enhancement: add option to slice input contigs

[jbadomics]

Torsten-
An idea for enhancement: would be great to have an option for barrnap to write fasta file(s) containing just the detected rRNA sequences, i.e. to slice the input contigs file at coordinates reported in the .gff output - would facilitate much faster BLAST...just a thought.

Otherwise very handy tool, thanks for maintaining! :)

Jon

[tseemann]

Do you mean you want to produce a FASTA file with the search results, ie. the sequence of each of the hits?

You can do this with

barrnap genome.fna > barrnap.gff
bedtools getfasta -fi genome.fna -bed barrnap.gff -s > barrnap.fasta

But I agree it would be useful to have an option to do it. I'll aim to add it @jbadomics