check file names (16cdb916) · Commits · github_fork / Universc

launch_universc.sh

+66 −61

Original line number	Diff line number	Diff line
		@@ -478,64 +478,6 @@ elif [ "$technology" == "icell8" ]; then
		fi

		#auto detect read file format (if one file each)
		if [[ ${#read1[@]} == 1 ]]
		then
		echo " checking file format for $read1 ..."
		if [ -f $read1 ]
		then
		echo $read1
		elif [ -f ${read1}.fq ]
		then
		read1=${read1}.fq
		echo $read1
		elif [ -f ${read1}.fastq ]
		then
		read1=${read1}.fastq
		echo $read1
		elif [ -f ${read1}.fq.gz ]
		then
		gunzip -k ${read1}.fq.gz
		read1=${read1}.fq
		echo $read1
		elif [ -f ${read1}.fastq.gz ]
		then
		gunzip -k ${read1}.fq.gz
		read1=${read1}.fastq
		echo $read1
		else
		echo $read1 not found
		fi
		fi

		if [[ ${#read2[@]} == 1 ]]
		then
		echo " checking file format for $read2 ..."
		if [ -f $read2 ]
		then
		echo $read2
		elif [ -f ${read2}.fq ]
		then
		read2=${read2}.fq
		echo $read2
		elif [ -f ${read2}.fastq ]
		then
		read2=${read2}.fastq
		echo $read2
		elif [ -f ${read2}.fq.gz ]
		then
		gunzip -k ${read2}.fq.gz
		read2=${read2}.fq
		echo $read2
		elif [ -f ${read2}.fastq.gz ]
		then
		gunzip -k ${read2}.fq.gz
		read2=${read2}.fastq
		echo $read2
		else
		echo $read2 not found
		fi
		fi

		for i in ${!read1[@]}
		do
		read=${read1[$i]}
		@@ -570,7 +512,7 @@ done
		for i in ${!read2[@]}
		do
		read=${read2[$i]}
		echo " checking file format for $read1 ..."
		echo " checking file format for $read2 ..."
		if [ -f $read ]
		then
		echo $read
		@@ -598,8 +540,71 @@ read=${read2[$i]}
		read2[$i]=$read
		done

		echo files: $read1 $Read1$ and $read2 $Read2$
		echo " checking file name for $read1 ..."
		for i in ${!read1[@]}
		do
		read=${read1[$i]}
		case $read in
		#check if contains lane before read
		(_L0[0123456789][0123456789]_R[12]) echo " $read compatible with lane";;
		(*) echo " converting $read..."
		#rename file
		echo " assuming 1 lane if none given"
		rename "s/_R1/_L001_R1/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R1/_L001_R1/g"`
		read1[$i]=$read
		echo " renaming $read ...";;
		esac
		case $read in
		#check if contains sample before lane
		(_S[123456789]_L0) echo " $read compatible with sample";;
		(*) echo " converting $read ..."
		#rename file
		j=$((${i}+1))
		rename "s/_L0/_S${j}_L0/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${j}_L0/g"`
		read1[$i]=$read
		echo " renaming $read ...";;
		esac
		done

		echo " checking file name for $read2 ..."
		for i in ${!read2[@]}
		do
		read=${read2[$i]}
		case $read in
		#check if contains lane before read
		(_L0[0123456789][0123456789]_R[12]) echo " $read compatible with lane";;
		(*) echo " converting $read..."
		#rename file
		echo " assuming 1 lane if none given"
		rename "s/_R2/_L001_R2/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R2/_L001_R2/g"
		read2[$i]=$read
		echo " renaming $read ...";;
		esac
		case $read in
		#check if contains sample before lane
		(_S[123456789]_L0) echo " $read compatible with sample";;
		(*) echo " converting $read ..."
		#rename file
		j=$((${i}+1))
		rename "s/_L0/_S${j}_L0/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${j}_L0/g"`
		read2[$i]=$read
		echo " renaming $read ...";;
		esac
		done

		echo " files: ${read1[@]} $Read1$"
		echo " ${read2[@]} $Read2$"

		#test exit
		exit 0
		#checking the quality of fastq file names
		SAMPLE=""
		LANE=()

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