Loading launch_universc.sh +102 −15 Original line number Diff line number Diff line Loading @@ -139,22 +139,18 @@ for op in "$@"; do ;; -f|--file) shift if [[ "$1" != "" ]]; then for i in $1/*; do if [[ "$i" == *"_R1_"* ]]; then if [[ ! "$i" == *".gz" ]] || [[ ! -f ${i%.*} ]]; then read1+=("$i") fi elif [[ "$i" == *"_R2_"* ]]; then if [[ ! "$i" == *".gz" ]] || [[ ! -f ${i%.*} ]]; then read2+=("$i") fi fi done next=true if [[ "$1" != "" ]] then arg=$1 while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do read1+=("${1}_R1_001") read2+=("${1}_R2_001") shift elif [[ -z $file ]]; then echo "Error: file input missing for --file" arg=$1 done skip=true else echo "Error: File input missing --file or --read1" exit 1 fi ;; Loading Loading @@ -278,6 +274,97 @@ if [[ ${#read2[@]} -eq 0 ]] && [[ $setup == "false" ]]; then exit 1 fi #check for file type (extension) for files ##allows incomplete file names and processing compressed files for i in ${!read1[@]} do read=${read1[$i]} if [[ $verbose == "true" ]]; then echo " checking file format for $read1 ..." fi if [ -f $read ] && [ ! -h $read ] then if [[ $read != *"gz" ]] then gunzip -k $read #update file variable read=`echo $read | sed -e "s/\.gz//g"` fi if [[ $read != *"fastq" ]] || [[ $read != *"fq" ]] then echo "Warning: file $read expected to be in fastq format" fi echo $read elif [ -f ${read}.fq ] && [ ! -h $read ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] && [ ! -h $read ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo $read not found fi read1[$i]=$read done for i in ${!read2[@]} do read=${read2[$i]} if [[ $verbose == "true" ]]; then echo " checking file format for $read2 ..." fi if [ -f $read ] && [ ! -h $read ] then if [[ $read != *"gz" ]] then gunzip -k $read #update file variable read=`echo $read | sed -e "s/\.gz//g"` fi if [[ $read != *"fastq" ]] || [[ $read != *"fq" ]] then echo "Warning: file $read expected to be in fastq format" fi echo $read elif [ -f ${read}.fq ] && [ ! -h $read ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] && [ ! -h $read ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo $read not found fi read2[$i]=$read done #renaming read1 and read 2 files if not compatible with the convention. if [[ $verbose == "true" ]]; then echo " checking file name for $read1 ..." Loading Loading
launch_universc.sh +102 −15 Original line number Diff line number Diff line Loading @@ -139,22 +139,18 @@ for op in "$@"; do ;; -f|--file) shift if [[ "$1" != "" ]]; then for i in $1/*; do if [[ "$i" == *"_R1_"* ]]; then if [[ ! "$i" == *".gz" ]] || [[ ! -f ${i%.*} ]]; then read1+=("$i") fi elif [[ "$i" == *"_R2_"* ]]; then if [[ ! "$i" == *".gz" ]] || [[ ! -f ${i%.*} ]]; then read2+=("$i") fi fi done next=true if [[ "$1" != "" ]] then arg=$1 while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do read1+=("${1}_R1_001") read2+=("${1}_R2_001") shift elif [[ -z $file ]]; then echo "Error: file input missing for --file" arg=$1 done skip=true else echo "Error: File input missing --file or --read1" exit 1 fi ;; Loading Loading @@ -278,6 +274,97 @@ if [[ ${#read2[@]} -eq 0 ]] && [[ $setup == "false" ]]; then exit 1 fi #check for file type (extension) for files ##allows incomplete file names and processing compressed files for i in ${!read1[@]} do read=${read1[$i]} if [[ $verbose == "true" ]]; then echo " checking file format for $read1 ..." fi if [ -f $read ] && [ ! -h $read ] then if [[ $read != *"gz" ]] then gunzip -k $read #update file variable read=`echo $read | sed -e "s/\.gz//g"` fi if [[ $read != *"fastq" ]] || [[ $read != *"fq" ]] then echo "Warning: file $read expected to be in fastq format" fi echo $read elif [ -f ${read}.fq ] && [ ! -h $read ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] && [ ! -h $read ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo $read not found fi read1[$i]=$read done for i in ${!read2[@]} do read=${read2[$i]} if [[ $verbose == "true" ]]; then echo " checking file format for $read2 ..." fi if [ -f $read ] && [ ! -h $read ] then if [[ $read != *"gz" ]] then gunzip -k $read #update file variable read=`echo $read | sed -e "s/\.gz//g"` fi if [[ $read != *"fastq" ]] || [[ $read != *"fq" ]] then echo "Warning: file $read expected to be in fastq format" fi echo $read elif [ -f ${read}.fq ] && [ ! -h $read ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] && [ ! -h $read ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] && [ ! -h $read ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo $read not found fi read2[$i]=$read done #renaming read1 and read 2 files if not compatible with the convention. if [[ $verbose == "true" ]]; then echo " checking file name for $read1 ..." Loading
