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linsalrob / genbank_to

Convert genbank files to a swath of other formats
MIT License
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Handling join() featureseg #2

Open tseemann opened 1 year ago

tseemann commented 1 year ago 
ncbi-acc-download MW367468

genbank_to -g MW367468.gbk --gff3 out.gff

# GEBBANK
CDS complement(join(23549..23700,1..220))

# GFF
CDS     1       23700   .       -

This plasmid is not oriented correctly so the rep gene spans the origin. Be good if this listed as 2 exons in the GFF

linsalrob commented 1 year ago

Compound features are a real problem to deal with, here is a solution we made for PhiSPy

Currently we use bcbio-gff for writing the GFF3 and we will work on a solution for bcbio since it doesn't currently handle compound features. We might consider moving to gffutils or another GFF3 library as well.

Update pending.