comparison scripts/TEMP_Absence.sh @ 12:ca36262102d8 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50

11:e19d9742c99b

        -s     Directory where all the scripts are
        -o     Path to output directory. Default is current directory
        -r     Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path
        -t     2bit file for the reference genome (can be downloaded from UCSC Genome Browser)
        -f     An integer specifying the length of the fragments (inserts) of the library. Default is 500
        -c     An integer specifying the number of CUPs used. Default is 4
        -h     Show help message

EOF
echo -en "\e[0m"
}

# taking options
while getopts "hi:c:f:o:r:s:t:" OPTION
do
        case $OPTION in
                h)
                        usage && exit 1
		;;

		        TEBED=$OPTARG
		;;
	        t)
		        REF=$OPTARG
		;;
                ?)
                        usage && exit 1
                ;;
        esac
done

then
        usage && exit 1
fi
[ ! -z "${CPU##*[!0-9]*}" ] || CPU=4
[ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
[ ! -z $OUTDIR ]  || OUTDIR=$PWD

mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m"
cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1
touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1

checkExist "mv"
checkExist "sort"
checkExist "touch"
checkExist "awk"
checkExist "grep"
checkExist "bwa"
checkExist "samtools"
echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m"

name=`basename $BAM`

# Identify breakpoints using soft-clipping information
perl $BINDIR/pickSoftClipping.over.pl $i.excision.cluster.rpmk $REF > $i.excision.cluster.rpmk.sfcp
perl $BINDIR/refine_breakpoint.ex.pl

# Estimate excision sites frequencies
perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup
perl $BINDIR/summarize_excision.pl

12:ca36262102d8

        -s     Directory where all the scripts are
        -o     Path to output directory. Default is current directory
        -r     Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path
        -t     2bit file for the reference genome (can be downloaded from UCSC Genome Browser)
        -f     An integer specifying the length of the fragments (inserts) of the library. Default is 500
        -x     The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA MEM.
        -c     An integer specifying the number of CPUs used. Default is 4
        -h     Show help message

EOF
echo -en "\e[0m"
}

# taking options
while getopts "hi:c:f:o:r:s:t:x:" OPTION
do
        case $OPTION in
                h)
                        usage && exit 1
		;;

		        TEBED=$OPTARG
		;;
	        t)
		        REF=$OPTARG
		;;
	        x)
		        SCORE=$OPTARG
		;;
                ?)
                        usage && exit 1
                ;;
        esac
done

then
        usage && exit 1
fi
[ ! -z "${CPU##*[!0-9]*}" ] || CPU=4
[ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
[ ! -z "${SCORE##*[!0-9]*}" ] || SCORE=0
[ ! -z $OUTDIR ]  || OUTDIR=$PWD

mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m"
cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1
touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1

checkExist "mv"
checkExist "sort"
checkExist "touch"
checkExist "awk"
checkExist "grep"
checkExist "twoBitToFa"
checkExist "bwa"
checkExist "samtools"
echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m"

name=`basename $BAM`

# Identify breakpoints using soft-clipping information
perl $BINDIR/pickSoftClipping.over.pl $i.excision.cluster.rpmk $REF > $i.excision.cluster.rpmk.sfcp
perl $BINDIR/refine_breakpoint.ex.pl

# Estimate excision sites frequencies
if [[ $SCORE -eq 0 ]]
then
    perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup
else
    perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.excision.cluster.rpmk.refined.bp $SCORE > $i.excision.cluster.rpmk.refined.bp.refsup
fi

perl $BINDIR/summarize_excision.pl