annotate mtls_analyze/annotate_mtls.R @ 4:b465306d00ba draft default tip

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debug = F
# Read in Data
if (debug == T) {
  mtls <- read.delim("~/code/scorchR-annotate_mtls/mtls.xls", quote="", stringsAsFactors=F)
  annotation <- read.delim("~/code/scorchR-annotate_mtls/gene_annotation.txt", header=T, stringsAsFactors=F)
  threshold <- 100000  
} else {
  cmd <- commandArgs(trailingOnly = T)
  mtls <- read.delim(cmd[1], quote="", stringsAsFactors=F)
  annotation <- read.delim(cmd[2], header=T, stringsAsFactors=F)
  threshold <- as.numeric(cmd[3])
}



# Get the median summit
summits <- sapply(strsplit(mtls[ ,"summit"], split="_"), function(x) {median(as.numeric(x))})
# Extract every tss
tss <- apply(annotation,1,function(x) {
  if (x["strand"]=="+"){
    return(as.numeric(x["txStart"]))
    }else{
      return(as.numeric(x["txEnd"]))
      }
  })


# Get each Chromosome
chromosomes <- unique( mtls[,"chr"])

# Set up output:
trgt <- character(length = length(summits))

# Loop through Chromosomes
for (chromosome in chromosomes){
  cat(chromosome, "\n")
  chr.ix.tss <- which(annotation[ ,"chrom"]==chromosome)
  chr.ix.summits <- which(mtls[ ,"chr"]==chromosome)
  

  cat(length(chr.ix.summits), " -summits\n",
      length(chr.ix.tss), " -tss\n")
  if (length(chr.ix.summits)>0 && length(chr.ix.tss)>0) {
  # Loop through Summits
  for(summit.ix in chr.ix.summits) {
    #cat("Summit = ", summit.ix, class(summit.ix),"\n")
    distances <- abs(tss[chr.ix.tss] - summits[summit.ix])
    closest.ix.tss <- which(distances == min(distances))[1]
    if(!is.na(closest.ix.tss) && !is.na(distances[closest.ix.tss])) {
    #print(closest.ix.tss)
    if (distances[closest.ix.tss] < threshold) {
      
      trgt[summit.ix] <- annotation[chr.ix.tss, "name2"][closest.ix.tss]
   
#       cat("A distance of ",
#           distances[closest.ix.tss],
#           " was found for the mtl summit located at: ",
#           chromosome,
#           ": ",
#           summits[summit.ix],
#           " and TSS located at: ",
#           chromosome,
#           ": ",
#           tss[chr.ix.tss][closest.ix.tss],
#           "\n")
    }
    }
  }
  } else {
    cat("chromosome", chromosome, " either has no transcripts or no peaks in this experiment. \n")
  }
  output <- cbind(mtls, trgt)
}

write.table(output, file="annotated_mtls.xls", sep="\t",row.names=F, quote=F)