371 lines
9.4 KiB
Bash
Executable file
371 lines
9.4 KiB
Bash
Executable file
#!/bin/bash
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### Environment Setting
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pkgver=0.0.2
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DirHome=$(pwd)
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DirRaw=$DirHome/00_raw
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DirQcTrim=$DirHome/01_fastp
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DirAssembly=$DirHome/02_spades
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DirFasta=$DirHome/03_assemblied
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DirMap=$DirHome/04_diamond
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DirPre=$DirHome/05_pre
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DirSplit=$DirHome/06_split
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DirMerge=$DirHome/07_merge
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DirAlign=$DirHome/08_macse
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PathSplitfsata=/usr/bin/splitfasta-cpp
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PathMacse=/usr/share/java/macse.jar
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PathSortdiamond=/usr/bin/sortdiamond
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ARG_C='scaffolds'
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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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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-2.0-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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\t--macse\t\tMacse jarfile path\n \
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\t--sortdiamond\tsortdiamond file path\n \
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\t--splitfasta\tsplitfasta file path\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.aa.fas \n"
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}
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if [ $# -eq 0 ]; then
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show_help
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exit 1
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else
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ARGS=$(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 [ $? != 0 ]; then
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echo "Failed to parse options." >&2
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exit 1
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fi
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eval set -- "$ARGS"
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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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"") 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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case "$2" in
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"") shift 2 ;;
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*) ARG_G=$2; shift 2 ;;
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esac ;;
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-f|--functions)
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case "$2" in
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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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show_help
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shift ;;
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-l|--list)
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case "$2" in
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"") shift 2 ;;
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*) ARG_L=$2; shift 2 ;;
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esac ;;
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-m|--memory)
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case "$2" in
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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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case "$2" in
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"") shift 2 ;;
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*) ARG_R=$2; shift 2 ;;
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esac ;;
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-t|--threads)
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case "$2" in
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"") shift 2 ;;
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*) ARG_T=$2; shift 2 ;;
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esac ;;
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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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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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fi
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### Get and check some arguments
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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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"ARG_F")
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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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;;
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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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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: $cmd_name command not found."
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exit 1
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fi
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}
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### Quality control && Trimming
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if [ "$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 $ARG_T
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done
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fi
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### De novo assembly
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if [ "$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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spades.py --pe1-1 $DirQcTrim/${full_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${full_names[$i]}_R2.fastq.gz -t $ARG_T -m $ARG_M --careful --phred-offset 33 -o $DirAssembly/${full_names[$i]}
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# -k 96,107,117,127 \
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done
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fi
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### Moving scaffords or Contigs out
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "fasta" ]; then
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## Check if the contigs type is specified
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check_var "ARG_C"
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check_var "ARG_L"
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## Prepare
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mkdir -p $DirFasta
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## Move the assemblied fasta file to the folder
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if [ "$ARG_C" = "scaffolds" ] || [ "$ARG_C" = "contigs" ] ; then
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for (( i=0; i<$length_fn; i++ )); do
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cp $DirAssembly/${full_names[$i]}/$ARG_C.fasta $DirFasta/$ARG_C/${full_names[$i]}.fasta
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done
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fi
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fi
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### Mapping
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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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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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## Index reference database
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cd $DirFasta/$ARG_C
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diamond makedb --db Reference --in $ARG_R
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cd -
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## Blastx for mapping DNA sequences to protein reference sequence
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cd $DirFasta/$ARG_C
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for (( i=0; i<$length_fn; i++ )); do
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diamond blastx -d Reference.dmnd -q ${full_names[$i]}.fasta -o ${full_names[$i]}.m8 \
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--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen gaps ppos qframe qseq
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# subject: reference; query: align-aimed
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#1: qseqid: Query Seq-id
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#2: sseqid: Subject Seq - id
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#3: pident: Percentage of identical matches
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#4: length: Alignment length
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#5: mismatch: Number of mismatches
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#6: gapopen: Number of gap openings
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#7: qstart: Start of alignment in query
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#8: qend: End of alignment in query
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#9: sstart: Start of alignment in subject
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#10: send: End of alignment in subject
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#11: evalue: Expect value
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#12: bitscore: Bit score
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#13: qlen: Query sequence length
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#14: slen: Subject sequence length
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#15: gaps: Total number of gaps
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#16: ppos: Percentage of positive - scoring matches
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#17: qframe: Query frame (frames in blast?)
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#18: qseq: Aligned part of query sequence
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done
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cd -
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mv $DirFasta/$ARG_C/*.m8 $DirMap
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
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mkdir -p $DirPre
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check_var "ARG_L"
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check_path "PathSortdiamond"
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# extract fasta file from diamond balst style output
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for (( i=0; i<$length_fn; i++ )); do
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$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
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done
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
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mkdir -p $DirSplit
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cd $DirPre
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check_var "ARG_L"
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check_path "PathSplitfasta"
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# split fasta into different folders based on sequence names
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for (( i=0; i<$length_fn; i++ )); do
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$PathSplitfsata ${full_names[$i]}.fasta
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done
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# mv to destdir
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find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
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cd -
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
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## Check if the genes is specified
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check_var "ARG_G"
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mkdir -p $DirMerge
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cd $DirSplit
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# merge different taxa sequences in same gene to one fasta
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for (( i=0; i<$length_gn; i++ ))
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do
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cd ${genes[$i]}
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cat * > ../${genes[$i]}.fasta
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cd ..
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done
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# mv to destdir
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mv *.fasta ../$DirMerge
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cd -
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fi
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if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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## Check if the genes is specified
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check_var "ARG_G"
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check_command "java"
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check_command "parallel"
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check_path "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 the sequence based on codon
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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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fi
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