#REMcMaster.sh Is to perform all REMc task and to operate from source directory REMc
# Gain permissions to the perl scripts for GTF
currentDir="$PWD"
GTFpath="$currentDir/GTF"
chmod -R u+rwx "$GTFpath"
#Step 0 Perform JoinInteractExps3dev.R to create the "REMcRdy_lm_only.csv" and "Shift_only.csv" files
Rscript JoinInteractExps3dev.R 

#Step1 Perform REMc java utility using file input file REMcRdy_lm_only.csv 
#and producing REMcRdy_lm_only.csv-finalTable.csv
sh ./REMcJar2.sh
wait
#wait isn't holding process until Jar is complete. Should take at least 3minuites

#Step 2 
if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
    #Jarflag= 1
    #echo "Jarflag =  $Jarflag"
echo "REMcJar... .sh completed"
else
echo "REMcJar failed"
wait
exit
fi
echo "start Step2"
#Step2 If REMcJar successfully produces "REMcRdy_lm_only.csv-finalTable.csv" 
  #then add shift values back to the "REMcRdy_lm_only.csv-finalTable.csv"
  #and output it as "REMcWithShift.csv" to be used to produce the REMc Heatmaps.
if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
    Rscript ./AddShiftVals2.R 
    wait
    echo "AddShiftVals2.R executed"
 fi

#Step3 Execute REMcHeatmaps_zscores.R contingent upon "REMcWithShift.csv" being created.
cd REMcHeatmaps
if [ -f "REMcWithShift.csv" ]; then
      echo "REMcWithShift.csv exists."
fi

rm *.pdf  #Remove .pdf files to be sure of a clean 'slate'

cd ..
      Rscript REMcHeatmaps_zscores.R
      echo "REMcHeatmaps executed"
      wait
cd REMcHeatmaps
            pdftk *.pdf output compiledREMcHeatmaps.pdf

#Step3b Execute REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R contingent upon "REMcWithShift.csv" being created in ../REMcHeatmapsWithHomology.
#cp ./Homology/REMcWithShift.csv ./REMcHeatmapsWithHomology/REMcWithShift.csv
cp ./REMcWithShift.csv ../REMcHeatmapsWithHomology/
cd ../REMcHeatmapsWithHomology
if [ -f "REMcWithShift.csv" ]; then
      echo "REMcWithShift.csv exists."
fi
      rm ./Homology/*.pdf  #Remove .pdf files to be sure of a clean 'slate'
      rm ./Homology/*.csv  #Remove .csv files to be sure of a clean 'slate'

      Rscript REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R REMcWithShift.csv Homology 17_0503_DAmPs_Only.txt Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
    
      echo "REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R executed"
      wait
cd Homology
      pdftk *.pdf output compiledREMcHomologyHeatmaps.pdf
      
echo "pdftk executed"
cd ../..
    
#Step4 Begin the process of GTF contingent upon "REMcRdy_lm_only.csv-finalTable.csv"
# being produced by "REMcJar.sh" (Step1)
if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
     python3 DconJG2.py REMcRdy_lm_only.csv-finalTable.csv GTF/Process/
    #python2 DconJG.py REMcRdy_lm_only.csv-finalTable.csv 12 GTF/Process/
else
    echo "DconJG2.py failed"
    wait
    exit

fi

if [ -f "GTF/Process/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
  echo "Begin copying REMcRdy_lm_only to /Function and /Component"
  cp -r GTF/Process/REMcRdy_lm_only GTF/Function/
  echo "Copy to Function complete"
  wait
  cp -r GTF/Process/REMcRdy_lm_only GTF/Component/
  echo "Copy to Component complete"

  wait

else
    echo "COPY failed"
    wait
    exit

fi

if [ -f "GTF/Function/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
   echo "Begin concurrent running of GTF tasks"
   sh ./mProcess.sh &
   sh ./mFunction.sh &
   sh ./mComponent.sh &

   echo "GTF ontologies run in background"

else
    echo "GTFontologies failed"
    
fi

wait

Rscript CompileGTF.R
wait 

echo "REMcMaster3.sh Finished"