Merge branch 'kai' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert

#set options

lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file

lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called

<<<<<<< HEAD

lastcall=`[ -e $lastcallfile ] &&  cat $lastcallfile || echo ""`

=======

lastcall=`[[ -e $lastcallfile ]] &&  cat $lastcallfile || echo ""`

lastcall_b=`echo ${lastcall} | cut -f1 -d' '`

lastcall_u=`echo ${lastcall} | cut -f2 -d' '`

lastcall_p=`echo ${lastcall} | cut -f3 -d' '`

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes

barcodefile=""

crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger

#check if this is a test run

if [[ $testrun == "true" ]]; then

<<<<<<< HEAD

    reference=${SDIR}/test/cellranger_reference/cellranger-tiny-ref/3.0.0

    if [[ -z $id ]]; then

        id=test-tiny-${technology}

    fi

    if [[ $technology == "10x" ]]; then

        gunzip -k ${SDIR}test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

        read1=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")

        read2=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

    elif [[ $technology == "nadia" ]]; then

        gunzip -k test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq

        read1=("test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")

        read2=("test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")

    elif [[ $technology == "icell8" ]]; then

        gunzip -k test/shared/mappa-test/test_FL_R[12].fastq.gz

        read1=("test/shared/mappa-test/test_FL_R1.fastq")

        read2=("test/shared/mappa-test/test_FL_R2.fastq")

=======

    if [[ ${#read1[@]} -gt 0 ]] || [[ ${#read2[@]} -gt 0 ]]; then

        echo "Error: for test run, no R1 or R2 file can be selected."

        exit 1

    else

        echo "Error: for test run, option --technology must be 10x, nadia, or icell8"

	exit 1

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

    fi

fi

#adjustment lengths

barcodeadjust=`echo $(($barcodelength-$barcode_default))`

umiadjust=`echo $(($umilength-$umi_default))`

<<<<<<< HEAD

#prepare a proper barcode file

if [[ "$technology" != "10x" ]] && [[ -z $barcodefile ]]; then

    if [[ "$technology" == "nadia" ]]; then

        barcodefile=${barcodedir}/nadia_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            #creat a nadia barcode file

            echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} | sed 's/ /\n/g' | sort | uniq > ${barcodedir}/nadia_barcode.txt

        fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${barcodedir}/iCell8_barcode.txt

        if [[ ! -f ${barcodefile} ]]; then

            #create an iCell8 barcode file by copying from convert repo

            cat ${SDIR}/iCell8_barcode.txt > $barcodefile

            sed -i 's/^/AAAAA/g' ${barcodefile}

	    sort -u -o ${barcodefile} ${barcodefile}

        fi

    fi

elif [[ ! -z $barcodefile ]]; then

    cat ${barcodefile} >${barcodedir}/custom_barcode.txt

    barcodefile=${barcodedir}/custom_barcode.txt

    if [[ $barcodeadjust -gt 0 ]]; then

        sed -i "s/^.{${barcodeadjust}}//" ${barcodefile} #Trim the first n characters from the beginning of the sequence and quality

    elif [[ 0 -gt $barcodeadjust ]]; then

        As=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`

        sed -i "s/^/$As/" ${barcodefile} #Trim the first n characters from the beginning of the quality

    fi

fi

=======

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

##########

	    echo " total of $lock cellranger ${cellrangerversion} jobs are already running in ${cellrangerpath} with barcode length (${lastcall_b}), UMI length (${lastcall_u}), and whitelist barcodes (${lastcall_p})"

	    #check if a custom barcode is used for a run (which cannot be run in parallel)

<<<<<<< HEAD

            if [[ $lastcall == "custom" ]]; then

                echo "Error: cellranger is currently running with a custom barcode list"

                echo "other jobs cannot be run until the current job is complete"

                echo "remove $lockfile if $lastcall jobs have completed or aborted"

                exit 1

            elif [[ $lastcall == $technology ]]; then

=======

            if [[ ${barcode_length} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${barcodefile} == ${lastcall_p} ]]; then

