pro_string


def is_intronic_variant(variant: Variant) -> bool:
    """Return True if given Variant is intronic, otherwise return False.
    Supports single or multi-position variants.
    """
    if isinstance(variant.positions, Iterable):
        if any(position.is_intronic() for position in variant.positions):
            return True
    else:
        if variant.positions.is_intronic():
            return True

    return False


def fetch_clingen_genomic_hgvs(hgvs: str) -> str | None:
    """Fetch the genomic HGVS string from ClinGen.

    :param hgvs: The HGVS string to fetch
    :return: The genomic HGVS string on GRCh38, or None if not found
    """
    if CLINGEN_API_URL is None:
        msg = "CLINGEN_API_URL environment variable is not set and default is unavailable."
        _logger.error(msg)
        raise ValueError(msg)
    response = request_with_backoff(url=f"{CLINGEN_API_URL}?hgvs={hgvs}", timeout=30)
    if response.status_code == 200:
        data = response.json()
        for allele in data.get("genomicAlleles", []):
            if allele.get("referenceGenome") == "GRCh38":
                for coordinates in allele.get("hgvs", []):
                    if coordinates.startswith("NC_"):
                        return coordinates
    return None


def _create_pre_mapped_hgvs_strings(
    raw_description: str,
    layer: AnnotationLayer,
    tx: TxSelectResult | None = None,
    alignment: AlignmentResult | None = None,
    accession_id: str | None = None,
) -> list[str]:
    """Generate a list of (pre-mapped) HGVS strings from one long string containing many valid HGVS substrings

    Currently, the provided transcript is used as the reference for the hgvs string, but this is inaccurate
    because pre-mapped variants should be relative to the user-provided target sequence, not an external accession.
    Any offset between the transcript and target sequence is not taken into account here (the variant position
    is relative to the target sequence).

    :param raw_description: A string containing valid HGVS sub-strings
    :param layer: An enum denoting the targeted annotation layer of these HGVS strings
    :param tx: A TxSelectResult object defining the transcript we are mapping to (or None).
    :param alignment: An AlignmentResult object defining the alignment we are mapping to (or None).
    :param accession_id: An accession id describing the reference sequence (for accession-based target gene variants)
    :return: A list of HGVS strings prior to being mapped to the `tx` or `alignment`
    """
    if layer is AnnotationLayer.PROTEIN and tx is None:
        msg = f"Transcript result must be provided for {layer} annotations (Transcript was `{tx}`)."
        raise ValueError(msg)
    if layer is AnnotationLayer.GENOMIC and alignment is None and accession_id is None:
        msg = f"Alignment result or accession ID must be provided for {layer} annotations (Alignment was `{alignment}`)."
        raise ValueError(msg)

    raw_variant_strings = _parse_raw_variant_str(raw_description)
    variants, errors = parse_variant_strings(raw_variant_strings)

    hgvs_strings = []
    for variant, error in zip(variants, errors, strict=True):
        if error is not None:
            msg = f"Variant could not be parsed by mavehgvs: {error}"
            raise ValueError(msg)

        # ga4gh hgvs_tools does not support intronic variants, so they will err out when vrs allele translator is called
        # therefore skip them there
        if is_intronic_variant(variant):
            msg = f"Variant is intronic and cannot be processed: {variant}"
            raise ValueError(msg)

        if accession_id:
            hgvs_strings.append(accession_id + ":" + str(variant))
        # Ideally we would create an HGVS string namespaced to GA4GH. The line below
        # creates such a string, but it is not able to be parsed by the GA4GH VRS translator.
        # hgvs_strings.append('ga4gh:' + sequence_id + ':' + str(variant))
        elif layer is AnnotationLayer.PROTEIN:
            assert tx  # noqa: S101. mypy help
            hgvs_strings.append(tx.np + ":" + str(variant))
        elif layer is AnnotationLayer.GENOMIC:
            assert alignment  # noqa: S101. mypy help
            hgvs_strings.append(
                get_chromosome_identifier(alignment.chrom) + ":" + str(variant)
            )
        else:
            msg = (
                f"Could not generate HGVS strings for invalid AnnotationLayer: {layer}"
            )
            raise ValueError(msg)

