Adding options for ligation junction and setting scripts directory; fixing bug...

# [topDir]/mega     - Location of result of processing the mega map

#

# Juicer version 1.5

juicer_version="1.5.6" 

juicer_version="1.5.7" 

# top level directory, can also be set in options

topDir=$(pwd)

# restriction enzyme, can also be set in options

# can also be set in options via -D 

juiceDir="/aidenlab"

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-h]"

genomeHelp="   genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-S stage] [-b ligation] [-D Juicer scripts directory] [-f] [-h]"

genomeHelp="   genomeID is either defined in the script, e.g. \"hg19\" or \"mm10\" or the path to the chrom.sizes file"

dirHelp="   [topDir] is the top level directory (default \"$topDir\") and must contain links to all merged_nodups files underneath it"

siteHelp="   [site] must be defined in the script, e.g.  \"HindIII\" or \"MboI\" (default \"$site\"); alternatively, this can be the restriction site file"

stageHelp="* [stage]: must be one of \"final\", \"postproc\", or \"early\".\n    -Use \"final\" when the reads have been combined into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"

excludeHelp="   -x: exclude fragment-delimited maps from Hi-C mega map (will run much faster)"

ligationHelp="* [ligation junction]: use this string when counting ligation junctions"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

excludeHelp="   -f: include fragment-delimited maps in Hi-C mega map (will run slower)"

helpHelp="   -h: print this help and exit"

printHelpAndExit() {

    echo "$dirHelp"

    echo "$siteHelp"

    echo "$stageHelp"

    echo "$ligationHelp"

    echo "$excludeHelp"

    echo "$helpHelp"

    exit "$1"

}

while getopts "d:g:hxs:S:" opt; do

while getopts "d:g:hfs:S:b:D:" opt; do

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;

	d) topDir=$OPTARG ;;

	s) site=$OPTARG ;;

	x) exclude=1 ;;

	b) ligation=$OPTARG ;;

        D) juiceDir=$OPTARG ;;

        f) exclude=0 ;;

	S) stage=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done

## Set ligation junction based on restriction enzyme

if [ -z "$ligation" ]; then

    case $site in

	HindIII) ligation="AAGCTAGCTT";;

	DpnII) ligation="GATCGATC";;

	    echo "$site not listed as recognized enzyme, so trying it as site file."

	    echo "Ligation junction is undefined";;

    esac

fi

if [ -z "$site_file" ]

then

if [ -z $final ] && [ -z $postproc ]

then

# Create top statistics file from all inter.txt files found under current dir

    awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt

    awk -f ${juiceDir}/scripts/common/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt

    echo "(-: Finished creating top stats files."

    cp ${outputdir}/inter.txt ${outputdir}/inter_30.txt

    sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

    echo "(-: Finished sorting all merged_nodups files into a single merge."

    rm -r ${tmpdir}

    ${juiceDir}/scripts/statistics.pl -q 1 -o${outputdir}/inter.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt

    ${juiceDir}/scripts/statistics.pl -q 30 -o${outputdir}/inter_30.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt 

    ${juiceDir}/scripts/common/statistics.pl -q 1 -o${outputdir}/inter.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt

    ${juiceDir}/scripts/common/statistics.pl -q 30 -o${outputdir}/inter_30.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt 

    if [ -n "$exclude" ]

    then

	${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

	${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

	${juiceDir}/scripts/common/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

	${juiceDir}/scripts/common/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

    else

	${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

	${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

	${juiceDir}/scripts/common/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

	${juiceDir}/scripts/common/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

    fi

fi

if [ -z $early ]

then

# Create loop lists file for MQ > 30

    ${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

    ${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic

    ${juiceDir}/scripts/common/juicer_hiccups.sh -j ${juiceDir}/scripts/common/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

    ${juiceDir}/scripts/common/juicer_arrowhead.sh -j ${juiceDir}/scripts/common/juicer_tools -i $outputdir/inter_30.hic

fi

echo "(-: Successfully completed making mega map. Done. :-)"