Loading launch_universc.sh +43 −2 Original line number Original line Diff line number Diff line Loading @@ -1385,13 +1385,12 @@ fi #generate missing indexes if required (generating I1 and I2) #generate missing indexes if required (generating I1 and I2) if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-ci" ]] ; then if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] ; then echo "dual indexes I1 and I2 required for $technology" echo "dual indexes I1 and I2 required for $technology" if [[ ${#index2[@]} -le 1 ]]; then if [[ ${#index2[@]} -le 1 ]]; then echo " automatically generating I1 and I2 index files from file headers" echo " automatically generating I1 and I2 index files from file headers" index1=("${read1[@]}") index1=("${read1[@]}") index2=("${read1[@]}") index2=("${read1[@]}") #for ii in $(seq 1 1 ${#read1[@]}); do for ii in ${!read1[@]}; do for ii in ${!read1[@]}; do #iterate over read1 inputs #iterate over read1 inputs R1_file=${read1[$(( $ii -1 ))]} R1_file=${read1[$(( $ii -1 ))]} Loading Loading @@ -1433,6 +1432,48 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ fi fi fi fi if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "strt-seq-c1" ]]; then echo "dual indexes I1 and I2 required for $technology" if [[ ${#index2[@]} -le 1 ]]; then echo " automatically generating I1 index files from file headers" index1=("${read1[@]}") for ii in ${!read1[@]}; do #iterate over read1 inputs R1_file=${read1[$(( $ii -1 ))]} R2_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_R2/' ) I1_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ $verbose ]]; then echo $R1_file echo $R2_file echo $I1_file fi # copies index 1 to next line (1st to 2nd) and deletes 3rd line (only if index 1 doesn't contain '+' character) cat $R1_file | sed -E "/x/! s/ (.):(.):(.):(.*)$/ \1:\2:\3:\4$\n\4/g" > $I1_file linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d: -f1 | awk 'NR==1{p=$1;next} END{print $1-p}') if [[ $linediff -eq 5 ]];then #remove lines if matched only sed "3~5d" > $I1_file else cat $R1_file | sed -E "s/ (.):(.):(.):(.*)\+(.*)$/ \1:\2:\3:\4+\5\n\4/g" | sed "3~5d" > $I1_file fi indexlength=$(($(head $I1_file -n 2 | tail -n 1 | wc -c) -1)) qualscores=$(seq 1 $indexlength | xargs -I {} printf I) if [[ $verbose ]]; then echo index of length $indexlength gives quality score $qualscores fi sed -i "4~4s/^.*$/${qualscores}/g" $I1_file index1+=("$I1_file") done if [[ $verbose ]]; then echo index1: $index1 fi else echo " index found" fi fi #inverting R1 and R2 for specific technologies #inverting R1 and R2 for specific technologies if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then #invert read1 and read2 #invert read1 and read2 Loading Loading
launch_universc.sh +43 −2 Original line number Original line Diff line number Diff line Loading @@ -1385,13 +1385,12 @@ fi #generate missing indexes if required (generating I1 and I2) #generate missing indexes if required (generating I1 and I2) if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-ci" ]] ; then if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] ; then echo "dual indexes I1 and I2 required for $technology" echo "dual indexes I1 and I2 required for $technology" if [[ ${#index2[@]} -le 1 ]]; then if [[ ${#index2[@]} -le 1 ]]; then echo " automatically generating I1 and I2 index files from file headers" echo " automatically generating I1 and I2 index files from file headers" index1=("${read1[@]}") index1=("${read1[@]}") index2=("${read1[@]}") index2=("${read1[@]}") #for ii in $(seq 1 1 ${#read1[@]}); do for ii in ${!read1[@]}; do for ii in ${!read1[@]}; do #iterate over read1 inputs #iterate over read1 inputs R1_file=${read1[$(( $ii -1 ))]} R1_file=${read1[$(( $ii -1 ))]} Loading Loading @@ -1433,6 +1432,48 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ fi fi fi fi if [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "strt-seq-c1" ]]; then echo "dual indexes I1 and I2 required for $technology" if [[ ${#index2[@]} -le 1 ]]; then echo " automatically generating I1 index files from file headers" index1=("${read1[@]}") for ii in ${!read1[@]}; do #iterate over read1 inputs R1_file=${read1[$(( $ii -1 ))]} R2_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_R2/' ) I1_file=$(echo $R1_file | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ $verbose ]]; then echo $R1_file echo $R2_file echo $I1_file fi # copies index 1 to next line (1st to 2nd) and deletes 3rd line (only if index 1 doesn't contain '+' character) cat $R1_file | sed -E "/x/! s/ (.):(.):(.):(.*)$/ \1:\2:\3:\4$\n\4/g" > $I1_file linediff=$(grep -n "^+" $I1_file | head -n 2 | cut -d: -f1 | awk 'NR==1{p=$1;next} END{print $1-p}') if [[ $linediff -eq 5 ]];then #remove lines if matched only sed "3~5d" > $I1_file else cat $R1_file | sed -E "s/ (.):(.):(.):(.*)\+(.*)$/ \1:\2:\3:\4+\5\n\4/g" | sed "3~5d" > $I1_file fi indexlength=$(($(head $I1_file -n 2 | tail -n 1 | wc -c) -1)) qualscores=$(seq 1 $indexlength | xargs -I {} printf I) if [[ $verbose ]]; then echo index of length $indexlength gives quality score $qualscores fi sed -i "4~4s/^.*$/${qualscores}/g" $I1_file index1+=("$I1_file") done if [[ $verbose ]]; then echo index1: $index1 fi else echo " index found" fi fi #inverting R1 and R2 for specific technologies #inverting R1 and R2 for specific technologies if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then #invert read1 and read2 #invert read1 and read2 Loading