    return hgvs_strings


def _create_post_mapped_hgvs_strings(
    raw_description: str,
    layer: AnnotationLayer,
    tx: TxSelectResult | None = None,
    alignment: AlignmentResult | None = None,
    accession_id: str | None = None,
) -> list[str]:
    """Generate a list of (post-mapped) HGVS strings from one long string containing many valid HGVS substrings.

    For protein annotations, these strings must be adjusted to match the offset defined by the start of the
    transcript sequence. For genomic annotations, these strings must be adjusted to match the coordinates of
    the reference alignment.

    :param raw_description: A string containing valid HGVS sub-strings
    :param layer: An enum denoting the targeted annotation layer of these HGVS strings
    :param tx: A TxSelectResult object defining the transcript we are mapping to (or None)
    :param alignment: An AlignmentResult object defining the alignment we are mapping to (or None)
    :param accession_id: An accession id describing the reference sequence (or None). Only used for accession-based variants.
    :return: A list of HGVS strings relative to the `tx` or `alignment`
    """
    if layer is AnnotationLayer.PROTEIN and tx is None:
        msg = f"Transcript result must be provided for {layer} annotations (Transcript was `{tx}`)."
        raise ValueError(msg)
    if layer is AnnotationLayer.GENOMIC and alignment is None and accession_id is None:
        msg = f"Alignment result or accession ID must be provided for {layer} annotations (Alignment was `{alignment}` and Accession ID was `{accession_id}`)."
        raise ValueError(msg)

    raw_variants = _parse_raw_variant_str(raw_description)
    variants, errors = parse_variant_strings(raw_variants)

    hgvs_strings = []
    for variant, error in zip(variants, errors, strict=True):
        if error is not None:
            msg = f"Variant could not be parsed by mavehgvs: {error}"
            raise ValueError(msg)

        # ga4gh hgvs_tools does not support intronic variants, so they will err out when vrs allele translator is called
        # therefore skip them there
        if is_intronic_variant(variant):
            msg = f"Variant is intronic and cannot be processed: {variant}"
            raise ValueError(msg)

        if layer is AnnotationLayer.PROTEIN:
            assert tx  # noqa: S101. mypy help

            variant = _adjust_protein_variant_to_ref(variant, tx)
            hgvs_strings.append(tx.np + ":" + str(variant))
        elif layer is AnnotationLayer.GENOMIC:
            if accession_id:
                pre_mapped_hgvs = accession_id + ":" + str(variant)
                # use ClinGen to align accession-based variants to genomic reference
                genomic_hgvs = fetch_clingen_genomic_hgvs(pre_mapped_hgvs)
                if genomic_hgvs:
                    hgvs_strings.append(genomic_hgvs)
                else:
                    msg = f"Could not fetch genomic HGVS on GRCh38 for accession-based variant: {pre_mapped_hgvs}"
                    raise ValueError(msg)
            else:
                assert alignment  # noqa: S101. mypy help

                variant = _adjust_genomic_variant_to_ref(variant, alignment)
                hgvs_strings.append(
                    get_chromosome_identifier(alignment.chrom) + ":" + str(variant)
                )
        else:
            msg = (
                f"Could not generate HGVS strings for invalid AnnotationLayer: {layer}"
            )
            raise ValueError(msg)

    return hgvs_strings


def _adjust_protein_variant_to_ref(
    variant: Variant,
    tx: TxSelectResult,
) -> Variant:
    if isinstance(variant.positions, Iterable):
        for position in variant.positions:
            position.position = position.position + tx.start
        return variant

    variant.positions.position = variant.positions.position + tx.start
    return variant


def _adjust_genomic_variant_to_ref(
    variant: Variant,
    alignment: AlignmentResult,
) -> Variant:
    """Adjust a variant relative to a provided alignment.

