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BioJulia / GenomicAnnotations.jl

MIT License
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gffstring mishandles transpliced genes #17

Closed ian-small closed 2 days ago

ian-small commented 4 days ago

'locus(gene).strand' in gffstring assumes all positions in the locus are on the same strand, which is not true for trans-spliced genes, e.g. join(11056..11919,complement(94283..95886)) is a valid GenBank locus that can now be faithfully represented using your much-appreciated rewrite of GenomicAnnotations.Locus, but which is rendered as gene 11056 11919 . + gene 94283 95886 . + by GFF.gffstring()

kdyrhage commented 2 days ago

Thanks for bringing up these issues; I only work with prokaryotic data so I rarely encounter more complex locus descriptors myself.