#This is a 'master associated' sh script to operate from the REMc source directory
#It is an altered Process.sh with a cd at start 

cd GTF/Process
#Begin the Original Process.sh
#!/bin/bash
# this one code will load the terms2tsv_v4.pl to add two more columns: one is the gene names, the other one is the cluster name column

set $1 = ORF_List_Without_DAmPs.txt #ORFs_w_DAmP_list.txt #ORF_List_Without_DAmPs.txt
set $2 = REMcRdy_lm_only/*.txt
#paths= ORF_List_Without_DAmPs.txt:REMcRdy_lm_only/*.txt
#if [ $argv -lt 2 ]; then
	
#echo "Usage: ./example_v4.sh backgroundFilePath geneListsFolder"

#else
	for i in ${*:2}       
	do
		#echo $1
		#echo $i
		./analyze_v2.pl -an gene_association.sgd -as P -o gene_ontology_edit.obo -b $1 $i
		./terms2tsv_v4.pl $i.terms > $i.tsv
	done
#fi
wait
echo "Process complete"
#Concatinatethe Process ontology outputs from the /REMcReady_lm_only folder
#python2 Concatenate_GTF_results.py ./REMcReady_lm_only/ ProcessResultsTest.txt
pwd 
python3 Concatenate_GTF_results.py REMcRdy_lm_only/ ProcessResults.txt
#python2 ConcatGTFdebug.py REMcRdy_lm_only/ ProcessResults.txt
#python2 ConcatGTFdebug.py REMcRdy_lm_only/ PresDebug4.txt

wait
echo "Process Concatenate complete"
pwd
#exit