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Hi,
Thank you for making and maintaining this very useful tool.
Working with genbank output from antiSMASH6.1.1, bioconvert genbank2gff3 fails when a tRNA feature is found as the first feature on the genome. The same genome directly from PGAP does not fail, because the /gene feature is listed before the /tRNA feature. This led me to look at the files which don't fail, and it turns out that the genbank2gff3 displays the wrong parent locus_tag for tRNAs when the order of features is unexpected (like tRNA before gene), without causing errors.
I believe that genbank format has freedom of feature order, so it could be an issue to rely on /gene being found first for the gff3 conversion, not only for tRNA and not only for antiSMASH output.
using /gene feature rather than locus_tag or similar, genbank2gff3 picks up the previous (and wrong) locus tag when /gene is not found before other feature.
The text was updated successfully, but these errors were encountered:
Hi,
Thank you for making and maintaining this very useful tool.
Working with genbank output from antiSMASH6.1.1, bioconvert genbank2gff3 fails when a tRNA feature is found as the first feature on the genome. The same genome directly from PGAP does not fail, because the /gene feature is listed before the /tRNA feature. This led me to look at the files which don't fail, and it turns out that the genbank2gff3 displays the wrong parent locus_tag for tRNAs when the order of features is unexpected (like tRNA before gene), without causing errors.
I believe that genbank format has freedom of feature order, so it could be an issue to rely on /gene being found first for the gff3 conversion, not only for tRNA and not only for antiSMASH output.
Version of bioconvert
1.0.0.post0
Command or code used
genbank input
Expected behaviour
CP109073 GenBank tRNA 243644 243717 . + . ID=OIE51_01175.tRNA.1;Parent=OIE51_01175;anticodon=tRNA-Pro
CP109073 GenBank gene 243644 243717 . + . ID=OIE51_01175;locus_tag=OIE51_01175
Your results
CP109073 GenBank tRNA 243644 243717 . + . ID=OIE51_01175.tRNA.1;Parent=OIE51_01170;anticodon=tRNA-Pro
CP109073 GenBank gene 243644 243717 . + . ID=OIE51_01175;locus_tag=OIE51_01175
What you think might have happened
using /gene feature rather than locus_tag or similar, genbank2gff3 picks up the previous (and wrong) locus tag when /gene is not found before other feature.
The text was updated successfully, but these errors were encountered: