In the GFF3 format, I believe
intron is a valid entry type along with
mRNA, etc. but is typically removed since it is redundant. Is there a tool that takes an input GFF3 file and adds the intron entries to it? Sometimes it's very helpful to have it in the file, even though the intron coordinates are implicit (for example if you want to map reads against exons and introns.)
If there's a program that does it out of the box I would like to know to avoid reinventing the wheel. In short, take a GFF3 file and print out all of its entries plus the
intron entries that are implicit in the original GFF3 file. thanks.
edit just found Is Is Feasible To Produce Intron Gff According To Utr Gff And Cds Gff? -- genometools seems to be a solution. It'd be nice if there were other, lighter scripts that do this, since it seems excessive to install/compile genometools just for this purpose if you don't already use genometools (though genometools looks very useful in general)