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added in resolutions flag to mega.sh map
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@nchernia
nchernia committed Aug 23, 2016
1 parent 05af18f commit ada6bde
Showing 1 changed file with 77 additions and 30 deletions.
107 changes: 77 additions & 30 deletions UGER/scripts/mega.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -49,15 +49,16 @@ groupname="a$(date +%s)"
# top level directory, can also be set in options
topDir=$(pwd)
# restriction enzyme, can also be set in options
site="DpnII"
site="MboI"
# genome ID, default to human, can also be set in options
genomeID="hg19"

## Read arguments
usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-hx]"
usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-r resolutions] [-hx]"
genomeHelp=" genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"
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"
resolutionsHelp=" [resolutions] is a comma-delimited list of resolutions, such as 10000,5000,1000,5f (default is 2.5M,1M,500K,250K,100K,50K,25K,10K,5K in base pair and 500f,250f,100f,50f,25f,10f,5f,2f,1f)"
excludeHelp=" -x: exclude fragment-delimited maps from Hi-C mega map (will run much faster)"
helpHelp=" -h: print this help and exit"

Expand All @@ -66,18 +67,20 @@ printHelpAndExit() {
echo "$genomeHelp"
echo "$dirHelp"
echo "$siteHelp"
echo "$resolutionsHelps"
echo "$excludeHelp"
echo "$helpHelp"
exit "$1"
}

while getopts "d:g:hxs:" opt; do
while getopts "d:g:r:hxs:" opt; do
case $opt in
g) genomeID=$OPTARG ;;
h) printHelpAndExit 0;;
d) topDir=$OPTARG ;;
s) site=$OPTARG ;;
x) exclude=1 ;;
r) resolutions=$OPTARG ;;
[?]) printHelpAndExit 1;;
esac
done
Expand Down Expand Up @@ -126,9 +129,28 @@ then
exit 100
fi

merged_names=$(find -L ${topDir} | grep merged_nodups.txt | tr '\n' ' ')
merged_names1=$(find -L ${topDir} | grep merged_nodups.txt)
merged_names=$(echo $merged_names1 | tr '\n' ' ')
inter_names=$(find -L ${topDir} | grep inter.txt | tr '\n' ' ')

if [[ $merged_names == *".txt.gz"* ]]
then
gzipped=1
echo "***! Mega map of gzipped files not yet supported, please unzip before running."
exit 100
# we need to unzip here
for i in $merged_names1
do
if [[ $i != *".txt.gz"* ]]
then
echo "***! Mixture of gzipped and unzipped merged_nodups files"
echo "Ensure that the merged_nodups are all either unzipped or gzipped then rerun"
echo "Files: $merged_names"
exit 100
fi
done
fi

## Create output directory, exit if already exists
if [[ -d "${outputdir}" ]]
then
Expand All @@ -150,13 +172,22 @@ if [ ! -d "$logdir" ]; then
chmod 777 $logdir
fi

if [ -n "$resolutions" ]; then
resolutions="-r $resolutions"
fi

## Arguments have been checked and directories created. Now begins
## the real work of the pipeline
qsub -o ${logdir}/header.out -j y -q short -r y -N ${groupname}cmd -cwd <<-EOF
date
echo "Juicer version:$juicer_version"
echo "$0 $@"
EOF