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                lock=$(($lock+1))

        echo " ${cellrangerpath} set for $technology"

    fi

<<<<<<< HEAD

    #generate backup for the default 10x whitelist

    if [[ ! -f 737K-august-2016.txt.backup ]] || [[ ! -f 3M-february-2018.txt.backup.gz ]]; then

        echo " generating backups for default 10x whitelist"

        cp -f 737K-august-2016.txt 737K-august-2016.txt.backup

       	cp -f 3M-february-2018.txt.gz 3M-february-2018.txt.backup.gz

=======

    #whitelist file name

    v2=737K-august-2016.txt

    v3=3M-february-2018.txt

        echo " generating backups for default 10x whitelist"

        cp -f ${v2} ${v2}.backup

       	cp -f ${v3}.gz ${v3}.backup.gz

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

        echo " backup generated"

    fi

    #convert whitelist to the apropriate barcode

    echo " converting whitelist"

<<<<<<< HEAD

    if [[ -z ${barcodefile} ]]; then

        #for version 2

        cp 737K-august-2016.txt.backup 737K-august-2016.txt

        #for version 3

        cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz

    else

=======

    if [[ ${barcodefile} == "default" ]]; then

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

        #for version 2

        cp ${v2}.backup ${v2}

        #for version 3

<<<<<<< HEAD

        cat 737K-august-2016.txt > 3M-february-2018.txt

        gzip -f 3M-february-2018.txt

        rm translation/3M-february-2018.txt.gz

        ln -s 3M-february-2018.txt.gz translation/3M-february-2018.txt.gz

=======

        cp ${v3}.backup.gz ${v3}.gz

    else

        #for version 2

        gzip -f ${v3}

        rm translation/${v3}.gz

        ln -s ${v3}.gz translation/${v3}.gz

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

    fi

    echo " whitelist converted"

echo "converting input files to confer cellranger format ..."

if [[ $convert == "false" ]]; then

    echo " input file format conversion skipped"

<<<<<<< HEAD

fi

echo " barcodes: ${barcodeadjust}bps at its head"

echo " UMIs: ${umiadjust}bps at its tail" 

#converting barcodes

echo " adjusting barcodes of R1 files"

if [[ $barcodeadjust != 0 ]] && [[ $convert == "true" ]]; then

    if [[ $barcodeadjust -gt 0 ]]; then

        for convFile in "${convFiles[@]}"; do

            echo " handling $convFile ..."

            sed -i "2~2s/^.{${barcodeadjust}}//" $convFile #Trim the first n characters from the beginning of the sequence and quality

            echo "  ${convFile} adjusted"

       done

    elif [[ 0 -gt $barcodeadjust ]]; then

        for convFile in "${convFiles[@]}"; do

            echo " handling $convFile ..."

            toS=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`

            toQ=`printf '%0.sI' $(seq 1 $(($barcodeadjust * -1)))`

            sed -i "2~4s/^/$toS/" $convFile #Trim the first n characters from the beginning of the sequence

            sed -i "4~4s/^/$toQ/" $convFile #Trim the first n characters from the beginning of the quality

=======

else

    echo " adjustment parameters:"

    echo "  barcodes: ${barcodeadjust}bps at its head"

            sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

            sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

            sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

            echo "  ${convFile} adjusted"

        done

    fi

fi

<<<<<<< HEAD

#UMI

echo " adjusting UMIs of R1 files"

if [[ 0 -gt $umiadjust ]]; then 

    for convFile in "${convFiles[@]}"; do

        echo " handling $convFile ..."

        toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

        toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

        keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

        sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

        sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

        sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

        echo "  ${convFile} adjusted"

    done

fi

=======

>>>>>>> 9b5b3a75da1d9f04a8f8f70cf4fadd8c27a959e7

##########