In the GFF3 format, I believe intron
is a valid entry type along with exon
, 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)
I tried to use gt gff3 --addintrons in the package GenomeTools to display intron feature in my gff3 file, my gff file might be not strict gff3 format, and it did not work for me, so I wrote one myself, wish it helpful to you. My suggestion is to insert the introns next to the exon using function spice
There is the AGAT solution too with
agat_sp_add_introns.pl
, it is supposed to work on every cases.Thanks for sharing, I'll fork this tool