    :param variant: A variant object relative to a scoreset's target sequence
    :param alignment: An AlignmentResult object denoting the alignment we are mapping to
    :return: A variant object that describes the variant relative to the provided alignment result
    """
    # adjust starts - hgvs uses 1-based numbering for c. sequences, while blat hits are 0-based
    starts = []
    if isinstance(variant.positions, Iterable):
        is_multi_position = True
        for position in variant.positions:
            starts.append(position.position - 1)
    else:
        is_multi_position = False
        starts.append(variant.positions.position - 1)

    # get hit
    query_subrange_containing_hit = None
    target_subrange_containing_hit = None
    for query_subrange, target_subrange in zip(
        alignment.query_subranges, alignment.hit_subranges, strict=True
    ):
        if all(
            start >= query_subrange.start and start < query_subrange.end
            for start in starts
        ):
            query_subrange_containing_hit = query_subrange
            target_subrange_containing_hit = target_subrange
            break

    if query_subrange_containing_hit is None or target_subrange_containing_hit is None:
        msg = f"Cannot process variant {variant} because it is not fully contained within the aligned portion of the query sequence"
        raise ValueError(msg)

    for idx, start in enumerate(starts):
        if alignment.strand is Strand.POSITIVE:
            # get variant start relative to the reference (the "hit")
            # distance from beginning of query to variant start position:
            query_to_start = start - query_subrange_containing_hit.start

            # distance from beginning of ref to the variant start position:
            ref_to_start = target_subrange_containing_hit.start + query_to_start
        else:
            # picture the rev comp of the query/variant as mapping to the positive strand of the ref
            # the start of the reverse complement of the variant is the end of the "original" variant
            # so we need to know where the end of the original variant is, relative to the query molecule
            end = start

            # subtract 1 from end of hit range, because blat ranges are 0-based [start, end)
            ref_to_start = (target_subrange_containing_hit.end - 1) - (
                end - query_subrange_containing_hit.start
            )

        # add distance from ref to variant start; hgvs is 1-based, so convert back to 1-based
        if is_multi_position:
            variant.positions[idx].position = ref_to_start + 1
        else:
            variant.positions.position = ref_to_start + 1

    # get reverse complement of sequence if the target maps to the negative strand of the reference
    if alignment.strand is Strand.NEGATIVE:
        # variant._sequences can be a string or an iterable
        if isinstance(variant._sequences, str):
            variant._sequences = str(Seq(variant._sequences).reverse_complement())
        elif variant._sequences is not None:
            revcomp_sequences_list = []
            for sequence in variant._sequences:
                revcomp_sequences_list.append(str(Seq(sequence).reverse_complement()))
            variant._sequences = revcomp_sequences_list

        # reverse order of positions tuple
        if is_multi_position:
            variant._positions = tuple(reversed(list(variant.positions)))

    # change prefix from c. to g. since variant is now relative to chr reference
    variant._prefix = "g"

    return variant


def _parse_raw_variant_str(raw_description: str) -> list[str]:
    """Parse a string which may contain many HGVS strings into a list of each one.

    :param raw_description: A string that may contain a list of variant descriptions or a single variant description
    :return: A list of HGVS strings
    """
    # some variant strings follow mavehgvs format, meaning they don't have a reference sequence id and colon preceding the c./g./n./p. prefix
    # the reference sequence information has previously been parsed for score sets with multiple targets,
    # so can discard the reference sequence id and colon if they are present
    # TODO check assumption of no colon unless reference sequence identifier is supplied!
    if ":" in raw_description:
        raw_description = raw_description.split(":")[1]
    if "[" in raw_description:
        prefix = raw_description[0:2]
        return [prefix + var for var in set(raw_description[3:-1].split(";"))]

    return [raw_description]


def _map_protein_coding_pro(
    row: ScoreRow,
    sequence_id: str,
    transcript: TxSelectResult,
) -> MappedScore:
    """Construct VRS object mapping for ``hgvs_pro`` variant column entry

