I have a GenBank (or even gff) file and want to count the number of bases found in introns/CDSs/intergenic space.
Does anyone know if there's any script already out there? I'll start writing mine (most probably using BioPerl). I'm just being lazy and also don't want to re-invent the wheel :D
My problem is that intron coordinates are only implied in my gff file (they're the regions inside a gene that are not CDSs). The same is also true for intergenic space. And last, there might be multiple splice variants per gene. I only want one of them...
you have to make your requirements more explicit - for example which splice variant do you want? in all I would say that there is probably no tool that does exactly what you want.
Albert, any variant would be good because I only want to have a rough estimate of the portion of genome found in introns/CDSs/intergenic space. Anyway, I've started writing my own script... I just wanted to make sure that I'm not re-inventing the wheel. Thank you all guys for your time!