Hi

I'm trying to make a Granges objet with all the internal exons of the genes annotated in a GTF file. I using this code:

txdb <- makeTxDbFromGFF("./gencode.vM9.chr_patch_hapl_scaff.annotation.gtf.sed", format="gtf")

exons <- exonsBy(txdb, by="tx")

internal_exons <- lapply(exons,
       function(x) if (length(x)>=3){x[3:length(x)-1] })

But it running really slow, is there any way to make it more efficient?
 

The more important problem is that internal_exons is not a convenient data structure. It will contain NULL values where the condition failed, instead of an empty set of ranges, and the list is semantically poor. Also, the looping obscures the code.

This is faster and cleaner:

internal_exons <- phead(ptail(exons, -2L), -1L)