    These arguments are a little lazy and could be pruned down later

    :param row: A row of output from a MaveDB score set
    :param sequence_id: The GA4GH accession for the provided sequence
    :param transcript: The transcript selection information for a score set
    :return: VRS mapping object if mapping succeeds
    """
    if (
        row.hgvs_pro in {"_wt", "_sy"}
        or is_missing_value(row.hgvs_pro)
        or len(row.hgvs_pro) == 3
    ):
        _logger.warning(
            "Can't process variant syntax %s for %s", row.hgvs_pro, row.accession
        )
        return MappedScore(
            accession_id=row.accession,
            score=row.score,
            error_message=f"Can't process variant syntax {row.hgvs_pro}",
        )

    if "fs" in row.hgvs_pro:
        _logger.warning(
            "Can't process variant syntax %s for %s because protein frameshift variants are not supported",
            row.hgvs_pro,
            row.accession,
        )
        return MappedScore(
            accession_id=row.accession,
            score=row.score,
            error_message="Protein frameshift variants are not supported",
        )

    # TODO: Handle edge cases without hardcoding URNs.
    # Special case for experiment set urn:mavedb:0000097
    if row.hgvs_pro.startswith("NP_009225.1:p."):
        vrs_variation = translate_hgvs_to_vrs(row.hgvs_pro)
        return MappedScore(
            accession_id=row.accession,
            score=row.score,
            annotation_layer=AnnotationLayer.PROTEIN,
            pre_mapped=vrs_variation,
            post_mapped=vrs_variation,
        )

    try:
        pre_mapped_hgvs_strings = _create_pre_mapped_hgvs_strings(
            row.hgvs_pro,
            AnnotationLayer.PROTEIN,
            tx=transcript,
        )
        pre_mapped_protein = _construct_vrs_allele(
            pre_mapped_hgvs_strings,
            AnnotationLayer.PROTEIN,
            sequence_id,
            True,
        )
    except Exception as e:
        _logger.warning(
            "An error occurred while generating pre-mapped protein variant for %s, accession %s: %s",
            row.hgvs_pro,
            row.accession,
            str(e),
        )
        return MappedScore(
            accession_id=row.accession, score=row.score, error_message=str(e)
        )

    try:
        post_mapped_hgvs_strings = _create_post_mapped_hgvs_strings(
            row.hgvs_pro,
            AnnotationLayer.PROTEIN,
            tx=transcript,
        )
        post_mapped_protein = _construct_vrs_allele(
            post_mapped_hgvs_strings,
            AnnotationLayer.PROTEIN,
            None,
            False,
        )
    except Exception as e:
        _logger.warning(
            "An error occurred while generating post-mapped protein variant for %s, accession %s: %s",
            row.hgvs_pro,
            row.accession,
            str(e),
        )
        return MappedScore(
            accession_id=row.accession,
            score=row.score,
            annotation_layer=AnnotationLayer.PROTEIN,
            pre_mapped=pre_mapped_protein,
            error_message=str(e).strip("'"),
        )

    return MappedScore(
        accession_id=row.accession,
        score=row.score,
        annotation_layer=AnnotationLayer.PROTEIN,
        pre_mapped=pre_mapped_protein,
        post_mapped=post_mapped_protein,
    )


def _map_genomic(
    row: ScoreRow,
    sequence_id: str,
    align_result: AlignmentResult | None,
) -> MappedScore:
    """Construct VRS object mapping for ``hgvs_nt`` variant column entry

