Accession based score set tweaks

pyproject.toml

@@ -36,14 +36,14 @@ dependencies = [
     "biopython",
     "tqdm",
     "click",
+    "cdot",
     "cool-seq-tool>=0.4.0.dev1",
     "ga4gh.vrs~=2.0.0-a6",
     "gene_normalizer[etl,pg]==0.3.0-dev2",
     "pydantic>=2",
     "python-dotenv",
     "setuptools>=68.0",  # tmp -- ensure 3.12 compatibility
     "mavehgvs==0.6.1",
-    "cdot",
 ]
 dynamic = ["version"]
 

src/dcd_mapping/main.py

@@ -159,7 +159,10 @@ async def map_scoreset(
 
     _emit_info("Selecting reference sequence...", silent)
     try:
-        transcript = await select_transcript(metadata, records, alignment_result)
+        if metadata.target_accession is None:
+            transcript = await select_transcript(metadata, records, alignment_result)
+        else:
+            transcript = None
     except TxSelectError as e:
         _emit_info(
             f"Transcript selection failed for scoreset {metadata.urn}",

src/dcd_mapping/transcripts.py

@@ -311,7 +311,7 @@ async def select_transcript(
     metadata: ScoresetMetadata,
     records: list[ScoreRow],
     align_result: AlignmentResult,
-) -> TxSelectResult | None:
+) -> TxSelectResult | str | None:
     """Select appropriate human reference sequence for scoreset.
 
     * Unnecessary for regulatory/other noncoding scoresets which report genomic
@@ -336,10 +336,14 @@ async def select_transcript(
             sequence=_get_protein_sequence(metadata.target_sequence),
         )
 
+    if metadata.target_accession:
+        return metadata.target_accession
+
     if metadata.target_gene_category != TargetType.PROTEIN_CODING:
         _logger.debug("%s is regulatory/noncoding -- skipping transcript selection")
         return None
     transcript_reference = await _select_protein_reference(metadata, align_result)
+
     if transcript_reference and metadata.target_sequence_type == TargetSequenceType.DNA:
         offset = _offset_target_sequence(metadata, records)
         if offset:

src/dcd_mapping/vrs_map.py

@@ -599,6 +599,9 @@ def _map_accession(
     # see if accession is in seqrepo
     # if not, get seq from cdot and add to seqrepo
     sequence_id = metadata.target_accession
+    if sequence_id is None:
+        raise ValueError
+
     store_accession(sequence_id)
 
     for row in records:
@@ -721,6 +724,9 @@ def vrs_map(
         _logger.warning(msg)
         return None
 
+    if metadata.target_accession:
+        return _map_accession(metadata, records, align_result)
+
     if metadata.target_gene_category == TargetType.PROTEIN_CODING and transcript:
         return _map_protein_coding(
             metadata,