bcbb icon indicating copy to clipboard operation
bcbb copied to clipboard

Did not find remapped ID location:

Open fbeghini opened this issue 6 years ago • 2 comments

I'm trying to parse a gff file downloaded from NCBI (GCA_001536265) and when I iterate on the parser it gives me this error Did not find remapped ID location: gene670, [[42143, 44074], [44736, 45087], [45979, 46332], [47064, 47369]], [42143, 47369]

Inspecting the GFF with GFFExaminer gives no error at all.

fbeghini avatar Jul 10 '18 12:07 fbeghini

Francesco -- sorry about the issues. In general, we've been recommeding using the gffutils parser, which is nicer and more actively maintained: https://github.com/daler/gffutils. Would you be able to try this out and see if it solves your parsing issues?

chapmanb avatar Jul 11 '18 14:07 chapmanb

Can I add annotation data from an external FASTA file to the GFF3 like the approach described here ?

fbeghini avatar Jul 12 '18 15:07 fbeghini