    These arguments are a little lazy and could be pruned down later

    :param row: A row of output from a MaveDB score set
    :param sequence_id: The GA4GH accession for the provided sequence
    :param align_result: The transcript selection information for a score set
    :return: VRS mapping object if mapping succeeds
    """
    namespace = infer_namespace(sequence_id)
    if namespace is None:
        if sequence_id.startswith("SQ."):
            # if the sequence id starts with SQ, it is a target sequence which is in the ga4gh namespace
            namespace = "ga4gh"
        else:
            return MappedScore(
                accession_id=row.accession,
                score=row.score,
                error_message=f"Namespace could not be inferred from sequence: {sequence_id}",
            )

    if (
        row.hgvs_nt in {"_wt", "_sy", "="}
        or "fs"
        in row.hgvs_nt  # TODO I think this line can be taken out, I don't think fs nomenclature can be used for nt anyway
        or len(row.hgvs_nt) == 3
    ):
        _logger.warning(
            "Can't process variant syntax %s for %s", row.hgvs_nt, row.accession
        )
        return MappedScore(
            accession_id=row.accession,
            score=row.score,
            error_message=f"Can't process variant syntax {row.hgvs_nt}",
        )

    if align_result is None:
        # for contig accession based score sets, no mapping is performed,
        # so pre- and post-mapped alleles are the same
        try:
            pre_mapped_hgvs_strings = (
                post_mapped_hgvs_strings
            ) = _create_pre_mapped_hgvs_strings(
                row.hgvs_nt,
                AnnotationLayer.GENOMIC,
                accession_id=sequence_id,
            )
            # accession-based pre-mapped alleles should be constructed like post-mapped alleles (sequence id is gathered from hgvs string rather than manually provided)
            pre_mapped_genomic = _construct_vrs_allele(
                pre_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                None,
                False,
            )
            post_mapped_genomic = _construct_vrs_allele(
                post_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                None,
                False,
            )
        except Exception as e:
            _logger.warning(
                "An error occurred while generating genomic variant for %s, accession %s: %s",
                row.hgvs_nt,
                row.accession,
                str(e),
            )
            return MappedScore(
                accession_id=row.accession, score=row.score, error_message=str(e)
            )

    elif namespace.lower() in ("refseq", "ncbi", "ensembl"):
        # nm/enst way
        try:
            pre_mapped_hgvs_strings = _create_pre_mapped_hgvs_strings(
                row.hgvs_nt,
                AnnotationLayer.GENOMIC,
                accession_id=sequence_id,
            )
            # accession-based pre-mapped alleles should be constructed like post-mapped alleles (sequence id is gathered from hgvs string rather than manually provided)
            pre_mapped_genomic = _construct_vrs_allele(
                pre_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                None,
                False,
            )
        except Exception as e:
            _logger.warning(
                "An error occurred while generating pre-mapped genomic variant for %s, accession %s: %s",
                row.hgvs_nt,
                row.accession,
                str(e),
            )
            return MappedScore(
                accession_id=row.accession, score=row.score, error_message=str(e)
            )
        try:
            post_mapped_hgvs_strings = _create_post_mapped_hgvs_strings(
                row.hgvs_nt,
                AnnotationLayer.GENOMIC,
                accession_id=sequence_id,
            )
            post_mapped_genomic = _construct_vrs_allele(
                post_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                None,
                False,
            )
        except Exception as e:
            _logger.warning(
                "An error occurred while generating post-mapped genomic variant for %s, accession %s: %s",
                row.hgvs_nt,
                row.accession,
                str(e),
            )
            return MappedScore(
                accession_id=row.accession,
                score=row.score,
                annotation_layer=AnnotationLayer.GENOMIC,
                pre_mapped=pre_mapped_genomic,
                error_message=str(e),
            )
    elif namespace.lower() == "ga4gh":
        # target seq way
        try:
            pre_mapped_hgvs_strings = _create_pre_mapped_hgvs_strings(
                row.hgvs_nt,
                AnnotationLayer.GENOMIC,
                alignment=align_result,
            )
            pre_mapped_genomic = _construct_vrs_allele(
                pre_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                sequence_id,
                True,
            )
        except Exception as e:
            _logger.warning(
                "An error occurred while generating pre-mapped genomic variant for %s, accession %s: %s",
                row.hgvs_nt,
                row.accession,
                str(e),
            )
            return MappedScore(
                accession_id=row.accession, score=row.score, error_message=str(e)
            )

