#! /bin/sh
######################################################################################
# Kritika Karri, 08.04.2017
# Way to run script:
#Usage: ./Run_Jobs.sh
#Example:
#./Run_Jobs.sh
# The result fo this script copies all the Diffexp_v2_genebody (.txt) files from DE analysis (HTSeq Method) and copies in the current directory. These files are then used as input bu the Pearson_Script.R to generate pearson correlation plots and matrices. 
# The . of this script is two folders: 1) Pearson_All (All genes were involved to calculate the pearson) 2) Pearson_Filtered (Genes filtered by rpkm  > 1 are used for calculating the pearson values)
module load gcc/7.2.0
#module load R/3.1.1
#module load R/3.2
#module load R/3.5.0

source ../00_Setup_Pipeline/01_Pipeline_Setup.sh

count=`ls -1 *.txt* 2>/dev/null  | wc -l`
if [ $count != 0 ]
then
rm -rf *.txt
rm -rf *.pdf
rm -rf *.csv
rm -rf DiffExp_*
rm -rf output 
fi

echo "Dataset_DIR:"
echo ${Dataset_DIR}
echo "Dataset_Label:"
echo ${Dataset_Label}
echo "SCRIPT_DIR:"
echo ${SCRIPT_DIR}
cd ..

Level_UP=$(pwd)

mkdir ${Level_UP}/14_final_summary/output

cd ${SCRIPT_DIR}
echo "Script_Directory"
echo ${SCRIPT_DIR}
echo "Level_UP:"
echo ${Level_UP}

	cp -rf  ${Level_UP}/04_TopHat_Paired_End/Job_Summary/TopHat2_Stats_BestMapped.txt  .
        cp -rf  ${Level_UP}/05_Read_Strandness/Job_Summary/Read_Strandness_Stats.txt .
        cp -rf  ${Level_UP}/06_CollectRnaSeqMetrics/Job_Summary/CollectRnaSeqMetrics_Stats.txt  .
        cp -rf  ${Level_UP}/07_CollectInsertSizeMetrics/Job_Summary/CollectInsertSizeMetrics_Plots.pdf .
        cp -rf  ${Level_UP}/08b_Extract_Counts_featureCounts/Job_Summary/featureCounts_summary_Illumina_GTF.txt  .
        cp -rf  ${Level_UP}/08b_Extract_Counts_featureCounts/Job_Summary/featureCounts_summary_LncRNA_Exon_Collapsed_GTF.txt  .
 	cp -rf ${Level_UP}/13b_Pearson_Correlation_featureCounts/PCA* .
        cp -rf ${Level_UP}/13c_Pearson_Correlation_featureCounts_lncRNA/PCA* .
	
	mv *.txt ${Level_UP}/14_final_summary/output
	mv *.pdf ${Level_UP}/14_final_summary/output
	mv *.csv ${Level_UP}/14_final_summary/output
	


#echo 'Setup_Pipeline_DIR :' $Setup_Pipeline_DIR
cc=$(find ../ -name "*b_DiffExp_*_featureCounts" | wc -l);
echo $cc
start=1
for((i=$start; i <=$cc; i++))
 { 	
	cp -rf ${Level_UP}/09b_DiffExp_${i}_featureCounts/Summary_Differential_Expression/SEGEX_Upload_Files/Individual/*_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt .
	cp -rf ${Level_UP}/09b_DiffExp_${i}_featureCounts/Summary_Differential_Expression/SEGEX_Upload_Files/Individual/*_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt .
	cp -rf ${Level_UP}/09c_DiffExp_${i}_lncRNA_featureCounts/Summary_Differential_Expression/SEGEX_Upload_Files/Individual/*_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt .
        cp -rf ${Level_UP}/09c_DiffExp_${i}_lncRNA_featureCounts/Summary_Differential_Expression/SEGEX_Upload_Files/Individual/*_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt .
}
	mv *.txt ${Level_UP}/14_final_summary/output	

echo "All files copied  Done "