source $usePath
$load_cluster
touchfile1=${megadir}/touch1
jid1=`qsub -terse -o ${logdir}/stats.out -e ${logdir}/stats.err -q short -r y -N ${groupname}_topstats <<-TOPSTATS
jid1=`qsub -terse -o ${logdir}/topstats.out -e ${logdir}/topstats.err -q short -r y -N ${groupname}_topstats <<-TOPSTATS
export LC_ALL=en_US.UTF-8
if ! awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt
then
Expand All @@ -172,15 +203,21 @@ TOPSTATS`
touchfile2=${megadir}/touch2
# Merge all merged_nodups.txt files found under current dir
jid2=`qsub -terse -o ${logdir}/merge.out -e ${logdir}/merge.err -q long -r y -N ${groupname}_merge -l m_mem_free=16g -hold_jid ${groupname}_topstats <<- MRGSRT
if [ ! -f "${touchfile1}" ]
then
echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."
exit 100;
fi
if ! sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt
if [ -n "$gzipped" ]
then
echo "***! Some problems occurred somewhere in creating sorted merged_nodups files."
# This code didn't work, doesn't sort appropriately unfortunately.
if ! gunzip -c $merged_names | sort -T ${tmpdir} -m -k2,2d -k6,6d > ${outputdir}/merged_nodups.txt
then
echo "***! Some problems occurred somewhere in merging sorted merged_nodups files."
exit 100
else
echo "(-: Finished sorting all merged_nodups files into a single merge."
rm -r ${tmpdir}
fi
elif ! sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt
then
echo "***! Some problems occurred somewhere in merging sorted merged_nodups files."
exit 100
else
echo "(-: Finished sorting all merged_nodups files into a single merge."
rm -r ${tmpdir}
Expand All @@ -189,10 +226,15 @@ touch $touchfile2
MRGSRT`
touchfile3=${megadir}/touch3
holdjobs1="-hold_jid ${groupname}_merge";
holdjobs1="-hold_jid ${groupname}_merge,${groupname}_topstats";
# Create statistics files for MQ > 0
jid3=`qsub -terse -o ${logdir}/inter0.out -e ${logdir}/inter0.err -q long -r y -N ${groupname}_inter0 $holdjobs1 <<- INTER0
if [ ! -f "${touchfile1}" ]
then
echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."
exit 100;
fi
if [ ! -f "${touchfile2}" ]
then
echo "***! Sort job failed, type qacct -j $jid2 to see what happened."
Expand All @@ -207,7 +249,12 @@ touchfile4=${megadir}/touch4
holdjobs2="-hold_jid ${groupname}_inter0";
# Create statistics files for MQ > 30
jid4=`qsub -terse -o ${logdir}/inter30.out -e ${megadir}/inter30.err -q long -r y -N ${groupname}_inter30 $holdjobs1 <<- INTER30
jid4=`qsub -terse -o ${logdir}/inter30.out -e ${logdir}/inter30.err -q long -r y -N ${groupname}_inter30 $holdjobs1 <<- INTER30
if [ ! -f "${touchfile1}" ]
then
echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."
exit 100;
fi
if [ ! -f "${touchfile2}" ]
then
echo "***! Sort job failed, type qacct -j $jid2 to see what happened."
Expand All @@ -229,18 +276,18 @@ then
echo "***! Statistics q=1 job failed, type qacct -j $jid3 to see what happened."
exit 100;
fi
exitcode=-999
myexitcode=1
if [ -z "$exclude" ]
then
echo "Launching ${juiceDir}/scripts/juicebox 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/juicebox pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
exitcode=\$?
echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
${juiceDir}/scripts/juicebox pre $resolutions -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
myexitcode=\$?
else
echo "Launching ${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
exitcode=\$?
echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"
${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}
myexitcode=\$?
fi
if [ "\${exitcode}" -eq 0 ]
if [ "\${myexitcode}" -eq 0 ]
then
touch $touchfile5
fi
Expand All @@ -256,18 +303,18 @@ then
echo "***! Statistics q=30 job failed, type qacct -j $jid4 to see what happened."
exit 100;
fi
exitcode=-999
myexitcode=1
if [ -z "${exclude}" ]
then
echo "Launching ${juiceDir}/scripts/juicebox 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/juicebox 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}
exitcode=\$?
echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -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/juicebox pre $resolutions -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}
myexitcode=\$?
else
echo "Launching ${juiceDir}/scripts/juicebox 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/juicebox pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
exitcode=\$?
echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"
${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}
myexitcode=\$?
fi
if [ "\${exitcode}" -eq 0 ]
if [ "\${myexitcode}" -eq 0 ]
then
touch $touchfile6
fi
Expand Down

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