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Fix protein layer generation and error handling in vrs_map #95

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Fix protein layer generation and error handling in vrs_map #95

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899f7ab
fix(vrs_map): only generate protein layer if protein strings are valid
bencap Apr 16, 2026
d681cbc
fix(vrs_map): avoid redundant error messages for protein alignment fa…
bencap Apr 16, 2026
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25 changes: 14 additions & 11 deletions src/dcd_mapping/vrs_map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -829,17 +829,20 @@ def _map_protein_coding(
error_message=str(transcript).strip("'"),
)
else:
if _hgvs_pro_is_valid(row.hgvs_pro) and protein_align_result is not None:
hgvs_pro_mappings = _map_protein_coding_pro(
row, psequence_id, transcript, protein_align_result
)
# This should not occur because protein align result is only None if transcript selection failed, which should be caught by the TxSelectError check above.
elif protein_align_result is None:
hgvs_pro_mappings = MappedScore(
accession_id=row.accession,
score=row.score,
error_message="Could not perform mapping for protein variant because transcript sequence is missing or could not be aligned to reference sequence",
)
if _hgvs_pro_is_valid(row.hgvs_pro):
if protein_align_result is not None:
hgvs_pro_mappings = _map_protein_coding_pro(
row, psequence_id, transcript, protein_align_result
)
# Only create this error message if there is not a valid hgvs nt mapping, because if there is a valid hgvs nt mapping,
# it indicates we expect protein alignemnt to fail and we don't want to create redundant error messages about missing
# transcript sequence or alignment failure
elif protein_align_result is None and not hgvs_nt_mappings:
hgvs_pro_mappings = MappedScore(
accession_id=row.accession,
score=row.score,
error_message="Could not perform mapping for protein variant because transcript sequence is missing or could not be aligned to reference sequence",
)
elif (
not hgvs_nt_mappings
): # only create error message if there is not an hgvs nt mapping
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