nfrPlot

#!/bin/bash
#PBS -l nodes=1:ppn=4

GENOME="mm9";
PLOTTITLE="REGIONS_INTEREST_HISTONE_PROFILE";

#### usage ####
usage() {
	echo Program: "nfrPlot (plot histone read density for a set of NFRs across multiple samples)"
	echo Author: BRIC, University of Copenhagen, Denmark
	echo Version: 1.0
	echo Contact: pundhir@binf.ku.dk
	echo "Usage: nfrPlot -i <file | stdin> -j <file> -k <string> -o <dir> [OPTIONS]"
	echo "Options:"
	echo " -i <file>   [input file having NFRs. Ouput from nfrAna script]"
	echo " -j <file>   [mapped reads in BAM format from all samples (seperated by a comma)]"
    echo " -k <string> [size factor for each input sample or BAM files]"
    echo " -o <dir>    [output directory to store results]"
    echo "[OPTIONS]"
    echo " -g <string> [genome (default: mm9)]"
    echo " -t <string> [name of the output histone read density plot (default: REGIONS_INTEREST_HISTONE_PROFILE)]"
	echo " -h          [help]"
	echo
	exit 0
}

#### parse options ####
while getopts i:j:k:o:g:t:h ARG; do
	case "$ARG" in
		i) NFRREGION=$OPTARG;;
		j) BAMFILES=$OPTARG;;
        k) SIZEFACTORS=$OPTARG;;
        o) OUTDIR=$OPTARG;;
        g) GENOME=$OPTARG;;
        d) PLOTTITLE=$OPTARG;;
		h) HELP=1;;
	esac
done

## usage, if necessary file and directories are given/exist
if [ -z "$NFRREGION" -o -z "$BAMFILES" -o -z "$SIZEFACTORS" -o -z "$OUTDIR" -o "$HELP" ]; then
	usage
fi

###################
#helperfunction
function wait_for_jobs_to_finish {
    for job in `jobs -p`
    do
        echo $job
        wait $job
    done
    echo $1
}

echoerr() { echo "$@" 1>&2; }
###############

## check input
echo -n "Check input.. "
IFS=","
BAMFILE=($BAMFILES)
BAMFILE_COUNT=${#BAMFILE[@]}
SIZEFACTOR=($SIZEFACTORS)
SIZEFACTOR_COUNT=${#SIZEFACTOR[@]}

if [ "$BAMFILE_COUNT" -ne "$SIZEFACTOR_COUNT" ]; then
    echo -n "Please provide size factor for each input bam file";
    usage
fi
echo "done"

echo -n "Create directory structure... "
if [ ! -d "$OUTDIR" ]; then
    mkdir -p $OUTDIR
fi
echo "done"

## determine, if the input NFRs are from a file or stdin
echo -n "Create NFR file depending on if the input is from file or STDIN... "
if [ -f "$NFRREGION" ]; then
    zless $NFRREGION | perl -ane '$line=(); foreach(@F) { chomp($_); $line.="$_\t"; } $line=~s/\t$//g; print "$line\n";' > $OUTDIR/NFR_INTEREST.bed
elif [ "$NFRREGION" == "stdin" ]; then 
    while read LINE; do echo ${LINE}; done | perl -ane '$line=(); foreach(@F) { chomp($_); $line.="$_\t"; } $line=~s/\t$//g; print "$line\n";' > $OUTDIR/NFR_INTEREST.bed
else
    usage
fi
echo "done"

echo -n "Analyze NFRs for histone read density... "
for (( i=0; i<${#BAMFILE[@]}; i++)); do
    ID=`echo ${BAMFILE[$i]} | perl -ane '$_=~s/^.*\///g; chomp($_); print "$_";'`;
    if [ "$i" -eq 0 ]; then
        OUTPUT="$ID (score)"
        OUTPUT1="$ID (block expr)\t$ID (nfr expr)"
    else
        OUTPUT="$OUTPUT\t$ID (score)"
        OUTPUT1="$OUTPUT1\t$ID (block expr)\t$ID (nfr expr)"
    fi
done
echo -e "#chr\tstart\tend\t$OUTPUT\t$OUTPUT1" > $OUTDIR/NFR_INTEREST.bed.stat

