## libraries
library(genomeIntervals)
library(Biostrings)

## read the reference file
ref <- readDNAStringSet("Ptrichocarpa_156.fa")

## read the gff3
annot <- readGff3("Ptrichocarpa_156_gene.gff3")

## keep only the genes
annot <- annot[annot$type=="gene",]

## process by scaffolds
fasta <- Reduce(append,lapply(levels(seq_name(annot)),function(scf,annot,ref){

  ## sel the annotations
  sel <- seq_name(annot)==scf

  ## get the starts and the ends
  seqs <- as(Views(ref[[scf]],annot[sel,1],annot[sel,2]),"DNAStringSet")

  ## get the gene ID
  names(seqs) <- getGffAttribute(annot[sel],"ID")

  ## check the strand
  n.sel <- strand(annot[sel]) == "-"
  append(seqs[!n.sel],reverseComplement(seqs[n.sel]))

},annot,ref))

## write it as fasta
writeXStringSet(fasta,file="Ptrichocarpa_156_gene_sequence.fa")