combine_imprinted_genes.R

   1 library(data.table)
   2
   3 args <- commandArgs(trailingOnly=TRUE)
   4
   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)]
  13
  14 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
  15 setkey(parent,"Gene")
  16 setkey(geneimprint,"Gene")
  17
  18 imprinted.genes <-
  19     union(parent[,Gene],geneimprint[,Gene])
  20
  21 write.table(file=args[length(args)],
  22             imprinted.genes,
  23             sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
  24