polish: add check function
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e8e40e4327
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01729e0726
1 changed files with 141 additions and 67 deletions
202
RGBEPP.sh
202
RGBEPP.sh
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@ -19,9 +19,33 @@ PathSortdiamond=/home/guoyi/Downloads/PhD/wes/sortdiamond
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HELP=false
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ARG_C='scaffolds'
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#ARG_F='all'
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ARG_M=16
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ARG_T=8
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### Get some arrays
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ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads: -n 'RGBEPP.sh' -- "$@")
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show_help(){
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# echo -e "\t\t\t\t\t\t\t\033[0;31mR\033[0m\033[0;92mG\033[0m\033[0;94mB\033[0m \033[0;33mE\033[0m\033[0;94mP\033[0m\033[0;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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echo -e "\t\t\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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Version: $pkgver\n \
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License: GPL-3.0-only\n \
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Author: Guoyi Zhang\n \
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-c\t--contigs\tcontings type: scaffolds or contigs\n \
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-g\t--genes\t\tgene file path\n \
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-f\t--functions\tfunctions type (optional): all clean \n \
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\t \t\tassembly fasta map pre split merge align\n \
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-h\t--help\t\tshow this information\n \
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-l\t--list\t\tlist file path\n \
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-m\t--memory\tmemory settings (optional, default 16 GB)\n \
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-r\t--reference\treference genome path\n \
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-t\t--threads\tthreads setting (optional, default 8 threads)\n \
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for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
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\t -r Reference.exons.aa.fas \n"
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}
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ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads:,macse:,sortdiamond:,splitfasta: -n 'RGBEPP.sh' -- "$@")
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if [ $? != 0 ]; then
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echo "Failed to parse options." >&2
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exit 1
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@ -32,7 +56,7 @@ while true; do
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case "$1" in
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-c|--contigs)
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case "$2" in
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"") ARG_C='scaffolds'; shift 2 ;;
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"") shift 2 ;;
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*) ARG_C=$2; shift 2 ;;
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esac ;;
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-g|--genes)
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@ -42,26 +66,12 @@ while true; do
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esac ;;
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-f|--functions)
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case "$2" in
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"") ARG_F='all'; shift 2 ;;
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"") shift 2 ;;
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*) ARG_F=$2; shift 2 ;;
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esac ;;
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-h|--help)
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# echo -e "\t\t\t\t\t\t\t\033[0;31mR\033[0m\033[0;92mG\033[0m\033[0;94mB\033[0m \033[0;33mE\033[0m\033[0;94mP\033[0m\033[0;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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echo -e "\t\t\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
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Version: $pkgver\n \
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License: GPL-3.0-only\n \
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Author: Guoyi Zhang\n \
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-c\t--contigs\tcontings type: scaffolds or contigs\n \
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-g\t--genes\t\tgene file path\n \
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-f\t--functions\tfunctions type (optional): all clean \n \
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\t \t\tassembly fasta map pre split merge align\n \
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-h\t--help\t\thelp: show this information\n \
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-l\t--list\t\tlist file path\n \
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-m\t--memory\tmemory settings (optional, default 16 GB)\n \
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-r\t--reference\treference genome path\n \
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-t\t--threads\tthreads setting (optional, default 8 threads)\n \
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for example: bash $0 -c scaffolds -f all -l list -g genes -r Reference.exons.aa.fas \n"
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HELP=true
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show_help
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HELP=true;
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shift ;;
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-l|--list)
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case "$2" in
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@ -70,7 +80,7 @@ while true; do
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esac ;;
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-m|--memory)
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case "$2" in
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"") ARG_M=16; shift 2 ;;
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"") shift 2 ;;
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*) ARG_M=$2; shift 2 ;;
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esac ;;
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-r|--reference)
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@ -80,26 +90,92 @@ while true; do
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esac ;;
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-t|--threads)
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case "$2" in
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"") ARG_T=8; shift 2 ;;
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"") shift 2 ;;
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*) ARG_T=$2; shift 2 ;;
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esac ;;
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--) shift; break ;;
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*) echo "Internal error!"; exit 1 ;;
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--macse)
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case "$2" in
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"") shift 2 ;;
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*) PathMacse=$2; shift 2 ;;
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esac ;;
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--sortdiamond)
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case "$2" in
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"") shift 2 ;;
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*) PathSortdiamond=$2; shift 2 ;;
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esac ;;
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--splitfasta)
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case "$2" in
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"") shift 2 ;;
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*) PathSplitfsata=$2; shift 2 ;;
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esac ;;
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--)
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show_help
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HELP=true
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shift; break ;;
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*) echo "Unknown option: $1"
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exit 1
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;;
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esac
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done
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### Get and check some arguments
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if [ "$HELP" = false ]; then
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if [ -z "$ARG_L" ]; then
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echo "List argument can't be empty"
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check_var() {
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local var_name="$1"
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local var_value="${!var_name}" # get value
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if [ -z "$var_value" ]; then
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echo "Error: $var_name is not set or is empty"
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exit 1
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else
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echo "$var_name is set to: $var_value"
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case "$var_name" in
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"ARG_G")
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readarray -t genes < "$var_value"
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length_gn=${#genes[@]}
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;;
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"ARG_L")
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readarray -t full_names < "$var_value"
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length_fn=${#full_names[@]}
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;;
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esac
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fi
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}
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check_path(){
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local path_name="$1"
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local path_value="${!path_name}" # get value
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# expand ~
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path_value=$(eval echo "$path_value")
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if [ -e "$path_value" ]; then
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echo "$path_name exists at: $path_value"
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else
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echo "Error: $path_name does not exist at: $path_value"
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exit 1
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fi
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}
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readarray -t full_names < "$ARG_L"
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readarray -t genes < "$ARG_G"
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length_fn=${#full_names[@]}
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length_gn=${#genes[@]}
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check_command() {
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local cmd_name="$1"
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if command -v "$cmd_name" >/dev/null 2>&1; then
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echo "$cmd_name command exists."
