R/deseq2/dodseq.r

   1 #!/usr/bin/env littler
   2
   3 if (length(argv)<2) {
   4     cat("Usage ./dodseq.r <prefix.featureCounts.txt> <Nctl,Nexp> [prefix]\n")
   5     quit()
   6 }
   7 inFile <- argv[1]
   8 ExpCnt <- as.numeric(unlist(strsplit(argv[2],',',fixed=T)))
   9 outP <- argv[3]
  10 if (length(argv)==2) {
  11     outP <- unlist(strsplit(inFile,'.',fixed=T))[1]
  12 }
  13 cat(sep='',"[!]From [",inFile,"],Design [",ExpCnt[1],':',ExpCnt[2],"],Prefix [",outP,"].\n")
  14
  15 countdata <- read.table(inFile, header=TRUE, row.names=1)
  16 countdata <- countdata[ ,6:ncol(countdata)]
  17 colnames(countdata) <- gsub("^alnSTAT\\.", "", colnames(countdata))
  18 colnames(countdata) <- gsub("Aligned\\.sortedByCoord\\.out\\.[sb]am$", "", colnames(countdata))
  19 countdata <- as.matrix(countdata)
  20
  21 tFileDim <- dim(countdata)
  22 tExpSize <- ExpCnt[1]+ExpCnt[2]
  23 if ( tFileDim[2] != tExpSize ) {
  24     cat("[x]Design size",tExpSize,"not matching with file column size",tFileDim[2],"!\n[!]File columns:[")
  25     cat(sep=',',colnames(countdata))
  26     cat("].\n")
  27     quit()
  28 }
  29
  30 print(head(countdata))
  31 cat(colnames(countdata),"\n")
  32 cat(dim(countdata),"\n")