creates a fasta file with 300bp chunks from the start of all exons larger than 300 bp

retro-lgexonFinder.R

setwd("~/Desktop/retrogenes/data/")
gff <- read.csv("exons.csv", header = F, as.is=T) #This is a parsed GFF3 file that contains the lines for exons

# lets get big ones >300 bp

gff <- gff[gff[, 3] - gff[, 2] > 300, ]
setwd("~/Desktop/retrogenes/data/chromosomes") #This is the directory that contains the chromosomes of the genome

library(ape)
seq <- name <- list()
LGS <- totals <- vector()

counter <- 0
fileName <- "NONE"
fileName <- paste(gff[1, 1], "-2.fa", sep="")
chromosome <- read.dna(fileName, format = 'fasta', as.character = T)  #This opens the first chromosome

for(i in 1:nrow(gff)){
    if(gff[i, 1] != substr(fileName, 1, stop=nchar(fileName) - 5)){
      LGS <- c(LGS, fileName)
      totals <- c(totals, counter)
      fileName <- paste(gff[i, 1], "-2.fa", sep="")
      chromosome <- read.dna(fileName, format = 'fasta', as.character = T)
      print(paste("Working on:", fileName))
      counter <- 0      
    }
    counter <- counter + 1
    print(paste("exon:", counter))
    seq[[i]] <- paste(chromosome[gff[i, 2]:(gff[i, 2]+300)], collapse="")
    name[[i]] <- paste(gff[i, 1], gff[i,2])
    fileName <- paste(gff[i, 1], "-2.fa", sep="")
}
LGS <- c(LGS, fileName)
totals <- c(totals, counter)
names(totals) <- LGS
totals
names(seq) <- name
write.dna(seq, format = "fasta", file = "300+bpExons.fa", colw=300)   #This saves the final file