GenBank output not found.

[Taalouane]

Hi,

For each input assembly I have used, Kaptive did not produce the Genbank file for the region (s) in the assembly that match the best locus of interest match.

Do you have any idea how I could get the Genbank file to output the region of interest?

Thanks !

[kelwyres]

Hi,

Many apologies- there is a mistake on the Kaptive instructions page- Kaptive doesn't produce a Genbank file as output, only a fasta file. I will update the instructions page. If you would like to generate a Genbank annotation you could try using Prokka with the relevant Kaptive database as a protein reference.

Apologies again for the confusion and thanks for highlighting our mistake!
Kelly

[tomdstanton]

This can be built into kaptive convert if there is enough interest.
GeneResult objects can be coerced into Bio.SeqFeature objects by adding the class method as_seqfeature() and LocusPiece objects can be coerced into Bio.SeqRecord objects by adding the class method as_seqrecord(). The TypingResult objects would then yield Bio.SeqRecord objects for locus pieces by adding the class method as_seqrecord(). However I'm unsure how we would deal with genes outside of the locus; I am open to suggestions.