Quiver_01.sh

#!/bin/bash
# Script to generate PBS sub files for quiver analysis
# 07/25/2016
# Andrew Severin <severin@iastate.edu>

function printUsage () {
    cat <<EOF

Synopsis

    $scriptName [-h | --help] <ReferenceGenomeToPolish>

Description

    This is a bash script that will take all *.bax.h5 files in a folder and generate a list of pbalign commands, then generate a submission script for each one with the required modules loaded. The submission file is formatted to run on condo with 48 hours walltime on default queue.
	The output will be named with the commands_file name along with the number suffix.

        -h, --help
        Brings up this help page

    <ReferenceGenomeToPolish>
       This fasta file contains the genome that you wish to polish with the raw read data (bax.h5).


Author

    Andrew Severin, Genome Informatics Facilty, Iowa State University
    severin@iastate.edu
    25 July, 2016


EOF
}
if [ $# -lt 1 ] ; then
        printUsage
        exit 0
fi

GENOME="$1"

ls *bax.h5 | xargs -I xx echo "pbalign --forQuiver xx $1 aligned_reads.xx.cmp.h5" > pbalign.commands

INFILE="pbalign.commands"



function readlines () {
    local N=1
    local line
    local rc="1"
    for i in $(seq 1 $N); do
        read line
        if [ $? -eq 0 ]; then
            echo "$line"
            rc="0"
        else
            break
        fi
    done
    return $rc
}
netid=$(whoami)
num=1
while chunk=$(readlines ${LINES}); do
cat <<JOBHEAD > ${INFILE%%.*}_${num}.sub
#!/bin/bash
#PBS -l nodes=1:ppn=16
#PBS -l walltime=48:00:00
#PBS -N ${INFILE%%.*}_${num}
#PBS -o \${PBS_JOBNAME}.o\${PBS_JOBID} -e \${PBS_JOBNAME}.e\${PBS_JOBID}
#PBS -m ae -M $netid@iastate.edu
cd \$PBS_O_WORKDIR
ulimit -s unlimited
chmod g+rw \${PBS_JOBNAME}.[eo]\${PBS_JOBID}
module use /shared/modulefiles 
module load LAS/parallel/20150922 
module load python/2.7.10
module load SMRTAnalysis/2.3.0
JOBHEAD
echo -e "${chunk}" >> ${INFILE%%.*}_${num}.sub
echo -e "qstat -f \"\$PBS_JOBID\" | head" >> ${INFILE%%.*}_${num}.sub
echo -e "\nwalltime" >> ${INFILE%%.*}_${num}.sub
((num++))
done<"${INFILE}"
sed -i '/^$/d' ${INFILE}