Commit aa89c591 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add print

parent 739ef6e9

launch_universc.sh

+24 −33
Original line number Diff line number Diff line
@@ -54,7 +54,6 @@ fi 
#reading in options

read1=()

read2=()

verbose=false

keep=false

convert=true

skip=false
@@ -255,7 +254,7 @@ for op in "$@";do 
            ;;

    esac

done

if [[ $verbose == "true" ]]

if [[ $verbose == "true ]]

    then

    echo " checking options ..."

fi
@@ -505,28 +504,27 @@ elif [ "$technology" == "icell8" ]; then 
fi



#auto detect read file format (if one file each)

for j in ${!read1[@]}

for i in ${!read1[@]}

do

i=$(($j+1))

read=${read1[$i]}

    echo " checking file format for $read1 ..."

    if [ -f $read ] && [ ! -h $read ]

    if [ -f $read ]

        then

        echo $read

    elif [ -f ${read}.fq ] && [ ! -h $read ]

    elif [ -f ${read}.fq ]

    then

        read=${read}.fq

        echo $read

    elif [ -f ${read}.fastq ] && [ ! -h $read ]

    elif [ -f ${read}.fastq ]

        then

        read=${read}.fastq

        echo $read

    elif [ -f ${read}.fq.gz ] && [ ! -h $read ]

    elif [ -f ${read}.fq.gz ]

        then

        gunzip -k ${read}.fq.gz

        read=${read}.fq

        echo $read

    elif [ -f ${read}.fastq.gz ] && [ ! -h $read ]

    elif [ -f ${read}.fastq.gz ]

        then

        gunzip -k ${read}.fastq.gz

        read=${read}.fastq
@@ -537,28 +535,27 @@ read=${read1[$i]} 
read1[$i]=$read

done



for j in ${!read2[@]}

for i in ${!read2[@]}

do

i=$(($j+1))

read=${read2[$i]}

    echo " checking file format for $read2 ..."

    if [ -f $read ] || [ ! -h $read ]

    if [ -f $read ]

        then

        echo $read 

    elif [ -f ${read}.fq ] && [ ! -h $read ]

    elif [ -f ${read}.fq ]

    then

        read=${read}.fq

        echo $read 

    elif [ -f ${read}.fastq ] && [ ! -h $read ]

    elif [ -f ${read}.fastq ]

        then

        read=${read}.fastq

        echo $read 

    elif [ -f ${read}.fq.gz ] && [ ! -h $read ]

    elif [ -f ${read}.fq.gz ]

        then

        gunzip -k ${read}.fq.gz

        read=${read}.fq

        echo $read 

    elif [ -f ${read}.fastq.gz ] && [ ! -h $read ]

    elif [ -f ${read}.fastq.gz ]

        then

        gunzip -k ${read}.fastq.gz

        read=${read}.fastq
@@ -570,9 +567,8 @@ read2[$i]=$read 
done



echo " checking file name for $read1 ..."

for j in ${!read1[@]}

for i in ${!read1[@]}

do

i=$(($j+1))

read=${read1[$i]}

case $read in

    #check if contains lane before read
@@ -599,7 +595,7 @@ case $read in 
        echo "   renaming $read ...";;

esac

case $read in

    #check if contains suffix

    #check if contains sample before lane

    (*_R1_001.*) echo " $read compatible with suffix";;

    (*) echo "  converting $read ..."

        #rename file
@@ -624,9 +620,8 @@ fi 
done



echo " checking file name for $read2 ..."

for j in ${!read2[@]}

for i in ${!read2[@]}

do

i=$(($j+1))

read=${read2[$i]}

case $read in

    #check if contains lane before read
@@ -653,15 +648,13 @@ case $read in 
        echo "   renaming $read ...";;

esac

case $read in

    #check if contains suffix

    #check if contains sample before lane

    (*_R1_001.*) echo " $read compatible with suffix";;

    (*) echo "  converting $read ..."

        #rename file

        rename "s/_R1.*\./_R1_001\./" $read

        rename "s/_R1.*\./_R1_001\./" $read

        #update file variable

        read=`echo $read | sed -e  "s/_R1.*\./_R1_001\./g"`

        read=`echo $read | sed -e  "s/_R1.*\./_R1_001\./g"`

        read2[$i]=$read

        echo "   renaming $read";;

esac
@@ -674,7 +667,7 @@ if [ ! -f $read ] || [ -h $read ] 
    then

    echo "  warning: file $read not in current directory"

    echo "   creating link to full path"

    ln -s -f $path $read

    ln -s -f $read $path

    read2[$i]=$read

fi

done
@@ -746,9 +739,8 @@ fi 
mkdir -p $crIN

if [ -d $crIN ]

    then

    for j in ${!read1[@]}

    for i in ${!read1[@]}

    do

    i=$(($j+1))

        read=${read1[$i]}

        if [ -f $crIN/$read ] 

            then
@@ -762,9 +754,8 @@ if [ -d $crIN ] 
             echo "file $crIN/$read kept"

        fi

    done

    for j in ${!read2[@]}

    for i in ${!read2[@]}

    do

    i=$(($j+1))

        read=${read2[$i]}

        if [ -f $crIN/$read ]

            then
@@ -851,13 +842,13 @@ if [[ $convert == "true" ]] 
            echo "        handling $fq"

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

                echo "        converting barcodes"

                sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read

                echo sed -i '2~4s/^/AAAA/' ${crIN}/$fq #Add AAAA to every read

                echo "        converting quality scores"

                sed -i '4~4s/^/IIII/'  ${crIN}/$fq #Add quality scores for added bases

                echo sed -i '4~4s/^/IIII/'  ${crIN}/$fq #Add quality scores for added bases

                echo "        converting UMI"

                sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/'  ${crIN}/$fq #Replace last 6 bases with AA

                echo sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/'  ${crIN}/$fq #Replace last 6 bases with AA

                echo "        converting quality scores"

                sed -i '4~4s/......$/II/'  ${crIN}/$fq #Replace quality scores for added bases

                echo sed -i '4~4s/......$/II/'  ${crIN}/$fq #Replace quality scores for added bases

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

                echo "converting barcodes"

                sed -i '2~4s/^/AAAAA/'  ${crIN}/$fq #Add AAAAA to every read

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