#ReNameFiles2.sh renames files in the /ZScores and /QC folders of each EXP_ to reflect the user labeling of the Exp_'s
#The ZScores_Interaction.csv file is required by many processes and therefore its name must be preserved
pwd
#Preserve ZScores_Interaction.csv in ZScores_Interaction.csvx temporary file
cp ZScores_Interaction.csv ZScores_Interaction.csvx
#Determine which /Exp_ this script is called from
cd ../
ExpDir="${PWD##*/}"
cd ZScores

if [ "$ExpDir" = "Exp1" ];then j=1;fi #Cannot have spaces in declaratives. Must have spaces in compare statements
if [ "$ExpDir" = "Exp2" ];then j=2;fi #Must use j to make value an integer
if [ "$ExpDir" = "Exp3" ];then j=3;fi
if [ "$ExpDir" = "Exp4" ];then j=4;fi
echo $j  #j makes value an integer for use in the following extraction of data from StudyInfo.csv spreadsheet
#-------------
#Extract the user's experiment Name stored in StudyInfo.csv found in../Code folder
eCollection=( $(cut -d ',' -f2 ../../Code/StudyInfo.csv) )
expName="${eCollection[$j]}"
echo $expName

#Remove double quotes that are an artifact of the .csv spreadsheet cells
temp=`echo $expName | sed 's/.\(.*\)/\1/' | sed 's/\(.*\)./\1/'`
expName=$temp
echo $expName  #display the extracted user experiment label without the double quotes

#Rename csv files
#The Sumary...csv files have a leading "white space" that the basename removes. Therefore must directly rename the #Summary files without the whitespace.
mv  " "SummaryStats_BackgroundStrains.csv SummaryStats_BackgroundStrains.csv
mv  " "SummaryStats_ALLSTRAINS.csv SummaryStats_ALLSTRAINS.csv
for i in $(ls *.csv); do
mv $i $(basename $i .csv)___$expName.csv
done

#restore ZScores_Interaction.csv
mv ZScores_Interaction.csvx ZScores_Interaction.csv

#Rename pdf files
for i in $(ls *.pdf); do
mv $i $(basename $i .pdf)___$expName.pdf    
done

#Rename .html files
for i in $(ls *.html); do
mv $i $(basename $i .html)___$expName.html   
done

pwd
echo $expName

#Rename csv files
cd QC #Step into the ../QC directory
#Rename csv files#Rename csv files
for i in $(ls *.csv); do
mv $i $(basename $i .csv)___$expName.csv
done
#Rename pdf files
for i in $(ls *.pdf); do
mv $i $(basename $i .pdf)___$expName.pdf    
done
#Rename .html files
for i in $(ls *.html); do
mv $i $(basename $i .html)___$expName.html   
done

cd .. #Return to ../ZScores folder