I have a gff3 file produced by an analysis step (specifically InterPro, but that's not terribly relevant here). Since that tool took a fasta file of proteins, all of the analysis results have coordinates respective to the analysed protein sequences

I'm trying to get these results to show up in a browser like JBrowse, the easiest way of doing this I found was to rebase the coordinates against the parent genome. E.g. if there was a match_part from 1-100 of cdsA which is comprised of bases 200..300, then we'd update the match_part to be 200..300, and change the parent reference to the parent genome.

I have a small tool that does this, but was wondering if anyone has a better solution (I just want to display them properly in JBrowse), or fully featured existing implementation of a rebasing tool like this?

Example

I have a gff file with my gene calls, like so:

##gff-version 3
##sequence-region Merlin 1 172788
Merlin  GeneMark.hmm    gene    2   691 -856.563659 +   .   ID=Merlin_1
Merlin  GeneMark.hmm    gene    1067    2011    -1229.683915    -   .   ID=Merlin_3

From this, those gene sequences were extracted, translated to protein sequences, and then run through some analysis step which generated some results/matches. In this case they're InterProScan results

Merlin  feature polypeptide 1   229 .   +   .   ID=Merlin_1
Merlin  Gene3D  protein_match   2   50  2.9E-21 +   .   ID=match%2477_2_50;Name=G3DSA:3.90.176.10;Target=Merlin_1 2 50;date=23-02-2015;status=T

In order to have these results visible, properly, in JBrowse, those coordinates need to be adjusted such that they reflect their coordinates respective to the parent genome.

The feature with ID=Merlin_1, should be moved 1 base to the right, as the gene that was analysed to produce that match starts at base 2.

A hit with ID=Merlin_3, going from bases 1..11 (in the InterPro results) would need to be changed to the minus strand, and moved to 2000..2011 according to the parent genome.