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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Is there a script to convert a gbk back to gff ? #575

Closed avilaHugo closed 3 years ago

avilaHugo commented 3 years ago

Dear developers, I was wondering if there is a way to convert a gbk file into the default gff3 file generated by prokka. After a prokka run a colleague of mine did a manual curation of several genes and I would like to get the gff3 file from this corrected annotation. First I thought about running the prokka a second time passing the gbk file as a reference (--proteins), but maybe this process would generate differences in the position of the features. What do you think ?

I tried converting with some tools like emboss seqret but when i imput the generated gff3 to tools like panaroo they return fomat errors.

tseemann commented 3 years ago

I have some internal scripts which I sometimes use, but they are not in the Prokka codebase.

Until then I have asked Panaroo author to maybe support GBK: https://github.com/gtonkinhill/panaroo/issues/119

avilaHugo commented 3 years ago

I think that was the fastest response i ever had on github

Thanks !