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nfrDynAna2MatrixGene
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nfrDynAna2MatrixGene
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#!/bin/bash
#PBS -l nodes=1:ppn=4
GENOME="mm9"
#### usage ####
usage() {
echo Program: "nfrDynAna2MatrixGene (compute matrix containing activity features corresponding to genes in BED format)"
echo Author: BRIC, University of Copenhagen, Denmark
echo Version: 1.0
echo Contact: pundhir@binf.ku.dk
echo "Usage: nfrDynAna2MatrixGene -i <file> -j <file> [OPTIONS]"
echo "Options:"
echo " -i <file> [input nfr coordinates in BED format]"
echo " [output from nfrDynAna script]"
echo " -j <file> [input gene coordinates in BED format (can be stdin)]"
echo "[OPTIONS]"
echo " -g <string> [genome (default: mm9)]"
echo " -h [help]"
echo
exit 0
}
#### parse options ####
while getopts i:j:g:h ARG; do
case "$ARG" in
i) BED_FILE=$OPTARG;;
j) GENE_FILE=$OPTARG;;
g) GENOME=$OPTARG;;
h) HELP=1;;
esac
done
## usage, if necessary file and directories are given/exist
if [ -z "$BED_FILE" -o ! -f "$GENE_FILE" -o "$HELP" ]; then
usage
fi
## populating files based on input genome
if [ "$GENOME" == "mm9" ]; then
GENOME_FILE="/home/pundhir/project/genome_annotations/mouse.mm9.genome"
elif [ "$GENOME" == "hg19" ]; then
GENOME_FILE="/home/pundhir/project/genome_annotations/human.hg19.genome"
else
echo "Presently the program only support analysis for mm9 or hg19"
echo
usage
fi
## create temporary BED file if input is from stdin
if [ "$BED_FILE" == "stdin" ]; then
TMP=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1)
while read LINE; do
echo ${LINE}
done | perl -ane '$line=""; foreach(@F) { $line.="$_\t"; } $line=~s/\t$//g; print "$line\n";' > $TMP
BED_FILE=$TMP
fi
## perform gene centric analysis
<<"COMMENT"
COMMENT
NCOL_GENE_FILE=$(head -n 1 $GENE_FILE | perl -ane 'print scalar(@F);')
NCOL_BED_FILE=$(head -n 1 $BED_FILE | cut -f 1-3,5,16-35,44 | perl -ane 'print scalar(@F);')
#echo -e "$NCOL_GENE_FILE\t$NCOL_BED_FILE"
#cat $GENE_FILE | perl -ane '@enhancer_info=`grep -w $F[3] '$BED_FILE' | cut -f 1-3,5,16-35,44`; if(scalar(@enhancer_info)>0) { for($i=0; $i<scalar(@enhancer_info); $i++) { chomp($_); chomp($enhancer_info[$i]); print "$_\t$enhancer_info[$i]\t1\n"; } } else { chomp($_); print "$_\t.\t-1\t-1\t"; for($i=4;$i<='$NCOL_BED_FILE';$i++) { print ".\t"; } print "0\n"; }' > test1; exit
#intersectBed -a $GENE_FILE -b <(cut -f 1-3,5,18,24,30,35,44 $BED_FILE | grep -v "start") -wao | sortBed -i stdin |
