correct renaming of input files for multiple reads (5044ea65) · Commits · github_fork / Universc

launch_universc.sh

+18 −8

Original line number	Original line	Diff line number	Diff line
	@@ -862,7 +862,9 @@ if [[ $verbose ]]; then
	echo "key: ${keys[@]}"		echo "key: ${keys[@]}"
	fi		fi
	for key in ${keys[@]}; do		for key in ${keys[@]}; do
			if [[ $verbose ]]; then
	readkey=$key		readkey=$key
			fi
	list=()		list=()
	if [[ $readkey == "R1" ]]; then		if [[ $readkey == "R1" ]]; then
	list=("${read1[@]}")		list=("${read1[@]}")
	@@ -950,7 +952,10 @@ fi

	#####Input file curation 3: renaming read1, read2, index1, and index2 file name if not compatible with the launch_universc.sh#####		#####Input file curation 3: renaming read1, read2, index1, and index2 file name if not compatible with the launch_universc.sh#####
	for key in ${keys[@]}; do		for key in ${keys[@]}; do
	readkey=$keys		if [[ $verbose ]]; then
			echo "key: $key"
			fi
			readkey=$key
	list=""		list=""
	if [[ $readkey == "R1" ]]; then		if [[ $readkey == "R1" ]]; then
	list=("${read1[@]}")		list=("${read1[@]}")
	@@ -990,7 +995,7 @@ for key in ${keys[@]}; do
	echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
	echo " renaming $read ..."		echo " renaming $read ..."
	fi		fi
	rename "s/_$readkey/_L001_$readkey/" $read		rename -f "s/_$readkey/_L001_$readkey/" $read
	#update file variable		#update file variable
	read=`echo $read \| sed -e "s/_${readkey}/_L001_${readkey}/g"`		read=`echo $read \| sed -e "s/_${readkey}/_L001_${readkey}/g"`
	list[$j]=$read		list[$j]=$read
	@@ -1010,7 +1015,7 @@ for key in ${keys[@]}; do
	echo " renaming $read ..."		echo " renaming $read ..."
	fi		fi
	k=$((${j}+1))		k=$((${j}+1))
	rename "s/_L0/_S${k}_L0/" $read		rename -f "s/_L0/_S${k}_L0/" $read
	#update file variable		#update file variable
	read=`echo $read \| sed -e "s/_L0/_S${k}_L0/g"`		read=`echo $read \| sed -e "s/_L0/_S${k}_L0/g"`
	list[$j]=$read		list[$j]=$read
	@@ -1029,7 +1034,7 @@ for key in ${keys[@]}; do
	echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"		echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"
	echo " renaming $read ..."		echo " renaming $read ..."
	fi		fi
	rename "s/_${readkey}.*\./_${readkey}_001\./" $read		rename -f "s/_${readkey}.*\./_${readkey}_001\./" $read
	#update file variable		#update file variable
	read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`		read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`
	list[$j]=$read		list[$j]=$read
	@@ -1171,12 +1176,17 @@ for fq in "${read12[@]}"; do
	name=${name%.*}		name=${name%.*}
	fields=`echo ${name} \| grep -o "_" \| wc -l`		fields=`echo ${name} \| grep -o "_" \| wc -l`
	fields=$(($fields+1))		fields=$(($fields+1))
	sn=`echo ${name} \| cut -f1-$((${fields}-4)) -d'_'`		if [[ $fields -le 4 ]]; then
			name_fields=$(($fields+1))
			else
			name_fields=$fields
			fi
			sn=`echo ${name} \| cut -f1-$((${name_fields}-4)) -d'_'`
	lane=`echo ${name} \| cut -f$((${fields}-2)) -d'_' \| sed 's/L00//'`		lane=`echo ${name} \| cut -f$((${fields}-2)) -d'_' \| sed 's/L00//'`
	LANE+=($lane)		LANE+=($lane)
	if [[ ${fields} -le 4 ]]; then		if [[ ${fields} -le 4 ]]; then
	echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";		echo "Warning: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";
	exit 1		#exit 1
	elif [[ $fq != '.fastq' ]] && [[ $fq != '.fq' ]]; then		elif [[ $fq != '.fastq' ]] && [[ $fq != '.fq' ]]; then
	echo "Error: $fq does not have a .fq or .fastq extention."		echo "Error: $fq does not have a .fq or .fastq extention."
	exit 1		exit 1

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