Extract gene IDS from GFF3 based on coordinates from another file

Question

[JR]

I have determined some regions of interest in my genome and i want to extract the gene annotations that fall into that regions.

First, I have formatted my initial GFF3 file to obtain a bed file like:

Scaffold_1      1451750 1458451 ID=ANN00021
Scaffold_1      3553514 3558618 ID=ANN00054
Scaffold_2      4024794 4032517 ID=ANN00058

And i have other bed file with the genome regions:

Scaffold_1      133745072       133845072
Scaffold_1      133854352       133954352
Scaffold_1      133806326       133906326
Scaffold_1      133912327       134012327
Scaffold_2      64167277        64267277

I have tried with bedtools but I think cannot deal with my question.

I will appreciate any suggestion. Thanks!

[Ram]

I have tried with bedtools

Can you also tell us exactly what you tried and how it failed? I'd recommend you take a look at bedops - the manual helps visualize your expectations very well: https://bedops.readthedocs.io/en/latest/content/overview.html#about-bedops

[JR]

Thank you for the bedtops, sounds good. I will try to solve with that.

[shimbalama]

you just need a little python. ie, if range start < annotation start < range end. and same for annotation end. or just make a range and ask if it's in that range... if u are going to have to do this sort of thing regularly u need to learn py.