cat $GENE_FILE | perl -ane '@enhancer_info=`grep -w $F[3] '$BED_FILE' | cut -f 1-3,5,16-35,44`; if(scalar(@enhancer_info)>0) { for($i=0; $i<scalar(@enhancer_info); $i++) { chomp($_); chomp($enhancer_info[$i]); print "$_\t$enhancer_info[$i]\t1\n"; } } else { chomp($_); print "$_\t.\t-1\t-1\t"; for($i=4;$i<='$NCOL_BED_FILE';$i++) { print ".\t"; } print "0\n"; }' | perl -ane '
$id="$F[0]_$F[1]_$F[2]_$F[3]";
$mid=sprintf("%0.0f", ($F['$((NCOL_GENE_FILE+1))']+$F['$((NCOL_GENE_FILE+2))'])/2);
if($F[5]=~/\+/ && $F['$((NCOL_GENE_FILE+2))']>0) {
#$dist=$F[2]-$mid;
$dist=$mid-$F[1];
}
elsif($F[5]=~/\-/ && $F['$((NCOL_GENE_FILE+2))']>0) {
#$dist=$mid-$F[1];
$dist=$F[2]-$mid;
}
else {
$dist="NA";
}
if($i==0) {
foreach(@F[0..'$((NCOL_GENE_FILE-1))']) { $des.="$_\t"; $seen{$id}=1; }
$des=~s/\t$//g;
$stage.="$F['$((NCOL_GENE_FILE+3))']";
$h3k27ac.="$F['$((NCOL_GENE_FILE+6))']";
$h3k4me1.="$F['$((NCOL_GENE_FILE+12))']";
$pu1.="$F['$((NCOL_GENE_FILE+18))']";
$cebpa.="$F['$((NCOL_GENE_FILE+23))']";
if($F['$((NCOL_GENE_FILE+24))']=~/^\.$/ && $F['$((NCOL_GENE_FILE+6))']>0) {
$F['$((NCOL_GENE_FILE+24))']="other";
}
if($F['$((NCOL_GENE_FILE+6))']>0) {
$h3k4me1_pregm=$F['$((NCOL_GENE_FILE+11))'];
$h3k4me1_pregm_ko=$F['$((NCOL_GENE_FILE+15))'];
$h3k4me1_gmp=$F['$((NCOL_GENE_FILE+12))'];
$h3k27ac_pregm=$F['$((NCOL_GENE_FILE+5))'];
$h3k27ac_pregm_ko=$F['$((NCOL_GENE_FILE+9))'];
$h3k27ac_gmp=$F['$((NCOL_GENE_FILE+6))'];
$pu1_pregm=$F['$((NCOL_GENE_FILE+17))'];
$pu1_pregm_ko=$F['$((NCOL_GENE_FILE+20))'];
$pu1_gmp=$F['$((NCOL_GENE_FILE+18))'];
$cebpa_pregm=$F['$((NCOL_GENE_FILE+22))'];
$cebpa_gmp=$F['$((NCOL_GENE_FILE+23))'];
}
$cobound.="$F['$((NCOL_GENE_FILE+24))']";
$distance.="$dist";
}
elsif($i>0 && !defined($seen{$id})) {
if(defined($h3k4me1_pregm)) {
$fc_h3k4me1_gmp_pregm = ($h3k4me1_gmp+0.01)/($h3k4me1_pregm+0.01);
$fc_h3k4me1_ko_wt = ($h3k4me1_pregm_ko+0.01)/($h3k4me1_pregm+0.01);
$fc_h3k27ac_gmp_pregm = ($h3k27ac_gmp+0.01)/($h3k27ac_pregm+0.01);
$fc_h3k27ac_ko_wt = ($h3k27ac_pregm_ko+0.01)/($h3k27ac_pregm+0.01);
$fc_pu1_gmp_pregm = ($pu1_gmp+0.01)/($pu1_pregm+0.01);
$fc_pu1_ko_wt = ($pu1_pregm_ko+0.01)/($pu1_pregm+0.01);
$fc_cebpa_gmp_pregm = ($cebpa_gmp+0.01)/($cebpa_pregm+0.01);
} else {
$fc_h3k4me1_gmp_pregm = 1;
$fc_h3k4me1_ko_wt = 1;
$fc_h3k27ac_gmp_pregm = 1;
$fc_h3k27ac_ko_wt = 1;
$fc_pu1_gmp_pregm = 1;
$fc_pu1_ko_wt = 1;
$fc_cebpa_gmp_pregm = 1;
}
print "$des\t$stage\t$h3k27ac\t$h3k4me1\t$pu1\t$cebpa\t$cobound\t$distance\t";
