3 args <- commandArgs(trailingOnly=TRUE)
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)]
15 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
19 setkey(geneimprint,"Gene")
22 union(gsub("[\\*\\@]$","",parent[,Gene]),
23 gsub("[\\*\\@]$","",geneimprint[,Gene]))
25 gene.aliases <- fread(args[3])
26 setkey(gene.aliases,"alias")
29 sort(sapply(imprinted.genes,
30 function(x){if(is.na(gene.aliases[x,gene])) {
33 return(gene.aliases[x,gene])
36 write.table(file=args[length(args)],
38 sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)