RNGS:

#!/usr/bin/Rscript

#Usage:

#R CMD INSTALL RNGS_0.1.0.tar.gz

#Rscript  Rscript ~/R/lib64/R/library/RNGS/bin/RNGS_interactive_model.r


  cat("Do you want to download SRA files?\n")

  input<-file('stdin', 'r')
  row <- readLines(input, n=1)

  print(row)

  if(row=="Yes") {

    cat("please defne the url:\n")

    input<-file('stdin', 'r')
    input.file.dir <- readLines(input, n=1)

    #input.file.dir=row

    cat("please defne the output file directory:\n")

    input<-file('stdin', 'r')
    output.file.dir <- readLines(input, n=1)

    #out.file.dir=row

    #cat("please defne genome name:\n")

    #input<-file('stdin', 'r')
    #genome <- readLines(input, n=1)

    R_lib=.libPaths()[1]

    cmd1="bsub -P bbc -J \"RunRNGS\" -o %J.RunRNGS.log -e %J.RunRNGS.err -W 72:00 -n 8 -q general -u aimin.yan@med.miami.edu"
    cmd2=paste0("wget -c -r -nd -np -L ",input.file.dir," ","-P ",output.file.dir)

    system(paste0(cmd1," ",cmd2))

#    cmd2=paste0()

#    system(cmd2)

    cat("Finished downloading SRA ...\n")
    }else{

    cat("Do you want to convert SRA files to fastq files?\n")

    input<-file('stdin', 'r')
    row <- readLines(input, n=1)

    print(row)

    if(row=="Yes") {

      cat("please give input SRA file:\n")

      input<-file('stdin', 'r')
      input.file.dir <- readLines(input, n=1)

      #input.file.dir=row

      cat("please define the output file directory for this conversion:\n")

      input<-file('stdin', 'r')
      output.file.dir <- readLines(input, n=1)

      R_lib=.libPaths()[1]

      cmd1="bsub -P bbc -J \"fastq-dump\" -o %J.fastq-dump.log -e %J.fastq-dump.err -W 72:00 -n 8 -q general -u aimin.yan@med.miami.edu"
      cmd2=paste0("fastq-dump --split-3 ",input.file.dir," ","-O ",output.file.dir)

      system(paste0(cmd1," ",cmd2))

      #cmd2=paste0()
      #system(cmd2)

      system("wait")
      cat("Finished converting SRA ...\n")

    }else{

      cat("Do you want to use STAR to perform alignment?\n")

      input<-file('stdin', 'r')
      row <- readLines(input, n=1)

      print(row)

      if(row=="Yes") {


        cat("Is your RNA-Seq data un-stranded?\n")

        input<-file('stdin', 'r')
        row <- readLines(input, n=1)

        if(row=="Yes"){
          strand="--outSAMstrandField introMotif"
        }else
        {
         strand=""
        }

        cat("please give input fastq file dir:ex(/scratch/projects/bbc/aiminy_project/DoGsFastq)\n")
        #/projects/scratch/bbc/GOSJ/ExampleData/
        input<-file('stdin', 'r')
        input.file.dir <- readLines(input, n=1)

        library(RNGS)
        re<-RNGS:::GetFastqFiles(input.file.dir)

        #print(class(re))
        #print(dim(re))
        #print(re)

         cat("please specify gene annotation file(GTF),ex(/projects/ctsi/bbc/Genome_Ref/Homo_sapiens/UCSC/hg19/Annotation/Genes/gene.gtf)\n or
/projects/ctsi/bbc/Genome_Ref/Homo_sapiens/UCSC/hg19/Annotation/Genes/refGene.txt\n")
         #/nethome/yxb173/Genome_Ref/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf
         input<-file('stdin', 'r')
         input.gtf.file <- readLines(input, n=1)

         cat("please specify STARindex file :ex(/projects/ctsi/bbc/Genome_Ref/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/)\n")
         #/nethome/yxb173/Genome_Ref/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/
         input<-file('stdin', 'r')
         STAR.index.file <- readLines(input, n=1)


         cat("please define the output file directory for this alignment:ex(/scratch/projects/bbc/aiminy_project/DoGsAlignmentStar/)\n")
         #/projects/scratch/bbc/GOSJ/ExampleData/
         input<-file('stdin', 'r')
         output.file.dir <- readLines(input, n=1)


         if (!dir.exists(output.file.dir))
         {
           dir.create(output.file.dir)
         }


