fix(seq): return spliced cDNA for transcripts instead of genomic (#187)#227
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Elarwei001 wants to merge 4 commits into
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fix(seq): return spliced cDNA for transcripts instead of genomic (#187)#227Elarwei001 wants to merge 4 commits into
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…erse#187) Ensembl's sequence/id endpoint returns the genomic span by default, which for a transcript ID includes introns rather than the spliced transcript sequence. gget seq therefore returned the wrong sequence for any ENST/transcript query. Request type=cdna for transcript IDs across all three code paths: - non-isoform bulk request: classify IDs via lookup/id and split into a cDNA batch (transcripts) and a genomic batch (genes/other), falling back to the previous genomic-only behaviour if the lookup fails - isoform gene branch: fetch each transcript as cDNA - isoform non-gene branch: cDNA for transcripts, genomic otherwise The cDNA response carries no "desc" field, so coerce a missing desc to an empty string when building the FASTA header. Regenerate the test7/ test8 fixtures to the spliced-transcript output. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #227 +/- ##
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+ Coverage 56.14% 56.63% +0.48%
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Files 29 29
Lines 9244 9260 +16
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+ Hits 5190 5244 +54
+ Misses 4054 4016 -38 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add network-free, mocked tests covering the scverse#187 fix (gget seq returns the spliced cDNA for transcript/ENST IDs instead of the genomic span): - versioned ENST id (.N) is version-stripped and fetched as type=cdna - non-coding/ncRNA transcript uses the same cDNA path - mixed gene+transcript batch splits into a genomic and a cDNA request - isoforms=True for both a gene (cDNA per transcript) and a transcript - translate=True for a transcript queries UniProt with the transcript ID - graceful handling when an entry has no desc, and when an ID is absent from the Ensembl response All Ensembl/UniProt calls are mocked so the new tests are deterministic and offline; existing live tests are left unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
for more information, see https://pre-commit.ci
Add targeted, network-free tests for the previously-uncovered branches of the scverse#187 fix (patch coverage was 82.6%, 4 lines in gget/gget_seq.py): - lookup/id classification failure -> falls back to a genomic request - isoforms=True on a gene where one transcript's cDNA fetch fails -> the error is logged and the remaining transcripts are still returned - isoforms=True on a transcript whose cDNA fetch fails -> error logged, no sequence returned These exercise the three `except RuntimeError` handlers that were not hit before, bringing patch coverage of the fix to ~100%. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #187
Summary
Ensembl's
sequence/idendpoint returns the genomic span by default, which for a transcript ID includes introns rather than the spliced transcript sequence. As a resultgget seqreturned the wrong sequence for any ENST/transcript query.What it does
Requests
type=cdnafrom the Ensemblsequence/idendpoint for transcript IDs so transcript queries return the spliced cDNA. Gene IDs are unaffected and still return the genomic sequence.Changes
lookup/idand split into a cDNA batch (transcripts) and a genomic batch (genes/other), falling back to the previous genomic-only behaviour if the lookup fails.descfield, so a missing desc is coerced to an empty string when building the FASTA header.test7/test8fixtures to the spliced-transcript output.Testing
ENST00000392653now returns cDNA (len 677, no chromosome desc) instead of the genomic span (len 1393). Mixed gene+transcript batches correctly split (transcript→cDNA, gene→genomic).pytest tests/test_seq.py— 10 passed.