Mouse reference names: mm9 maps to a nonexistent GRCm37, and GRCm38/GRCm39 accessions misparse

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
74/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python
Domain
bioinformatics

Research direction

Start with the reference-name mappings and matching logic in varcode/reference.py, then look for existing tests of infer_genome. Check the listed accession versions against pyensembl’s assembly_catalog.json and the NCBI data mentioned in the issue. Done means mm9 and each listed GCA/GCF accession resolve to the expected assembly, without treating GRCm39 accessions as GRCm38 releases.

Written by the indexing model from the issue text.

Description

Found while fixing #668 (#689); varcode 11.5.1 branch, pyensembl 2.32.3. infer_genome(name):

name result expected
mm9 ValueError: Failed to infer genome assembly name for mm9 NCBIM37 (UCSC mm9 is NCBI Build 37; pyensembl serves NCBIM37 in releases 54–67)
NCBIM37 NCBIM37, release 67 (works)
GCA_000001635.8 (GRCm38.p6) ValueError: Invalid Ensembl releases 8, must be greater than 40 GRCm38
GCA_000001635.9 (GRCm39) ValueError: Invalid Ensembl releases 9, must be greater than 40 GRCm39
GCF_000001635.26 (GRCm38.p6) Failed to infer genome assembly name GRCm38
GCF_000001635.27 (GRCm39) Failed to infer genome assembly name GRCm39
GCF_000001635.24 (GRCm38.p4) GRCm38 (works)

Causes, in varcode/reference.py:

  1. ucsc_to_ensembl_reference_names maps mm9 to "GRCm37", which isn't a name pyensembl knows. _collect_candidate_matches only walks pyensembl's canonical names, so mm9 never matches.
  2. ensembl_reference_aliases["GRCm38"] includes the unversioned "GCA_000001635". Since it is an exact alias, _split_release reads any versioned accession GCA_000001635.N as "GRCm38, Ensembl release N". That breaks every GRCm38 GCA accession as well as GRCm39's, and as a substring it would also claim GRCm39 files named by accession for GRCm38. The GCF list stops at GRCm38.p4 (.24), and GRCm39 has no accession aliases.

Suggested fix: map mm9 to NCBIM37. Replace the unversioned GCA with versioned accessions taken from pyensembl's assembly_catalog.json, the shared metadata: GRCm38 GCA_000001635.2–.8, GRCm39 GCA_000001635.9. Add the GCF accessions for GRCm38.p5/p6 (.25, .26) and GRCm39 (.27), checked against NCBI. Test that each accession resolves to its own assembly, and that GRCm39's accession is never read as a GRCm38 release.

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