[FEAT] genbank or gff as input

[alexweisberg]

Is your feature request related to a problem? Please describe.
Often I already have annotations for a genome, including gene calls/ORFs with locus_tags. Running Integron_Finder on the fasta file results in reannotating ORFs, and it would be nice to save time on that as well as have the preexisting locus tag IDs in the output. The gembase format used by Integron_Finder seems to have changed from that used by macsyfinder and is fairly involved. It would be nice if Integron_Finder could take a genbank gbk file or gff file as input, and report the output in terms of that file.

The --annot-parser option looks promising, however (I could be wrong) it doesn't look like it supports more than a single replicon in the input. If this option took a replicon id as a fifth part of the tuple that seems like it would work as a good alternative.

Describe the solution you'd like
Integron_Finder taking genbank or gff files as input rather than fasta nucleotide

Thanks!