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else
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echo "Error: $cmd_name command not found."
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exit 1
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fi
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}
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if [ "$HELP" = false ]; then
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check_command "cp"
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check_command "cd"
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check_command "mv"
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check_command "find"
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check_command "mkdir"
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fi
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### Quality control && Trimming
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@ -109,6 +185,15 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "clean" ]; then
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## Prepare
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mkdir -p $DirQcTrim
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check_var "ARG_L"
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check_command "fastp"
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readarray -t full_names < "$ARG_L"
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length_fn=${#full_names[@]}
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readarray -t genes < "$ARG_G"
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length_gn=${#genes[@]}
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## Quality control and trimming using fastp
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for (( i=0; i<$length_fn; i++ )); do
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fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j $DirQcTrim/${full_names[$i]}.json -h $DirQcTrim/${full_names[$i]}.html -o $DirQcTrim/${full_names[$i]}_R1.fastq.gz -O $DirQcTrim/${full_names[$i]}_R2.fastq.gz -w $ARG_T
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@ -123,6 +208,9 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "assembly" ]; then
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## Prepare
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mkdir -p $DirAssembly
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check_var "ARG_L"
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check_command "spades.py"
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## De novo assembly using spades
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for (( i=0; i<$length_fn; i++ )); do
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mkdir -p $DirAssembly/${full_names[$i]}
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@ -137,10 +225,8 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "fasta" ]; then
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## Check if the contigs type is specified
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if [ -z "$ARG_C" ] ; then
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echo "Argument of contig type missing."
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exit 1
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fi
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check_var "ARG_C"
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check_var "ARG_L"
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## Prepare
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mkdir -p $DirFasta
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@ -159,10 +245,9 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
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## Check if the reference or contigs type is specified
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if [ -z "$ARG_R" ] || [ -z "$ARG_C" ] ; then
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echo "Argument of reference or contig type missing."
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exit 1
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fi
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check_var "ARG_C"
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check_var "ARG_R"
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check_command "diamond"
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## Prepare
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mkdir -p $DirMap
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@ -205,7 +290,12 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
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mkdir -p $DirPre
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check_var "ARG_L"
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checkPath "PathSortdiamond"
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for (( i=0; i<$length_fn; i++ )); do
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$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
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done
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@ -215,6 +305,10 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
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mkdir -p $DirSplit
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cd $DirPre
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check_var "ARG_L"
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checkPath "PathSplitfasta"
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for (( i=0; i<$length_fn; i++ )); do
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$PathSplitfsata ${full_names[$i]}.fasta
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done
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@ -225,10 +319,7 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
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## Check if the genes is specified
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if [ -z "$ARG_G" ] ; then
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echo "Argument of genes list missing."
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exit 1
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fi
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check_var "ARG_G"
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mkdir -p $DirMerge
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cd $DirSplit
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@ -246,34 +337,17 @@ fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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## Check if the genes is specified
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if [ -z "$ARG_G" ] ; then
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echo "Argument of genes list missing."
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exit 1
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fi
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check_var "ARG_G"
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check_command "java"
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check_command "parallel"
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checkPath "PathMacse"
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# current_thread=0
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mkdir -p $DirAlign
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mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
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cd $DirMerge
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align_by_macse() {
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java -jar $PathMacse -prog alignSequences -seq $1.fasta -out_AA ../$DirAlign/AA/$1.fasta -out_NT ../$DirAlign/NT/$1.fasta &
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}
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export -f align_by_macse
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parallel -j $ARG_T align_by_macse ::: "${genes[@]}"
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# for (( i=0; i<$length_gn; i++ ))
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# do
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# java -jar $PathMacse -prog alignSequences -seq ${genes[$i]}.fasta -out_AA ../$DirAlign/AA/${genes[$i]}.fasta -out_NT ../$DirAlign/NT/${genes[$i]}.fasta &
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# ((current_thread++))
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# if [ $current_thread -eq $ARG_T ]; then
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# wait
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# current_thread=0
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# fi
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# done
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parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
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cd -
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