Loading launch_universc.sh +8 −8 Original line number Diff line number Diff line Loading @@ -1176,36 +1176,36 @@ for key in ${keys[@]}; do rename -f "s/_${readkey}.(.*).gz/_${readkey}_001\.\$1.gz/g" ${read} fi if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fastq') ]]; then rename -f "s/_${readkey}.(.*)/_${readkey}_001\.\$1/" ${read}*.fastq rename -f "s/_${readkey}\.(.*)/_${readkey}_001\.\$1/" ${read}*.fastq fi if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fq') ]]; then rename -f "s/_${readkey}.(.*)/_${readkey}_001\.\$1/" ${read}*.fq rename -f "s/_${readkey}\.(.*)/_${readkey}_001\.\$1/" ${read}*.fq fi if [[ ${read} == *.fastq ]]; then rename -f "s/_${readkey}(.*).fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz rename -f "s/_${readkey}*\.fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz fi if [[ ${read} == *.fq ]]; then rename -f "s/_${readkey}(.*).fq/_${readkey}_001\.fq/" ${read} rename -f "s/_${readkey}*\.fq/_${readkey}_001\.fq/" ${read} fi #update file variable if [[ ${read} == *.gz ]] || [[ ${read} == *.fastq ]] || [[ ${read} == *.fq ]] || [[ -f ${read} ]]; then #assumes read name already contains . in file extension read=`echo $read | sed -e "s/_${readkey}.*\./_${readkey}_001\./g"` read=`echo $read | sed -e "s/_${readkey}*\./_${readkey}_001\./g"` else #replace everything after read key (R1, R2, I1, I2) with 001 suffix (detects file later) rename -f "s/_${readkey}.*/_${readkey}_001/g" ${read} read=`echo $read | sed -e "s/_${readkey}.*/_${readkey}_001/g"` read=`echo $read | sed -e "s/_${readkey}*/_${readkey}_001/g"` fi #remove characters after read key (R1, R2, I1, I2) required as above if [[ ${read} != *_${readkey}_001.* ]] && [[ ${read} != *.* ]]; then rename -f "s/_${readkey}_*\./_${readkey}_001\./" ${read} read=`echo $read | sed -e "s/_${readkey}.*\./_${readkey}_001\./g"` read=`echo $read | sed -e "s/_${readkey}*\./_${readkey}_001\./g"` elif [[ ${read} != *_${readkey}_001 ]] || [[ ${read} != *_${readkey}*00#1 ]]; then rename -f "s/_${readkey}*_001/_${readkey}_001/" ${read#} read=`echo $read | sed -e "s/_${readkey}*_001/_${readkey}_001/g"` fi if [[ ${read} == *_${readkey}_*_001.* ]]; then rename -f "s/_${readkey}.*_001\./_${readkey}_001\./" ${read} rename -f "s/_${readkey}*_001\./_${readkey}_001\./" ${read} read=`echo $read | sed -e "s/_${readkey}*_001\./_${readkey}_001\./g"` fi Loading Loading
launch_universc.sh +8 −8 Original line number Diff line number Diff line Loading @@ -1176,36 +1176,36 @@ for key in ${keys[@]}; do rename -f "s/_${readkey}.(.*).gz/_${readkey}_001\.\$1.gz/g" ${read} fi if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fastq') ]]; then rename -f "s/_${readkey}.(.*)/_${readkey}_001\.\$1/" ${read}*.fastq rename -f "s/_${readkey}\.(.*)/_${readkey}_001\.\$1/" ${read}*.fastq fi if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fq') ]]; then rename -f "s/_${readkey}.(.*)/_${readkey}_001\.\$1/" ${read}*.fq rename -f "s/_${readkey}\.(.*)/_${readkey}_001\.\$1/" ${read}*.fq fi if [[ ${read} == *.fastq ]]; then rename -f "s/_${readkey}(.*).fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz rename -f "s/_${readkey}*\.fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz fi if [[ ${read} == *.fq ]]; then rename -f "s/_${readkey}(.*).fq/_${readkey}_001\.fq/" ${read} rename -f "s/_${readkey}*\.fq/_${readkey}_001\.fq/" ${read} fi #update file variable if [[ ${read} == *.gz ]] || [[ ${read} == *.fastq ]] || [[ ${read} == *.fq ]] || [[ -f ${read} ]]; then #assumes read name already contains . in file extension read=`echo $read | sed -e "s/_${readkey}.*\./_${readkey}_001\./g"` read=`echo $read | sed -e "s/_${readkey}*\./_${readkey}_001\./g"` else #replace everything after read key (R1, R2, I1, I2) with 001 suffix (detects file later) rename -f "s/_${readkey}.*/_${readkey}_001/g" ${read} read=`echo $read | sed -e "s/_${readkey}.*/_${readkey}_001/g"` read=`echo $read | sed -e "s/_${readkey}*/_${readkey}_001/g"` fi #remove characters after read key (R1, R2, I1, I2) required as above if [[ ${read} != *_${readkey}_001.* ]] && [[ ${read} != *.* ]]; then rename -f "s/_${readkey}_*\./_${readkey}_001\./" ${read} read=`echo $read | sed -e "s/_${readkey}.*\./_${readkey}_001\./g"` read=`echo $read | sed -e "s/_${readkey}*\./_${readkey}_001\./g"` elif [[ ${read} != *_${readkey}_001 ]] || [[ ${read} != *_${readkey}*00#1 ]]; then rename -f "s/_${readkey}*_001/_${readkey}_001/" ${read#} read=`echo $read | sed -e "s/_${readkey}*_001/_${readkey}_001/g"` fi if [[ ${read} == *_${readkey}_*_001.* ]]; then rename -f "s/_${readkey}.*_001\./_${readkey}_001\./" ${read} rename -f "s/_${readkey}*_001\./_${readkey}_001\./" ${read} read=`echo $read | sed -e "s/_${readkey}*_001\./_${readkey}_001\./g"` fi Loading