        #
         R_lib=.libPaths()[1]

         cat("please define the number of core to be used:\n")
         #8
         input<-file('stdin', 'r')
         Ncores <- readLines(input, n=1)


          cmd1="bsub -P bbc -J \"STAR-alignment\" -o %J.STAR-alignment.log -e %J.STAR-alignment.err -W"
          cmd2="72:00 -n 8 -q bigmem -R 'rusage[mem=36864] span[hosts=1]' -u aimin.yan@med.miami.edu"

          cmd3=paste("STAR",strand,"--genomeLoad NoSharedMemory --runThreadN",Ncores,"--sjdbGTFfile",collapse = " ")
          cmd4=paste(input.gtf.file,"--outFileNamePrefix",collapse = " ")

          cmd44=paste("--genomeDir",STAR.index.file,collapse = " ")


          cmd11="bsub -w \"done(\"STAR-alignment\")\" -P bbc -J \"samtools-sort\" -o %J.samtools-sort.log -e %J.samtools-sort.err -W"

          #cmd.wait="wait"

          #CONVERTING SAM DIRECTLY TO A SORTED BAM FILE

          #cmd6=paste("samtools view -bS -@", Ncores)



          #system(paste0(cmd1," ",cmd2))


          for(i in 1:dim(re)[1]){
           cmd5=paste("--readFilesIn",re[i,1],re[i,2],collapse = " ")

           sample.name=unlist(strsplit(basename(re[i,1]),"_"))[1]

           cmd.each.sample=paste0(output.file.dir,"STAR_",sample.name)

           system(paste(cmd1,cmd2,cmd3,cmd4,cmd.each.sample,cmd44,cmd5,collapse = " "))

           #system(cmd.wait)

           #cmd7=paste0(cmd.each.sample,"Aligned.out.sam | samtools sort -@ ",Ncores," - ",paste0(cmd.each.sample,"STAR_out.sorted"))

           #cmd8=paste0(cmd.each.sample,"STAR_out.sorted")

           cmd6=paste0("sh ",R_lib,"/RNGS/bin/Sam2BamAndSorting.sh ",cmd.each.sample," ",Ncores)

           system(paste(cmd11,cmd2,cmd6,collapse = " "))

          }



        # #cmd2=paste0()
        # #system(cmd2)
        #
        # system("wait")



         #system(paste(cmd1,cmd6,cmd7,cmd8,collapse = " "))


          #table_cmd3 = cbind(com="samtools index", file=paste0(out_dir1,"/STAR_out.sorted.bam"))

        # cat("Finished converting SRA ...\n")

      }else{


        cat("Do you want to get count using the sorted Bam files ?\n")

        input<-file('stdin', 'r')
        row <- readLines(input, n=1)

        print(row)

        if(row=="Yes"){


          cat("please give input bam file:\n")
          #/projects/scratch/bbc/GOSJ/ExampleData/STAR_SRR1660309STAR_out.sorted.bam
          input<-file('stdin', 'r')
          input.bam.file <- readLines(input, n=1)

          #library(RNGS)
          #re<-GetFastqFiles(input.file.dir)

          #print(class(re))
          #print(dim(re))
          #print(re)

          cat("please specify gene annotation file(GTF):\n")
          #/nethome/axy148/Annotation_ref/Homo_sapiens.GRCh38.84.processed.sorted.2.gtf

          input<-file('stdin', 'r')
          input.gtf.file <- readLines(input, n=1)


          cat("please define the output file directory for this alignment:\n")
          #/projects/scratch/bbc/GOSJ/ExampleData/
          input<-file('stdin', 'r')
          output.file.dir <- readLines(input, n=1)

          R_lib=.libPaths()[1]

          cat("Do you want to keep \"--keepMultiMapped\" :\n")
          #Yes or No
          input<-file('stdin', 'r')
          choose.count <- readLines(input, n=1)

          if(choose.count=="Yes"){
          output.file.dir<-paste0(output.file.dir,basename(input.bam.file),"_QoRTCounts_1")
          cmd11="bsub -P bbc -J \"QoRT-count-1\" -o %J.QoRT-count-1.log -e %J.QoRT-count-1.err -W"
          cmd2="72:00 -n 8 -q bigmem -R 'rusage[mem=36864] span[hosts=1]' -u aimin.yan@med.miami.edu"
          cmd6=paste("sh",paste0(R_lib,"/RNGS/bin/UseQoRTs2GetCounts1.sh"),input.bam.file,input.gtf.file,output.file.dir,collapse = " ")}else
          {
            output.file.dir<-paste0(output.file.dir,basename(input.bam.file),"_QoRTCounts_2")
            cmd11="bsub -P bbc -J \"QoRT-count-2\" -o %J.QoRT-count-2.log -e %J.QoRT-count-2.err -W"
            cmd2="72:00 -n 8 -q bigmem -R 'rusage[mem=36864] span[hosts=1]' -u aimin.yan@med.miami.edu"
            cmd6=paste("sh",paste0(R_lib,"/RNGS/bin/UseQoRTs2GetCounts2.sh"),input.bam.file,input.gtf.file,output.file.dir,collapse = " ")
          }

          system(paste(cmd11,cmd2,cmd6,collapse = " "))

        }else{quit()}
      }
    }
    }