extractMotifs

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

GENOME="mm9";

usage() {
	echo Program: "extractMotifs (extract motifs of interest from a motif file)"
	echo Author: BRIC, University of Copenhagen, Denmark
	echo Version: 1.0
	echo Contact: pundhir@binf.ku.dk
	echo "Usage: extractMotifs -i <file> -j <string> [OPTIONS]"
	echo "Options:"
	echo " -i <file>   [input file containing motifs (or stdin)]"
	echo " -j <string> [name of motifs needs to be extracted]"
    echo "             [if multiple, separate them by a comma]"
    echo "[OPTIONS]"
    echo " -S          [soft match to motif name, regexp based (default: hard match)]"
    echo "             [id before a '/', eg. E2F1_MOUSE.H10MO.A in E2F1_MOUSE.H10MO.A/hocomoco]"
	echo " -h          [help]"
	echo
	exit 0
}

#### parse options ####
while getopts i:j:Sh ARG; do
	case "$ARG" in
		i) MOTIFFILE=$OPTARG;;
        j) MOTIF=$OPTARG;;
        S) SOFTMATCH=1;;
		h) HELP=1;;
	esac
done

## usage, if necessary file and directories are given/exist
if [ -z "$MOTIFFILE" -o -z "$MOTIF" -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
}
###############

if [ "$GENOME" == "mm9" ]; then
    GENOME_FILE="/home/pundhir/project/genome_annotations/mouse.mm9.genome"
    REPEAT_FILE="/home/pundhir/project/genome_annotations/mouse.mm9.simpleRepeat.gz"
    GENOME_MOTIF="mm9r"
elif [ "$GENOME" == "hg19" ]; then
    GENOME_FILE="/home/pundhir/project/genome_annotations/human.hg19.genome"
    REPEAT_FILE="/home/pundhir/project/genome_annotations/human.hg19.simpleRepeat.gz"
    GENOME_MOTIF="hg19r"
elif [ "$GENOME" == "danRer7" ]; then
    GENOME_FILE="/home/pundhir/project/genome_annotations/zebrafish.danRer7.genome"
    REPEAT_FILE="/home/pundhir/project/genome_annotations/zebrafish.danRer7.simpleRepeat.gz"
    GENOME_MOTIF="danRer7r"
else
    echo "Presently the program only support analysis for mm9, hg19 or danRer7."
    echo
    usage
fi

## create temporary BED file if input is from stdin
if [ "$MOTIFFILE" == "stdin" ]; then
    TMP=$(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";' > $TMP
    MOTIFFILE=$TMP
fi

oIFS=$IFS
IFS=","
MOTIFS=($MOTIF)
IFS=$oIFS

if [ -z "$SOFTMATCH" ]; then
    for (( i=0; i<${#MOTIFS[@]}; i++ )); do
        MOTIFS[$i]=$(echo ${MOTIFS[$i]} | perl -ane 's/\//\\\//g; print $_;')
        zless $MOTIFFILE | perl -ane '
            if($_=~/'${MOTIFS[$i]}'\//) {
                @t=split(/\s+/,$_);
                $t[1]=~s/^.*\(/'${MOTIFS[$i]}'(/g;
                $line=();
                foreach(@t) { $line.="$_\t"; }
                $line=~s/\t$//g;
                print "$line\n"; $start=1;
            }
            elsif($_=~/^\>/) { $start=0; }
            elsif($start) { print $_; }
        '
    done
else
    for (( i=0; i<${#MOTIFS[@]}; i++ )); do
        MOTIFS[$i]=$(echo ${MOTIFS[$i]} | perl -ane 's/\//\\\//g; print $_;')
        zless $MOTIFFILE | perl -ane '
            if($_=~/'${MOTIFS[$i]}'.*\//) {
                @t=split(/\s+/,$_);
                $t[1]=~s/^.*\(/'${MOTIFS[$i]}'(/g;
                $line=();
                foreach(@t) { $line.="$_\t"; }
                $line=~s/\t$//g;
                print "$line\n"; $start=1;
            }
            elsif($_=~/^\>/) { $start=0; }
            elsif($start) { print $_; }
        '
    done
fi

if [ ! -z "$TMP" ]; then
    rm $TMP
fi

#wait
#wait_for_jobs_to_finish "Wait for jobs to finish... "
#echo "done"