3 args <- commandArgs(trailingOnly=TRUE)
5 geneimprint <- fread(args[1])
6 parent <- fread(args[2])
7 ### fix up the 0 prefixed chromosomes
8 parent[,chr:=gsub("^0","",chromosome)]
9 ### remove aliases in ()
10 parent[,Gene:=gsub("\\s*\\([^\\)]+\\)\\s*","",gene)]
11 ### remove aliases after ,
12 parent[,Gene:=gsub("\\s*,\\s*.+","",Gene)]
14 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
16 setkey(geneimprint,"Gene")
19 union(parent[,Gene],geneimprint[,Gene])
21 write.table(file=args[length(args)],
23 sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)