args <- commandArgs(trailingOnly=TRUE)
geneimprint <- fread(args[1])
+geneimprint <- geneimprint[!grepl(" ",Gene),]
parent <- fread(args[2])
### fix up the 0 prefixed chromosomes
parent[,chr:=gsub("^0","",chromosome)]
parent[,Gene:=gsub("\\s*,\\s*.+","",Gene)]
parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
+
+
setkey(parent,"Gene")
setkey(geneimprint,"Gene")
imprinted.genes <-
- union(parent[,Gene],geneimprint[,Gene])
+ union(gsub("[\\*\\@]$","",parent[,Gene]),
+ gsub("[\\*\\@]$","",geneimprint[,Gene]))
+
+gene.aliases <- fread(args[3])
+setkey(gene.aliases,"alias")
+
+imprinted.genes <-
+ sort(sapply(imprinted.genes,
+ function(x){if(is.na(gene.aliases[x,gene])) {
+ return(x)
+ } else {
+ return(gene.aliases[x,gene])
+ }}))
write.table(file=args[length(args)],
imprinted.genes,