autoParams

#!/bin/bash

# Automagic script to launch motifParams on many regulators

if [ "$#" -lt 2 ]; then
    echo 'autoParams MOTIF_DIR FASTA_FILE'
    exit 65
fi

MOTIF_DIR=$1
FASTA_FILE=$2

for reg in $(ls -d $MOTIF_DIR/*/)
do
    regulator=$(echo $reg | awk 'BEGIN {FS = "/"}; {print ( $(NF-1) )}')
	for meme in $(ls -d $reg/*/)
	do
	    echo $regulator
	    ./motifParams $meme/meme.txt $FASTA_FILE
	done
done