        try:
            post_mapped_hgvs_strings = _create_post_mapped_hgvs_strings(
                row.hgvs_nt,
                AnnotationLayer.GENOMIC,
                alignment=align_result,
            )
            post_mapped_genomic = _construct_vrs_allele(
                post_mapped_hgvs_strings,
                AnnotationLayer.GENOMIC,
                None,
                False,
            )
        except Exception as e:
            _logger.warning(
                "An error occurred while generating post-mapped genomic variant for %s, accession %s: %s",
                row.hgvs_nt,
                row.accession,
                str(e),
            )
            return MappedScore(
                accession_id=row.accession,
                score=row.score,
                annotation_layer=AnnotationLayer.GENOMIC,
                pre_mapped=pre_mapped_genomic,
                error_message=str(e),
            )
    else:
        msg = f"Unsupported reference sequence namespace: {namespace}"
        raise UnsupportedReferenceSequenceNameSpaceError(msg)

    return MappedScore(
        accession_id=row.accession,
        score=row.score,
        annotation_layer=AnnotationLayer.GENOMIC,
        pre_mapped=pre_mapped_genomic,
        post_mapped=post_mapped_genomic,
    )


def _get_allele_sequence(allele: Allele) -> str:
    """Get sequence for Allele

    :param allele: VRS allele
    :return: sequence
    :raise ValueError: if sequence is none
    """
    dp = get_seqrepo()
    start = allele.location.start
    end = allele.location.end
    sequence = dp.get_sequence(
        f"ga4gh:{allele.location.sequenceReference.refgetAccession}", start, end
    )
    if sequence is None:
        raise ValueError
    return sequence


def store_sequence(sequence: str) -> str:
    """Store sequence in SeqRepo.

    :param sequence: raw sequence (ie nucleotides or amino acids)
    :return: sequence ID (sans prefix, which is ``"ga4gh"``)
    """
    sequence_id = f"SQ.{sha512t24u(sequence.encode('ascii'))}"
    alias_dict_list = [{"namespace": "ga4gh", "alias": sequence_id}]
    sr = get_seqrepo()
    sr.sr.store(sequence, alias_dict_list)
    return sequence_id


def _hgvs_nt_is_valid(hgvs_nt: str) -> bool:
    """Check for invalid or unavailable nucleotide MAVE-HGVS variation

    :param hgvs_nt: MAVE_HGVS nucleotide expression
    :return: True if expression appears populated and valid
    """
    return (
        (not is_missing_value(hgvs_nt))
        and (hgvs_nt not in {"_wt", "_sy", "="})
        and (len(hgvs_nt) != 3)
    )


def _hgvs_pro_is_valid(hgvs_pro: str) -> bool:
    """Check for invalid or unavailable protein MAVE-HGVS variation

    :param hgvs_nt: MAVE_HGVS protein expression
    :return: True if expression appears populated and valid
    """
    return (
        (hgvs_pro not in {"_wt", "_sy"})
        and (not is_missing_value(hgvs_pro))
        and (len(hgvs_pro) != 3)
        and ("fs" not in hgvs_pro)
    )


def _map_protein_coding(
    metadata: TargetGene,
    records: list[ScoreRow],
    transcript: TxSelectResult | TxSelectError,
    align_result: AlignmentResult,
) -> list[MappedScore]:
    """Perform mapping on protein coding experiment results

