Adding ligation junction option #122, adding scripts option #124. Making no...

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

#

# Juicer version 1.5

juicer_version="1.5.6" 

juicer_version="1.5.7" 

## Set the following variables to work with your system

# Aiden Lab specific check

site="MboI"

# genome ID, default to human, can also be set in options

genomeID="hg19"

# by default exclude fragment delimited maps

exclude=1

## Read arguments                                                     

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-S stage] [-q queue] [-l long queue] [-Q queue time] [-L long queue time] [-x] [-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] [-q queue] [-l long queue] [-Q queue time] [-L long queue time] [-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 from 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:l:L:q:Q:" opt; do

while getopts "d:g:hfs:S:l:L:q:Q:b:D:" opt; do

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;

	d) topDir=$OPTARG ;;

	s) site=$OPTARG ;;

	x) exclude=1 ;;

	f) exclude=0 ;;

	S) stage=$OPTARG ;;

	l) long_queue=$OPTARG ;;

	L) long_queue_time=$OPTARG ;;

	q) queue=$OPTARG ;;

	Q) queue_time=$OPTARG ;;

	b) ligation=$OPTARG ;;

	D) juiceDir=$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

#source $usePath

$load_java

export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"

export _JAVA_OPTIONS="-Xms73728m -Xmx73728m"

if [ ! -f "${touchfile3}" ]

then

   echo "***! Statistics q=1 job failed."

   exit 1

fi

if [ -z "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools72g pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

if [ -z "$exclude" ] &&  ${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} 

then

   touch $touchfile5

elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools72g pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 

then

   touch $touchfile5 

fi

#source $usePath

$load_java	

export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"

export _JAVA_OPTIONS="-Xms73728m -Xmx73728m"

if [ ! -f "${touchfile4}" ]

then

   echo "***! Statistics q=30 job failed."

   exit 1

fi

if [ -z "${exclude}" ] &&  ${juiceDir}/scripts/juicer_tools72g 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} 

if [ -z "${exclude}" ] &&  ${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} 

then

   touch $touchfile6

elif [ -n "${exclude}" ] && ${juiceDir}/scripts/juicer_tools72g pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 

elif [ -n "${exclude}" ] && ${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} 

then

   touch $touchfile6

fi

	   exit 1

	fi

	${load_gpu}

	${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools72g -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID

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

	touch $touchfile7

	HICCUPS`

	dependhic30="${dependhic30}:$jid7"

   echo "***! HIC maps q=30 job failed."

   exit 1

fi

${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools72g -i $outputdir/inter_30.hic

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

touch $touchfile8

ARROWHEAD`

    dependhic30="${dependhic0}:$jid8"