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daler / gffutils

GFF and GTF file manipulation and interconversion
http://daler.github.io/gffutils
MIT License
282 stars 76 forks source link

address #159 #188

Closed daler closed 2 years ago

daler commented 2 years ago

The original helpers.canonical_transcripts was not well tested (or even used much as far as I know).

@EFraim, this uses your PR #156 but I was unable to update it myself and fix the merge conflict (because understandably your master branch as diverged in the 2 yrs since you've addressed this!)

Eventually I would like to modularize this to instead have a method on the FeatureDB that finds the canonical transcript for a gene, and have the sequence part dealt with separately, e.g., 

for gene in genes_of_interest:
    transcript = db.canonical_transcript(gene)

but that will be later...