    :param metadata: Target gene metadata from MaveDB API
    :param records: The list of MAVE variants in a given score set
    :param transcript: The transcript data for a score set, or an error message describing why an expected transcript is missing
    :param align_results: The alignment data for a score set
    :return: A list of mappings
    """
    if metadata.target_sequence_type == TargetSequenceType.DNA:
        sequence = str(
            Seq(metadata.target_sequence).translate(table="1", stop_symbol="")
        )
        psequence_id = store_sequence(sequence)
        gsequence_id = store_sequence(metadata.target_sequence)
    else:
        sequence = metadata.target_sequence
        psequence_id = gsequence_id = store_sequence(sequence)

    variations: list[MappedScore] = []
    for row in records:
        hgvs_nt_mappings = None
        hgvs_pro_mappings = None
        if _hgvs_nt_is_valid(row.hgvs_nt):
            hgvs_nt_mappings = _map_genomic(row, gsequence_id, align_result)

        if (
            isinstance(transcript, TxSelectError) and not hgvs_nt_mappings
        ):  # only create error message if there is not an hgvs nt mapping
            # TODO create pre mapped allele
            hgvs_pro_mappings = MappedScore(
                accession_id=row.accession,
                score=row.score,
                error_message=str(transcript).strip("'"),
            )
        else:
            if _hgvs_pro_is_valid(row.hgvs_pro):
                hgvs_pro_mappings = _map_protein_coding_pro(
                    row, psequence_id, transcript
                )
            elif (
                not hgvs_nt_mappings
            ):  # only create error message if there is not an hgvs nt mapping
                hgvs_pro_mappings = MappedScore(
                    accession_id=row.accession,
                    score=row.score,
                    error_message="Invalid protein variant syntax",
                )

        # append both pro and nt mappings if both available
        if hgvs_pro_mappings:
            variations.append(hgvs_pro_mappings)
        if hgvs_nt_mappings:
            variations.append(hgvs_nt_mappings)
    return variations


def _map_regulatory_noncoding(
    metadata: TargetGene,
    records: list[ScoreRow],
    align_result: AlignmentResult,
) -> list[MappedScore]:
    """Perform mapping on noncoding/regulatory experiment results

    :param metadata: Target gene metadata from MaveDB API
    :param records: list of MAVE experiment result rows
    :param align_result: An AlignmentResult object for a score set
    :return: A list of VRS mappings
    """
    variations: list[MappedScore] = []
    sequence_id = store_sequence(metadata.target_sequence)

    for row in records:
        hgvs_nt_mappings = _map_genomic(row, sequence_id, align_result)
        variations.append(hgvs_nt_mappings)

    return variations


def store_accession(
    accession_id: str,
) -> None:
    namespace = infer_namespace(accession_id)
    alias_dict_list = [{"namespace": namespace, "alias": accession_id}]
    cd = cdot_rest()
    sequence = cd.get_seq(accession_id)
    sr = get_seqrepo()
    sr.sr.store(sequence, alias_dict_list)


def _map_accession(
    metadata: TargetGene,
    records: list[ScoreRow],
    align_result: AlignmentResult
    | None,  # NP and NC accessions won't have alignment results
    transcript: TxSelectResult | None,
) -> list[MappedScore]:
    variations: list[MappedScore] = []
    sequence_id = metadata.target_accession_id
    if sequence_id is None:
        msg = " No target_accession_id was provided by target gene metadata. Target gene metadata must have a target_accession_id to map to VRS."
        raise MissingSequenceIdError(msg)

    store_accession(sequence_id)

    # TODO full list of protein accession id prefixes
    if metadata.target_accession_id.startswith(("NP", "ENSP")):
        for row in records:
            hgvs_pro_mappings = _map_protein_coding_pro(
                row,
                sequence_id,
                transcript,
            )
            variations.append(hgvs_pro_mappings)
    # TODO full list of transcript and contig accession id prefixes
    elif metadata.target_accession_id.startswith(("NM", "ENST", "NC")):
        for row in records:
            hgvs_nt_mappings = _map_genomic(row, sequence_id, align_result)
            variations.append(hgvs_nt_mappings)
    else:
        msg = f"Unrecognized accession prefix for accession id: {metadata.target_accession_id}"
        raise UnsupportedReferenceSequencePrefixError(msg)

    return variations


def _rle_to_lse(
    rle: ReferenceLengthExpression, location: SequenceLocation
) -> LiteralSequenceExpression:
    """Coerce ReferenceLengthExpression to LiteralSequenceExpression.