print "$fc_h3k4me1_gmp_pregm\t$fc_h3k4me1_ko_wt\t";
print "$fc_h3k27ac_gmp_pregm\t$fc_h3k27ac_ko_wt\t";
print "$fc_pu1_gmp_pregm\t$fc_pu1_ko_wt\t";
print "$fc_cebpa_gmp_pregm\n";
$des=(); $h3k27ac=(); $h3k4me1=(); $stage=(); $pu1=(); $cebpa=(); $cobound=(); $distance=();
$h3k4me1_pregm=(); $h3k4me1_pregm_ko=(); $h3k4me1_gmp=();
$h3k27ac_pregm=(); $h3k4me1_pregm_ko=(); $h3k27ac_gmp=();
$pu1_pregm=(); $pu1_pregm_ko=(); $pu1_gmp=();
$cebpa_pregm=(); $cebpa_gmp=();
foreach(@F[0..'$((NCOL_GENE_FILE-1))']) { $des.="$_\t"; $seen{$id}=1; }
$des=~s/\t$//g;
$stage.="$F['$((NCOL_GENE_FILE+3))']";
$h3k27ac.="$F['$((NCOL_GENE_FILE+6))']";
$h3k4me1.="$F['$((NCOL_GENE_FILE+12))']";
$pu1.="$F['$((NCOL_GENE_FILE+18))']";
$cebpa.="$F['$((NCOL_GENE_FILE+23))']";
if($F['$((NCOL_GENE_FILE+24))']=~/^\.$/ && $F['$((NCOL_GENE_FILE+6))']>0) {
$F['$((NCOL_GENE_FILE+24))']="other";
}
if($F['$((NCOL_GENE_FILE+6))']>0) {
$h3k4me1_pregm=$F['$((NCOL_GENE_FILE+11))'];
$h3k4me1_pregm_ko=$F['$((NCOL_GENE_FILE+15))'];
$h3k4me1_gmp=$F['$((NCOL_GENE_FILE+12))'];
$h3k27ac_pregm=$F['$((NCOL_GENE_FILE+5))'];
$h3k27ac_pregm_ko=$F['$((NCOL_GENE_FILE+9))'];
$h3k27ac_gmp=$F['$((NCOL_GENE_FILE+6))'];
$pu1_pregm=$F['$((NCOL_GENE_FILE+17))'];
$pu1_pregm_ko=$F['$((NCOL_GENE_FILE+20))'];
$pu1_gmp=$F['$((NCOL_GENE_FILE+18))'];
$cebpa_pregm=$F['$((NCOL_GENE_FILE+22))'];
$cebpa_gmp=$F['$((NCOL_GENE_FILE+23))'];
}
$cobound.="$F['$((NCOL_GENE_FILE+24))']";
$distance.="$dist";
}
else {
$stage.=";$F['$((NCOL_GENE_FILE+3))']";
$h3k27ac.=";$F['$((NCOL_GENE_FILE+6))']";
$h3k4me1.=";$F['$((NCOL_GENE_FILE+12))']";
$pu1.=";$F['$((NCOL_GENE_FILE+18))']";
$cebpa.=";$F['$((NCOL_GENE_FILE+23))']";
if($F['$((NCOL_GENE_FILE+24))']=~/^\.$/ && $F['$((NCOL_GENE_FILE+6))']>0) {
$F['$((NCOL_GENE_FILE+24))']="other";
$h3k4me1_pregm=+$F['$((NCOL_GENE_FILE+11))'];
$h3k4me1_pregm_ko=+$F['$((NCOL_GENE_FILE+15))'];
$h3k4me1_gmp=+$F['$((NCOL_GENE_FILE+12))'];
$h3k27ac_pregm=+$F['$((NCOL_GENE_FILE+5))'];
$h3k27ac_pregm_ko=+$F['$((NCOL_GENE_FILE+9))'];
$h3k27ac_gmp=+$F['$((NCOL_GENE_FILE+6))'];
$pu1_pregm=+$F['$((NCOL_GENE_FILE+17))'];
$pu1_pregm_ko=+$F['$((NCOL_GENE_FILE+20))'];
$pu1_gmp=+$F['$((NCOL_GENE_FILE+18))'];
$cebpa_pregm=+$F['$((NCOL_GENE_FILE+22))'];
$cebpa_gmp=+$F['$((NCOL_GENE_FILE+23))'];
}
$cobound.=";$F['$((NCOL_GENE_FILE+24))']";
$distance.=";$dist";
} $i++; END {
print "$des\t$stage\t$h3k27ac\t$h3k4me1\t$pu1\t$cebpa\t$cobound\t$distance\t";
