File refactoring

workflow/.old/templates/qhtcp/mFunction.sh

@@ -0,0 +1,32 @@
+#This is a 'master associated' sh script to operate from the /REMc source directory
+#It is an altered Function.sh with a cd at start 
+
+cd GTF/Function
+#Begin the Original Function.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 #ORF_List_Without_DAmPs.txt #ORFs_w_DAmP_list.txt
+set $2 = 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 F -o gene_ontology_edit.obo -b $1 $i
+		./terms2tsv_v4.pl $i.terms > $i.tsv
+	done
+wait
+echo "Function complete"
+#fi
+#Concatinatethe Process ontology outputs from the /REMcRdy_lm_only folder
+python3 Concatenate_GTF_results.py REMcRdy_lm_only/ FuctionResults.txt
+wait
+echo "FunctionConcatenate complete"
+pwd
+#exit