3 args <- commandArgs(trailingOnly=TRUE)
5 geneimprint <- fread(args[1])
6 geneimprint <- geneimprint[!grepl(" ",Gene),]
8 geneimprint <- geneimprint[Status!="Not Imprinted",]
9 geneimprint <- geneimprint[Status!="Unknown",]
11 parent <- fread(args[2])
12 ### fix up the 0 prefixed chromosomes
13 parent[,chr:=gsub("^0","",chromosome)]
14 ### remove aliases in ()
15 parent[,Gene:=gsub("\\s*\\([^\\)]+\\)\\s*","",gene)]
16 ### remove aliases after ,
17 parent[,Gene:=gsub("\\s*,\\s*.+","",Gene)]
19 parent <- parent[grepl("^[A-Z0-9]+$",Gene),]
23 setkey(geneimprint,"Gene")
26 union(gsub("[\\*\\@]$","",parent[,Gene]),
27 gsub("[\\*\\@]$","",geneimprint[,Gene]))
29 gene.aliases <- fread(args[3])
30 setkey(gene.aliases,"alias")
33 sort(sapply(imprinted.genes,
34 function(x){if(is.na(gene.aliases[x,gene])) {
37 return(gene.aliases[x,gene])
40 write.table(file=args[length(args)],
42 sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)