print "$fc_h3k4me1_gmp_pregm\t$fc_h3k4me1_ko_wt\t";
print "$fc_h3k27ac_gmp_pregm\t$fc_h3k27ac_ko_wt\t";
print "$fc_pu1_gmp_pregm\t$fc_pu1_ko_wt\t";
print "$fc_cebpa_gmp_pregm\n";
}' | perl -ane '
$cobound{"other"}{'stage'}=".";
$cobound{"pu1"}{'stage'}=".";
$cobound{"cebpa"}{'stage'}=".";
$cobound{"pu1,cebpa"}{'stage'}=".";
$cobound{"other"}{'count'}=0;
$cobound{"pu1"}{'count'}=0;
$cobound{"cebpa"}{'count'}=0;
$cobound{"pu1,cebpa"}{'count'}=0;
$cobound{"other"}{'h3k27ac'}=0;
$cobound{"pu1"}{'h3k27ac'}=0;
$cobound{"cebpa"}{'h3k27ac'}=0;
$cobound{"pu1,cebpa"}{'h3k27ac'}=0;
$cobound{"other"}{'h3k4me1'}=0;
$cobound{"pu1"}{'h3k4me1'}=0;
$cobound{"cebpa"}{'h3k4me1'}=0;
$cobound{"pu1,cebpa"}{'h3k4me1'}=0;
$cobound{"other"}{'pu1'}=0;
$cobound{"pu1"}{'pu1'}=0;
$cobound{"cebpa"}{'pu1'}=0;
$cobound{"pu1,cebpa"}{'pu1'}=0;
$cobound{"other"}{'cebpa'}=0;
$cobound{"pu1"}{'cebpa'}=0;
$cobound{"cebpa"}{'cebpa'}=0;
$cobound{"pu1,cebpa"}{'cebpa'}=0;
$cobound{"other"}{'distance'}=();
$cobound{"pu1"}{'distance'}=();
$cobound{"cebpa"}{'distance'}=();
$cobound{"pu1,cebpa"}{'distance'}=();
@stage=split(/\;/,$F[15]);
@h3k27ac=split(/\;/,$F[16]);
@h3k4me1=split(/\;/,$F[17]);
@pu1=split(/\;/,$F[18]);
@cebpa=split(/\;/,$F[19]);
@binding=split(/\;/,$F[20]);
@distance=split(/\;/,$F[21]);
#print "$_\n";
for($i=0; $i<scalar(@binding); $i++) {
#if($h3k27ac[$i] > $cobound{$binding[$i]}{'h3k27ac'}) {
$cobound{$binding[$i]}{'h3k27ac'}+=$h3k27ac[$i];
$cobound{$binding[$i]}{'h3k4me1'}+=$h3k4me1[$i];
$cobound{$binding[$i]}{'pu1'}+=$pu1[$i];
$cobound{$binding[$i]}{'cebpa'}+=$cebpa[$i];
$cobound{$binding[$i]}{'distance'}.="$distance[$i];";
#}
$cobound{$binding[$i]}{'count'}++;
#print "Hello\t$binding[$i]\t$h3k27ac[$i]\t$h3k4me1[$i]\t$pu1[$i]\t$cebpa[$i]\n\n";
}
foreach(@F[0..15]) { print "$_\t"; }
#foreach $keys(keys(%cobound)) {
# if($cobound{$keys}{'count'}>0) {
# $cobound{$keys}{'h3k27ac'}=sprintf("%0.5f", $cobound{$keys}{'h3k27ac'}/$cobound{$keys}{'count'});
# $cobound{$keys}{'h3k4me1'}=sprintf("%0.5f", $cobound{$keys}{'h3k4me1'}/$cobound{$keys}{'count'});
# $cobound{$keys}{'pu1'}=sprintf("%0.5f", $cobound{$keys}{'pu1'}/$cobound{$keys}{'count'});
# $cobound{$keys}{'cebpa'}=sprintf("%0.5f", $cobound{$keys}{'cebpa'}/$cobound{$keys}{'count'});
# }
# print "Hi\t$keys\t$cobound{$keys}{'h3k27ac'}\t$cobound{$keys}{'h3k4me1'}\t$cobound{$keys}{'pu1'}\t$cobound{$keys}{'cebpa'}\n";
#}
if(!defined($cobound{"other"}{'distance'})) { $cobound{"other"}{'distance'}="NA"; } else { $cobound{"other"}{'distance'}=~s/\;$//g; }
