";" in gbk fields break read_gbk/gb2gff

thackl / gggenomes

A grammar of graphics for comparative genomics

https://thackl.github.io/gggenomes/

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";" in gbk fields break read_gbk/gb2gff #121

Closed thackl closed 2 years ago

thackl commented 2 years ago

$ gb2gff GCF_009738455.1_ASM973845v1_genomic.gbff | grep yfhX
writing directives
writing features
NZ_CP046527 .   gene    537002  537814  .   +   .   ID=gene-GN312_RS03255;Name=hcaB;Alias=phdD; yfhX;old_locus_tag...

Note the " ;yfhX" which is later parsed into an undefined value column.

thackl commented 2 years ago

Not sure if this is technically allowed in gff and just my regexp in read_gff is bad, but an easy fix for now is to not allow ";" in gff fields generated from the gbk file in the first place.