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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Did not find remapped ID location: #118

Open fbeghini opened 6 years ago

fbeghini commented 6 years ago

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.

chapmanb commented 6 years ago

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?

fbeghini commented 6 years ago

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