Fix #335 (part 1): wire GENCODE_BIOTYPE_ALIASES into read_gtf call#356
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GENCODE GTFs use gene_type / transcript_type where Ensembl uses gene_biotype / transcript_biotype. Before this fix, pointing pyensembl at a vanilla GENCODE GTF produced a sqlite database with empty biotype columns, so Transcript.is_protein_coding returned False for every transcript and downstream tools like varcode reported NoncodingTranscript for every variant effect (the original #335 user repro). gtfparse 2.7.0 introduced an attribute_aliases kwarg on read_gtf that renames source columns onto canonical names at parse time, plus a GENCODE_BIOTYPE_ALIASES constant for the two GENCODE->Ensembl renames. pyensembl now passes that constant unconditionally: * Pure Ensembl GTFs: alias sources don't exist, the rename is a no-op (gtfparse skips missing alias source columns). * GENCODE GTFs: gene_type / transcript_type get renamed to gene_biotype / transcript_biotype before they hit the sqlite schema. * Mixed (both column variants present): canonical wins, gtfparse warns. Bumps gtfparse dep floor to >=2.7.0. Companion to #350 / v2.9.6 (versioned protein-ID FASTA matching). With both shipped, the original #335 GENCODE genome example finally produces Substitution effects instead of NoncodingTranscript. Bump version to 2.9.8.
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coverage: 84.971%. remained the same — fix-335-part1-gencode-biotype-aliases into main |
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Summary
Closes the GTF half of #335. With both this PR and #350 / v2.9.6 (versioned protein-ID FASTA matching) deployed, the original repro from the issue (
Variant(...).effects()returningNoncodingTranscriptfor every transcript when wired to a GENCODE genome) finally produces correctSubstitutioneffects.Mechanism
gtfparse 2.7.0 (just released — openvax/gtfparse#67) introduced an
attribute_aliaseskwarg onread_gtfthat renames source columns onto canonical names at parse time, plus aGENCODE_BIOTYPE_ALIASESconstant for the two relevant GENCODE → Ensembl renames (gene_type→gene_biotype,transcript_type→transcript_biotype). pyensembl now passes that constant unconditionally:gene_type/transcript_typeget renamed togene_biotype/transcript_biotypebefore they hit pyensembl's sqlite schema.Dependency
Bumps
gtfparsedep floor from>=2.6.0to>=2.7.0—GENCODE_BIOTYPE_ALIASESandattribute_aliases=are new in 2.7.0.Out of scope
This is the biotype half of #335. The versioned-ID half was fixed in #350 / v2.9.6 (and refined again in #355 which is in flight). Together they're the full close.
Test plan
tests/test_gencode_biotype_aliases.pycovers:gene_type/transcript_type) lands in the sqlite DB with biotype columns populatedGenome.genes(biotype="protein_coding")andtranscripts(biotype="protein_coding")filter correctly against the renamed columnsTranscript.is_protein_codingreturns True for coding rows and False for lncRNA rows — the exact thing the ID version handling and GENCODE compatibility #335 user repro was failing onpytest tests/test_gencode_biotype_aliases.py tests/test_mouse.py tests/test_tair10_complete.py tests/test_biotype_filter.py tests/test_versions.py tests/test_versioned_protein_fasta.py— 24 passed locally./lint.shBumps version to 2.9.8.