update parsing R3 and I1 files for 10x 3` scRNA v1 (e6f5fe3d) · Commits · github_fork / Universc

launch_universc.sh

+20 −5

Original line number	Diff line number	Diff line
		@@ -1024,6 +1024,8 @@ fi


		#index 1
		r4_present="false"
		i1_present="false"
		if [[ $setup == "false" ]]; then
		if [[ ${#index1[@]} -ne ${#read1[@]} ]]; then
		if [[ ${#index1[@]} -gt 0 ]]; then
		@@ -1045,6 +1047,7 @@ if [[ $setup == "false" ]]; then
		R4_file=$(echo $read \| perl -pne 's/(.*)_R1/$1_R4/' )
		I1_file=$(echo $read \| perl -pne 's/(.*)_R1/$1_I1/' )
		if [[ -f $R4_file ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'.gz') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'.fastq') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then
		r4_present="true"
		if [[ $verbose ]]; then
		echo " file $R4_file found, replacing $R1_file ..."
		fi
		@@ -1062,6 +1065,7 @@ if [[ $setup == "false" ]]; then
		i1_list[$j]=$i1_read
		fi
		if [[ -f $I1_file ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'.gz') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'.fastq') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fq') ]]; then
		i1_present="true"
		if [[ $verbose ]]; then
		echo " file $I1_file found ..."
		fi
		@@ -1087,9 +1091,11 @@ if [[ $setup == "false" ]]; then
		fi

		#index 2
		r3_present="false"
		i2_present="false"
		if [[ $setup == "false" ]]; then
		#only check I2 for dual-indexed techniques
		if [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "sciseq2" ]] \|\| [[ "$technology" == "sciseq3" ]] \|\| [[ "$technology" == "scifiseq" ]] \|\| [[ "$technology" == "smartseq"* ]]; then
		if [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "sciseq2" ]] \|\| [[ "$technology" == "sciseq3" ]] \|\| [[ "$technology" == "scifiseq" ]] \|\| [[ "$technology" == "smartseq"* ]] \|\| [[ "$chemistry" == "SC3Pv1" && "$technology" == "10x" ]]; then
		if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then
		if [[ ${#index2[@]} -gt 0 ]]; then
		echo " Error: number of index1 files is not matching the number of index2 files"
		@@ -1110,6 +1116,7 @@ if [[ $setup == "false" ]]; then
		R3_file=$(echo $read \| perl -pne 's/(.*)_R1/$1_R3/' )
		I2_file=$(echo $read \| perl -pne 's/(.*)_R1/$1_I2/' )
		if [[ -f $R3_file ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'.gz') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'.fastq') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq') ]]; then
		r3_present="true"
		if [[ $verbose ]]; then
		echo " file $R3_file found, replacing $I2_file ..."
		fi
		@@ -1117,6 +1124,7 @@ if [[ $setup == "false" ]]; then
		i2_list[$j]=$i1_read
		fi
		if [[ -f $I2_file ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'.gz') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'.fastq') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then
		i2_present="true"
		if [[ $verbose ]]; then
		echo " file $I2_file found ..."
		fi
		@@ -1158,10 +1166,17 @@ if [[ $verbose ]]; then
		fi

		keys=("R1" "R2")
		if [[ ${#index2[@]} -gt 0 ]]; then
		keys=("R1" "R2" "I1" "I2")
		elif [[ ${#index1[@]} -gt 0 ]]; then
		keys=("R1" "R2" "I1")
		if [[ $r3_present == "true" ]]; then
		keys=(${keys[@]} "R3")
		fi
		if [[ $r4_present == "true" ]]; then
		keys=(${keys[@]} "R4")
		fi
		if [[ $i1_present == "true" ]]; then
		keys=(${keys[@]} "I1")
		fi
		if [[ $i2_present == "true" ]]; then
		keys=(${keys[@]} "I2")
		fi
		##########

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