    RLEs are helpful for long repeating sequences but a) unnecessary here and b)
    create incompatibilities with some data extraction further down so to simplify,
    we'll just turn them into equivalent LiteralSequenceExpressions.
    """
    sr = get_seqrepo()
    sequence_id = location.sequenceReference.refgetAccession
    start: int = location.start
    end = start + rle.repeatSubunitLength
    subsequence = sr.get_sequence(f"ga4gh:{sequence_id}", start, end)
    c = cycle(subsequence)
    derived_sequence = ""
    for _ in range(rle.length):
        derived_sequence += next(c)
    return LiteralSequenceExpression(sequence=derived_sequence)


def _construct_vrs_allele(
    hgvs_strings: list[str],
    layer: AnnotationLayer,
    sequence_id: str | None,
    pre_map: bool,
) -> Allele | Haplotype:
    alleles: list[Allele] = []
    for hgvs_string in hgvs_strings:
        _logger.info("Processing HGVS string: %s", hgvs_string)
        allele = translate_hgvs_to_vrs(hgvs_string)

        if pre_map:
            if sequence_id is None:
                msg = "Must provide sequence id to construct pre-mapped VRS allele"
                raise ValueError(msg)
            allele.location.sequenceReference.refgetAccession = sequence_id
        else:
            allele.location.sequenceReference.label = hgvs_string.split(":")[0]

        if "dup" in hgvs_string:
            allele.state.sequence = SequenceString(2 * _get_allele_sequence(allele))

        # TODO check assumption that c.= leads to an "N" in the sequence.root
        if allele.state.sequence.root == "N" and layer == AnnotationLayer.GENOMIC:
            allele.state.sequence = SequenceString(_get_allele_sequence(allele))

        if "=" in hgvs_string and layer == AnnotationLayer.PROTEIN:
            allele.state.sequence = SequenceString(_get_allele_sequence(allele))

        allele = normalize(allele, data_proxy=get_seqrepo())

        if isinstance(allele.state, ReferenceLengthExpression):
            _logger.debug(
                "Coercing state for %s into LSE: %s",
                hgvs_string,
                allele.state.model_dump_json(),
            )
            allele.state = _rle_to_lse(allele.state, allele.location)

        # Run ga4gh_identify to assign VA digest
        allele.id = ga4gh_identify(allele)
        alleles.append(allele)

    if not alleles:
        msg = f"Input variant hgvs_string(s) could not be translated to an allele: {hgvs_strings}."
        raise ValueError(msg)

    if len(alleles) > 1:
        return Haplotype(members=alleles)

    return alleles[0]


def vrs_map(
    metadata: TargetGene,
    align_result: AlignmentResult | None,
    records: list[ScoreRow],
    transcript: TxSelectResult | TxSelectError | None = None,
    silent: bool = True,
) -> list[MappedScore]:
    """Given a description of a MAVE scoreset and an aligned transcript, generate
    the corresponding VRS objects.

    :param metadata: target gene metadata from MaveDB API
    :param align_result: output from the sequence alignment process
    :param records: scoreset records
    :param transcript: output of transcript selection process
    :param silent: If true, suppress console output
    :return: A list of mapping results
    """
    if metadata.target_accession_id:
        return _map_accession(metadata, records, align_result, transcript)
    if metadata.target_gene_category == TargetType.PROTEIN_CODING and transcript:
        return _map_protein_coding(
            metadata,
            records,
            transcript,
            align_result,
        )
    return _map_regulatory_noncoding(
        metadata,
        records,
        align_result,
    )