## 1) prepare module gene lists as regulons

# modules recomputed by R Sancho 15020212

ls -1 | perl -lne 'if(/(\d+).txt./){ mkdir("D$1"); `mv "$1.txt.panther.txt" "D$1/regulonD$1.txt"` }'
ls -1 | perl -lne 'if(/(\d+).txt./){ mkdir("W$1"); `mv "$1.txt.panther.txt" "W$1/regulonW$1.txt"` }'

## 2) extract regulon sequences 
# NOTE: orths were not properly retrieved, hence not used; 
# brachy seqs were retrieved by mistake instead of barley
nohup make -f regulons.mk all -j 6 &> log.regulons.D
nohup make -f regulons.mk all -j 6 &> log.regulons.W


## 3) discover motifs
nohup make -f peak-regulons.mk all -j 6 &> log.peak.D
nohup make -f peak-regulons.mk all -j 6 &> log.peak.W


## 4) compute GO enrichment
nohup make -f go.mk all -j 6 &> log.go.D
nohup make -f go.mk all -j 6 &> log.go.W

perl report.pl modulesD
perl report.pl modulesW