loop incorporated to go through read1 files and read2 files in one go. (993f5f1e) · Commits · github_fork / Universc

launch_universc.sh

+139 −231

Original line number	Diff line number	Diff line
		@@ -293,12 +293,21 @@ if [[ $setup == "false" ]]; then
		fi
		fi

		#check for file type (extension) for files
		#check read1 and read2 files for their extensions
		##allows incomplete file names and processing compressed files
		for i in ${!read1[@]}; do
		read=${read1[$i]}
		for i in {1..2}; do
		readkey=R$i
		list=""
		if [[ $readkey == "R1" ]]; then
		list=("${read1[@]}")
		elif [[ $readkey == "R2" ]]; then
		list=("${read2[@]}")
		fi

		for j in ${!list[@]}; do
		read=${list[$j]}
		if [[ $verbose == "true" ]]; then
		echo " checking file format for $read1 ..."
		echo "checking file format for $read ..."
		fi
		if [[ -f $read ]] && [[ -h $read ]]; then
		if [[ $read == *"gz" ]]; then
		@@ -307,7 +316,8 @@ for i in ${!read1[@]}; do
		read=`echo $read \| sed -e "s/\.gz//g"`
		fi
		if [[ $read != "fastq" ]] && [[ $read != "fq" ]]; then
		echo "*Warning: file $read is assumed to be in fastq format*"
		echo "Error: file $read needs a .fq or .fastq extention."
		exit 1
		fi
		if [[ $verbose == "true" ]]; then
		echo " $read"
		@@ -319,7 +329,8 @@ for i in ${!read1[@]}; do
		read=`echo $read \| sed -e "s/\.gz//g"`
		fi
		if [[ $read != "fastq" ]] && [[ $read != "fq" ]]; then
		echo "*Warning: file $read is assubed to be in fastq format*"
		echo "Error: file $read needs a .fq or .fastq extention."
		exit 1
		fi
		if [[ $verbose == "true" ]]; then
		echo " $read"
		@@ -328,126 +339,32 @@ for i in ${!read1[@]}; do
		echo "Error: $read not found"
		exit 1
		fi
		read1[$i]=$read
		list[$j]=$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 is assubed to be in fastq format*"
		if [[ $readkey == "R1" ]]; then
		read1=("${list[@]}")
		elif [[ $readkey == "R2" ]]; then
		read2=("${list[@]}")
		fi
		if [[ $verbose == "true" ]]; then
		echo " $read"
		fi
		elif [[ -f $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 is assubed to be in fastq format*"
		fi
		if [[ $verbose = "true" ]]; then
		echo " $read"
		fi
		else
		echo "Error: $read not found"
		exit 1
		fi
		read2[$i]=$read
		done

		#renaming read1 and read 2 files if not compatible with the convention.
		if [[ $verbose == "true" ]]; then
		echo " checking file name for $read1 ..."
		#renaming read1 and read2 files if not compatible with the convention
		for i in {1..2}; do
		readkey=R$i
		list=""
		if [[ $readkey == "R1" ]]; then
		list=("${read1[@]}")
		elif [[ $readkey == "R2" ]]; then
		list=("${read2[@]}")
		fi

		for i in ${!read1[@]}; do
		read=${read1[$i]}
		if [[ -h $read ]]; then
		path=`readlink -f $read`
		if [[ $verbose == "true" ]]; then
		echo " *Warning: file $read not in current directory. Path to the file captured instead.*"
		echo " (file) $read"
		echo " (path) $path"
		fi
		read=${path}
		fi
		case $read in
		#check if contains lane before read
		_L0[0123456789][0123456789]_R1)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with lane"
		fi
		;;
		*)
		#rename file
		for j in ${!list[@]}; do
		read=${list[$j]}
		if [[ $verbose == "true" ]]; then
		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
		echo " renaming $read ..."
		echo " checking file name for $read ..."
		fi
		rename "s/_R1/_L001_R1/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R1/_L001_R1/g"`
		read1[$i]=$read
		;;
		esac
		case $read in
		#check if contains sample before lane
		_S[123456789]_L0)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with sample"
		fi
		;;
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		echo "*Warning: file $read does not have sample value in its name. Sample $j is assumed.*"
		echo " renaming $read ..."
		fi
		j=$((${i}+1))
		rename "s/_L0/_S${j}_L0/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${j}_L0/g"`
		read1[$i]=$read
		;;
		esac
		case $read in
		#check if contains sample before lane
		_R1_001.)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with suffix"
		fi
		;;
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"
		echo " renaming $read ..."
		fi
		rename "s/_R1.*\./_R1_001\./" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R1.*\./_R1_001\./g"`
		read1[$i]=$read
		;;
		esac
		done

