# 31 Dec 2010
# Run TRAP and PASTAA on 38405 hg18 merged-TSS regions, using TRANSFAC 9.3

# 25 Dec 2010
# Run TRAP and PASTAA on all TRANSFAC 9.3 PWMs, and on low-CpG and high-CpG merged hg18 knownGene TSS regions (-2/+1kb)

# From Helge -
#*Compile C scripts
#g++ PSCM_to_PSEM.c  -o PSCM_to_PSEM
#g++ TRAP.c  -o TRAP
#g++ PASTAA.c  -o PASTAA

#Run C programs
#./PSCM_to_PSEM  matrices.transfac.txt  >  matrices.energy.txt
#./TRAP  matrices.energy.txt  200bp_mouse_promoters.fasta  >  200bp_mouse_promoters.affinities.txt
#./PASTAA  200bp_mouse_promoters.affinities.txt  livergenes.txt  |  sort -k2,2 -rg  >  enrichment.txt
#=============================================================================

# 64-bit Linux, CentOS 5.5

BINDIR=/home/grobertson/linux_x86_64/PASTAA/PASTAA
WRKDIR=/...

FADIR=$WRKDIR
FA=kg-38405-merged-TSS.20101225.fa

MATRICES=transfac.9.3.matrix.dat.txt
ENERGIES=energies.$MATRICES
AFFINITIES=affinities.$ENERGIES

KDSEQIDS=114-KD-DE-SEQIDs.txt
CTLSEQIDS=346-CTL-DE-SEQIDs.txt

echo "fa: $FA"
echo "matrices: $MATRICES"
echo "energies: $ENERGIES"
echo "affinities: $AFFINITIES"
echo "KD-DE seqIDs: $KDSEQIDS"
echo "CTL-DE seqIDs: $CTLSEQIDS"

echo "1. Convert PWMs to energy matricies"
echo "use TRANSFAC 9.3 PWM file (TRAP needs integer PWMS!)"
echo "$BINDIR/PSCM_to_PSEM $WRKDIR/$MATRICES > $WRKDIR/$ENERGIES"
$BINDIR/PSCM_to_PSEM $WRKDIR/$MATRICES > $WRKDIR/$ENERGIES

echo
echo "2. Score affinities of TSS regions"
echo "$BINDIR/TRAP $WRKDIR/$ENERGIES $FADIR/$FA > $WRKDIR/$AFFINITIES"
$BINDIR/TRAP $WRKDIR/$ENERGIES $FADIR/$FA > $WRKDIR/$AFFINITIES

echo "rank TFs for a promoter FA set"
echo "114 KD-DE regions"
echo "$BINDIR/PASTAA $WRKDIR/$AFFINITIES $WRKDIR/$KDSEQIDS | sort -k2,2 -rg > $WRKDIR/enrichment.$KDSEQIDS"
$BINDIR/PASTAA $WRKDIR/$AFFINITIES $WRKDIR/$KDSEQIDS | sort -k2,2 -rg > $WRKDIR/enrichment.$KDSEQIDS

echo
echo "326 CTL-DE regions"
echo "$BINDIR/PASTAA $WRKDIR/$AFFINITIES $WRKDIR/$CTLSEQIDS | sort -k2,2 -rg > $WRKDIR/enrichment.$CTLSEQIDS"
$BINDIR/PASTAA $WRKDIR/$AFFINITIES $WRKDIR/$CTLSEQIDS | sort -k2,2 -rg > $WRKDIR/enrichment.$CTLSEQIDS

echo "done"