gff <- "../Pea Project/References/ref_DBM_FJ_V1.1_scaffolds.gff3"
fileName <- "~/Desktop/Tree-TipR/Plutella_SNPsOnly.vcf.gz"
getGenes <- function(fileName, gff, feature = "gene", nCores = 5){
allGR <- import.gff(gff)
if(feature == "gene"){
genes <- allGR[allGR$type == "gene"]
featureList <- split(genes, genes$Name)
}
if(feature == "exon"){
exons <- allGR[allGR$type == "exon"]
featureList <- split(exons, unlist(exons$Parent))
featureList <- mclapply(1:length(featureList), mc.cores = nCores, function(x){
gr <- featureList[[x]]
logi <- allGR$ID == gr$Parent[[1]]
logi[is.na(logi)] <- FALSE
gr$Name <- allGR[logi]$Name
gr
})
}
featureList[1:100]
}
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