get_expr.sh

#!/bin/bash


WHERE=$1

for file in $WHERE/*.txt
        do
        TAD=$(basename $file _list_genes.txt)
	mkdir -p $WHERE/$TAD
	for gene in $(cat $file)
		do
		head -n 1 /work/gad/shared/analyse/Integration/RNA_SEQ/normalized_counts.csv >> $WHERE/$TAD/$gene.txt
		grep $gene /work/gad/shared/analyse/Integration/RNA_SEQ/normalized_counts.csv >> $WHERE/$TAD/$gene.txt
	done
done