Fix KeyError: 'ID' in create_splice_sites for GTF-derived databases - #248
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Fix KeyError: 'ID' in create_splice_sites for GTF-derived databases#248youdie006 wants to merge 1 commit into
youdie006 wants to merge 1 commit into
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FeatureDB.create_splice_sites() uniquifies each new splice-site feature's ID by reading splice_site.attributes["ID"]. GTF-derived features carry gene_id/transcript_id/exon_id but have no ID attribute, so the read raises KeyError: 'ID'. The sibling create_introns() is unaffected because it never touches ID. The interfeatures() helper already guards its own ID rewrite with `if "ID" in ...attributes`, so this applies the same existing convention here. Guard the ID rewrite so it only runs when an ID is present. GTF input no longer crashes; GFF3 input (which has real IDs) keeps its uniquified IDs exactly as before. Fixes daler#239.
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Fixes #239
Problem
Calling
FeatureDB.create_splice_sites()on a database built from a GTF file raisesKeyError: 'ID'.Root cause
create_splice_sites()uniquifies each new splice-site feature's ID by readingsplice_site.attributes["ID"]. GTF-derived features carrygene_id/transcript_id/exon_idbut have noIDattribute, so the read raisesKeyError: 'ID'. The siblingcreate_introns()is unaffected because it never touchesID. (Theinterfeatures()helper already guards its own ID rewrite withif "ID" in ...attributes, so this fix simply applies the same existing convention here.)Fix
Guard the ID rewrite so it only runs when an ID is present. GTF input no longer crashes; GFF3 input (which has real IDs) keeps its uniquified IDs exactly as before.
Tests
Added
test_create_splice_sites_from_gtfusing the reporter's exact GTF example: a 3-exon transcript yields 4 splice sites without raising. Verified red (KeyError on old code) / green (passes with fix), and the existing GFF3test_create_splice_sitesis unchanged and still passes.Thanks to @kbseah for the clear report and reproducer.
This change was prepared with AI assistance and reviewed by me before submission. (No rush -- I understand the project merges in bursts, so review whenever convenient.)