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

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thackl opened this issue Mar 30, 2022 · 1 comment
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";" in gbk fields break read_gbk/gb2gff #121

thackl opened this issue Mar 30, 2022 · 1 comment
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thackl commented Mar 30, 2022 

$ 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 thackl added the bug Something isn't working label Mar 30, 2022
@thackl thackl self-assigned this Mar 30, 2022
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thackl commented Mar 30, 2022

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.

@thackl thackl closed this as completed in 4792ee4 Mar 30, 2022
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