combine_imprinted_genes.R

   1 library(data.table)
   2
   3 args <- commandArgs(trailingOnly=TRUE)
   4
   5 geneimprint <- fread(args[1])
   6 geneimprint <- geneimprint[!grepl(" ",Gene),]
   7 parent <- fread(args[2])
   8 ### fix up the 0 prefixed chromosomes
   9 parent[,chr:=gsub("^0","",chromosome)]
  10 ### remove aliases in ()
  11 parent[,Gene:=gsub("\\s*\\([^\\)]+\\)\\s*","",gene)]
  12 ### remove aliases after ,
  13 parent[,Gene:=gsub("\\s*,\\s*.+","",Gene)]
  14
  15 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
  16
  17
  18 setkey(parent,"Gene")
  19 setkey(geneimprint,"Gene")
  20
  21 imprinted.genes <-
  22     union(gsub("[\\*\\@]$","",parent[,Gene]),
  23           gsub("[\\*\\@]$","",geneimprint[,Gene]))
  24
  25 gene.aliases <- fread(args[3])
  26 setkey(gene.aliases,"alias")
  27
  28 imprinted.genes <-
  29     sort(sapply(imprinted.genes,
  30            function(x){if(is.na(gene.aliases[x,gene])) {
  31                            return(x)
  32                        } else {
  33                            return(gene.aliases[x,gene])
  34                        }}))
  35
  36 write.table(file=args[length(args)],
  37             imprinted.genes,
  38             sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
  39