		if [[ $verbose == "true" ]]; then
		echo " checking file name for $read2 ..."
		fi
		for i in ${!read2[@]}; do
		read=${read2[$i]}
		if [[ -h $read ]]; then
		path=`readlink -f $read`
		if [[ $verbose == "true" ]]; then
		@@ -459,7 +376,7 @@ for i in ${!read2[@]}; do
		fi
		case $read in
		#check if contains lane before read
		_L0[0123456789][0123456789]_R2)
		_L0[0123456789][0123456789]_$readkey)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with lane"
		fi
		@@ -470,10 +387,10 @@ for i in ${!read2[@]}; do
		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
		echo " renaming $read ..."
		fi
		rename "s/_R2/_L001_R2/" $read
		rename "s/_$raadkey/_L001_$readkey/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R2/_L001_R2/g"`
		read2[$i]=$read
		read=`echo $read \| sed -e "s/_${readkey}/_L001_${raedkey}/g"`
		list[$j]=$read
		;;
		esac
		case $read in
		@@ -486,19 +403,19 @@ for i in ${!read2[@]}; do
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		echo "*Warning: file $read does not have sample value in its name. Sample $j is assumed.*"
		echo "*Warning: file $read does not have sample value in its name. Sample $k is assumed.*"
		echo " renaming $read ..."
		fi
		j=$((${i}+1))
		rename "s/_L0/_S${j}_L0/" $read
		k=$((${j}+1))
		rename "s/_L0/_S${k}_L0/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${j}_L0/g"`
		read2[$i]=$read
		list[$j]=$read
		;;
		esac
		case $read in
		#check if contains sample before lane
		_R2_001.)
		_${readkey}_001.)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with suffix"
		fi
		@@ -509,48 +426,33 @@ for i in ${!read2[@]}; do
		echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"
		echo " renaming $read ..."
		fi
		rename "s/_R2.*\./_R2_001\./" $read
		rename "s/_${readkey}.*\./_${readkey}_001\./" $read
		#update file variable
		read=`echo $read \| sed -e "s/_R2.*\./_R2_001\./g"`
		read2[$i]=$read
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${raedkey}_001\./g"`
		list[$j]=$read
		;;
		esac
		done

		#checking the quality of fastq file names
		for fq in "${read1[@]}"; do
		name=`basename $fq \| cut -f1 -d'.' \| grep -o "_" \| wc -l \| xargs`
		sn=`basename $fq \| cut -f1-$(($name-3)) -d'_'`
		ln=`basename $fq \| cut -f$(($name-1)) -d'_' \| sed 's/L00//'`
		LANE+=($ln)
		if [[ $name < 4 ]]; then
		echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";
		exit 1
		elif [[ $fq != '.fastq' ]] && [[ $fq != '.fq' ]]; then
		echo "Error: $fq does not have a .fq or .fastq extention"
		exit 1
		fi

		if [[ $sn != $SAMPLE ]]; then
		if [[ -z $SAMPLE ]]; then
		SAMPLE=$sn
		else
		echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."
		exit 1
		fi
		if [[ $readkey == "R1" ]]; then
		read1=("${list[@]}")
		elif [[ $readkey == "R2" ]]; then
		read2=("${list[@]}")
		fi
		done
		for fq in "${read2[@]}"; do

		#checking the quality of fastq file names
		read12=("${read1[@]}" "${read2[@]}")
		for fq in "${read12[@]}"; do
		name=`basename $fq \| cut -f1 -d'.' \| grep -o "_" \| wc -l \| xargs`
		sn=`basename $fq \| cut -f1-$(($name-3)) -d'_'`
		ln=`basename $fq \| cut -f$(($name-1)) -d'_' \| sed 's/L00//'`
		LANE+=($ln)

		if [[ $name < 4 ]]; then
		echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";
		exit 1
		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
		fi

		@@ -598,7 +500,7 @@ elif [[ "$jobmode" != "local" ]] && [[ "$jobmode" != "sge" ]] && [[ "$jobmode" !
		exit 1
		fi

		#check if setup needs to be run before analysis
		#check if setup needs to be run before analysis (potentially overriding the user input)
		if [[ -z $setup ]]; then
		setup=false
		fi
		@@ -606,6 +508,13 @@ if [[ $lastcall != $technology ]]; then
		setup=true
		fi

		#check if convertion is needs to be run before analysis (potentially overriding the user input)
		if [[ $technology == "10x" ]]; then
		convert=false
		elif [[ ! -d $crIN ]] \|\| [[ $lastcall != $technology ]]; then
		convert=true
		fi

		#check if ID is present
		if [[ -z $id ]]; then
		if [[ ${#read1[@]} -ne 0 ]] \|\| [[ ${#read2[@]} -ne 0 ]]; then
		@@ -916,7 +825,6 @@ convFiles=()

		if [[ ! -d $crIN ]] \|\| [[ $lastcall != $technology ]]; then
		echo " directory $crIN created for converted files"
		convert=true
		if [[ -d $crIN ]]; then
		rm -rf $crIN
		fi

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