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Label ref seqs #22

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Merged
sallybg merged 2 commits into from
Sep 25, 2024
Merged

Label ref seqs #22

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604e94f
Add mapped reference seq label to vrs output
sallybg Sep 24, 2024
bf4a79d
Bump version number
sallybg Sep 24, 2024
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2 changes: 1 addition & 1 deletion src/dcd_mapping/version.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
"""Provide dcd mapping version"""

dcd_mapping_version = "2024.1.0"
dcd_mapping_version = "2024.1.1"
10 changes: 2 additions & 8 deletions src/dcd_mapping/vrs_map.py
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Expand Up @@ -623,6 +623,8 @@ def _construct_vrs_allele(
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]
Comment on lines +626 to +627
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@bencap bencap Sep 24, 2024

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There will always be a colon in the hgvs string right? Just making sure we don't ever raise a key error down below.

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@sallybg sallybg Sep 25, 2024

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There should always be a colon in the post-mapped hgvs string, as long as the hgvs string was created by the function _create_post_mapped_hgvs_strings.

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@sallybg sallybg Sep 25, 2024

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We are assuming that there's no colon in the transcript or chromosome name, though. I think that's a safe assumption, but if that assumption were to be wrong, then the post-mapped variant would not be created for the variant, and you're right that the associated error for that variant would be a KeyError.


if "dup" in hgvs_string:
allele.state.sequence = SequenceString(2 * _get_allele_sequence(allele))
Expand Down Expand Up @@ -675,14 +677,6 @@ def vrs_map(
:param silent: If true, suppress console output
:return: A list of mapping results
"""
# TODO address this hardcoding, and if we keep it, this should be a score set mapping error message
# if metadata.urn == "urn:mavedb:00000072-a-1":
# msg = f"No RefSeq accession is available for {metadata.urn}."
# if not silent:
# click.echo(msg)
# _logger.warning(msg)
# return None

Comment on lines -678 to -685
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@bencap bencap Sep 24, 2024

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Will this raise a mapping error now?

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@sallybg sallybg Sep 25, 2024

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This score set raises a mapping error without the hardcoding now. This was addressed in the first release of the mapper for mavedb, but I hadn't removed the commented out code.

if metadata.target_gene_category == TargetType.PROTEIN_CODING and transcript:
return _map_protein_coding(
metadata,
Expand Down