while read line; do
    #echo -n ${line}
    NFRCHR=`echo ${line} | perl -ane 'print "$F[0]";'`;
    NFRSTART=`echo ${line} | perl -ane 'print "$F[1]";'`;
    NFREND=`echo ${line} | perl -ane 'print "$F[2]";'`;
    NFRCOOR=`echo ${line} | perl -ane 'print "$F[0]:$F[1]-$F[2]";'`;
    NFRLEN=`echo ${line} | perl -ane '$len=($F[2]-$F[1])+1; print "$len";'`;
    STARTBLOCKCOOR=`echo ${line} | perl -ane 'print "$F[6]";'`;
    STARTBLOCKLEN=`echo ${line} | perl -ane '@t=split(/[\:\-]+/,$F[6]); $len=($t[2]-$t[1])+1; print "$len";'`;
    ENDBLOCKCOOR=`echo ${line} | perl -ane 'print "$F[8]";'`;
    ENDBLOCKLEN=`echo ${line} | perl -ane '@t=split(/[\:\-]+/,$F[8]); $len=($t[2]-$t[1])+1; print "$len";'`;
<<"COMMENT1"
COMMENT1
    for (( i=0; i<${#BAMFILE[@]}; i++)); do
        NFREXPR=`coor2reads -c $NFRCOOR -b ${BAMFILE[$i]} -s ${SIZEFACTOR[$i]} | perl -ane 'BEGIN { $expr=0.01; } $expr+=$F[4]; END { printf("%0.2f", $expr); }'`;
        STARTBLOCKEXPR=`coor2reads -c $STARTBLOCKCOOR -b ${BAMFILE[$i]} -s ${SIZEFACTOR[$i]} | perl -ane 'BEGIN { $expr=0.01; } $expr+=$F[4]; END { printf("%0.2f", $expr); }'`;
        ENDBLOCKEXPR=`coor2reads -c $ENDBLOCKCOOR -b ${BAMFILE[$i]} -s ${SIZEFACTOR[$i]} | perl -ane 'BEGIN { $expr=0.01; } $expr+=$F[4]; END { printf("%0.2f", $expr); }'`;
        NFRSCORE=`perl -e '$score=((('$STARTBLOCKEXPR'/'$STARTBLOCKLEN')+('$ENDBLOCKEXPR'/'$ENDBLOCKLEN'))/('$NFREXPR'/'$NFRLEN')); printf("%0.4f", log($score));'`
        BLOCKEXPRNORM=`perl -e '$expr=(('$STARTBLOCKEXPR'/'$STARTBLOCKLEN')+('$ENDBLOCKEXPR'/'$ENDBLOCKLEN')); printf("%0.2f", $expr);'`
        NFREXPRNORM=`perl -e '$expr=('$NFREXPR'/'$NFRLEN'); printf("%0.2f", $expr);'`
        #echo -e "$NFRCOOR\t$NFREXPR\t$NFRLEN\t$STARTBLOCKCOOR\t$STARTBLOCKEXPR\t$STARTBLOCKLEN\t$ENDBLOCKCOOR\t$ENDBLOCKEXPR\t$ENDBLOCKLEN\t$NFRSCORE"
        if [ "$i" -eq 0 ]; then
            OUTPUT="$NFRSCORE"
            OUTPUT1="$BLOCKEXPRNORM\t$NFREXPRNORM"
        else
            OUTPUT="$OUTPUT\t$NFRSCORE"
            OUTPUT1="$OUTPUT1\t$BLOCKEXPRNORM\t$NFREXPRNORM"
        fi
    done
    echo -e "$NFRCHR\t$NFRSTART\t$NFREND\t$OUTPUT\t$OUTPUT1"
done < $OUTDIR/NFR_INTEREST.bed >> $OUTDIR/NFR_INTEREST.bed.stat

#grep -v "#" $OUTDIR/NFR_INTEREST.bed.stat | perl -ane '$dip=log((exp($F[3]+$F[4])/2)/(exp($F[5]+$F[6])/2)); chomp($_); print "$_\t"; printf("%0.3f\n", $dip);' | sort -k 12rn,12 | perl -ane 'if($F[11]<-1) { print $_; }' | wc -l

echo "done"