options(stringsAsFactors=F)
args <- commandArgs(T)
LRM.in.lnc.file <- args[1]
LRM.info.file <- args[2]

LRM.in.lnc <- read.table(LRM.in.lnc.file, header=F)
colnames(LRM.in.lnc) <- c("transcript_id", "motif", "position", "sequence")
LRM.info <- read.table(LRM.info.file, header=T, sep="\t", check.names=F)
out <- merge(LRM.in.lnc, LRM.info, by.x="motif", by.y="motif identifier")[,c("position", "sequence", "motif name", "localization contribution", "description", "reference (PMID)")]
#sort by position
f <- function(x){return(as.integer(strsplit(x,"-")[[1]][1]))}
start <- unlist(lapply(out$position, f))
out <- out[order(start),]
write.table(out, LRM.in.lnc.file, row.names=F, col.names=T, sep="\t", quote=F)