if(!defined($cobound{"pu1"}{'distance'})) { $cobound{"pu1"}{'distance'}="NA"; } else { $cobound{"pu1"}{'distance'}=~s/\;$//g; }
if(!defined($cobound{"cebpa"}{'distance'})) { $cobound{"cebpa"}{'distance'}="NA"; } else { $cobound{"cebpa"}{'distance'}=~s/\;$//g; }
if(!defined($cobound{"pu1,cebpa"}{'distance'})) { $cobound{"pu1,cebpa"}{'distance'}="NA"; } else { $cobound{"pu1,cebpa"}{'distance'}=~s/\;$//g; }
printf("%d\t%d\t%d\t%d\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%0.5f\t%s\t%s\t%s\t%s\t", $cobound{"other"}{'count'}, $cobound{"pu1"}{'count'}, $cobound{"cebpa"}{'count'}, $cobound{"pu1,cebpa"}{'count'}, $cobound{"other"}{'h3k27ac'}, $cobound{"pu1"}{'h3k27ac'}, $cobound{"cebpa"}{'h3k27ac'}, $cobound{"pu1,cebpa"}{'h3k27ac'}, $cobound{"other"}{'h3k4me1'}, $cobound{"pu1"}{'h3k4me1'}, $cobound{"cebpa"}{'h3k4me1'}, $cobound{"pu1,cebpa"}{'h3k4me1'}, $cobound{"other"}{'pu1'}, $cobound{"pu1"}{'pu1'}, $cobound{"cebpa"}{'pu1'}, $cobound{"pu1,cebpa"}{'pu1'}, $cobound{"other"}{'cebpa'}, $cobound{"pu1"}{'cebpa'}, $cobound{"cebpa"}{'cebpa'}, $cobound{"pu1,cebpa"}{'cebpa'}, $cobound{"other"}{'distance'}, $cobound{"pu1"}{'distance'}, $cobound{"cebpa"}{'distance'}, $cobound{"pu1,cebpa"}{'distance'});
print "$F[22]\t$F[23]\t$F[24]\t$F[25]\t$F[26]\t$F[27]\t$F[28]\n";' | perl -ane '
$sum=$F[16]+$F[17]+$F[18]+$F[19];
chomp($_);
$class="none";
$distance="none";
if($sum>0) {
$max_index=1; $max=0; $i=1;
foreach(@F[20..23]) {
if($_ > $max) {
$max=$_;
$max_index=$i;
}
$i++;
}
#print "Hello\t$max_index\n\n";
if($max_index==1) { $class="other"; $distance=$F[36]; }
elsif($max_index==2) { $class="pu1"; $distance=$F[37]; }
elsif($max_index==3) { $class="cebpa"; $distance=$F[38]; }
else { $class="pu1,cebpa"; $distance=$F[39]; }
}
print "$_\t$distance\t$class\n";' > $BED_FILE.gene
<<"COMMENT"
intersectBed -a $GENE_FILE -b <(cut -f 1-3,16-35 $BED_FILE | grep -v start) -wao | sortBed -i stdin | cut -f 1-6,8-15,19-38 | perl -ane '
$id="$F[0]_$F[1]_$F[2]";
$line=();
for($i=0; $i<=13; $i++) {
$line.="$F[$i]\t";
}
$line=~s/\t$//g;
$seen{$id}{'gene'}=$line;
for($i=14; $i<=33; $i++) {
if($F[$i]=~/^\.$/) { $F[$i]=0; }
$seen{$id}{$i}+=$F[$i];
}
END {
foreach $id(keys(%seen)) {
print "$seen{$id}{'gene'}\t";
$line=();
for($i=14; $i<=33; $i++) {
$line.="$seen{$id}{$i}\t";
}
$line=~s/\t$//g;
print "$line\n";
}
}
' | sortBed -i stdin > $BED_FILE.gene_summary
COMMENT
## remove temporary file
if [ ! -z "$TMP" ]; then
rm $TMP
fi