compare two time course expression, find the changing genes, clustering them and find the enriched motif

cmpseries_pipeline.sh

if [[ $# -lt 2 ]] ; then
	echo "Usage: cmpseries_pipeline.sh SeriesA.tsv SeriesB.tsv"
	exit 0
fi
x=${1##*/} i=${x%.*} 
y=${2##*/}
j=${y%.*} 
resp="${i}_vs_${j}.resp.txt"
echo "respondGenes.py -i $1  $2  -o  $resp"
respondGenes.py -i $1  $2  -o  $resp
oi=$i.${resp%.*}.tsv 
echo "getsubset.py -i $resp -t $1 -o $oi"
getsubset.py -i $resp -t $1 -o $oi
oj=$j.${resp%.*}.tsv  
echo "getsubset.py -i $resp -t $2 -o $oj" 
getsubset.py -i $resp -t $2 -o $oj 
ocmp=${resp%.*}.cmp.tsv
echo "CmpSeries $oi $oj > $ocmp"
CmpSeries $oi $oj > $ocmp
diffgene="${ocmp%.*}.diff.tsv"
awk '$3<0.5' $ocmp  > $diffgene
diffi=${oi%.*}.diff.tsv
diffj=${oj%.*}.diff.tsv
getsubset.py -i $diffgene -t $1 > $diffi 
getsubset.py -i $diffgene -t $2 > $diffj
oakmeans=${diffgene%.*}.akmeans.tsv
akmeans.py -i $diffi $diffj -M -o $oakmeans 
awk -v o=${oakmeans%.*} 'NR >= 2 { print >> o".group."$6 }' $oakmeans
for f in *.group.* 
do
	hg19_genelist_corepromoter_motif_tfbs_enrichment.py -i $f -b $resp -o ${f}.motif.out
done