polish: use check function to check instead of setting help, check argc
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parent
01729e0726
commit
c0ea2c4318
1 changed files with 17 additions and 10 deletions
27
RGBEPP.sh
27
RGBEPP.sh
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@ -41,10 +41,18 @@ show_help(){
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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.exons.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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@ -71,7 +79,6 @@ while true; do
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esac ;;
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-h|--help)
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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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@ -109,8 +116,6 @@ while true; do
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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: $1"
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exit 1
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@ -118,6 +123,8 @@ while true; do
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esac
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done
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fi
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### Get and check some arguments
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check_var() {
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@ -139,6 +146,13 @@ check_var() {
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readarray -t full_names < "$var_value"
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length_fn=${#full_names[@]}
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;;
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"ARG_F")
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check_command "cp"
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check_command "cd"
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check_command "mv"
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check_command "find"
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check_command "mkdir"
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;;
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esac
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fi
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@ -170,13 +184,6 @@ check_command() {
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fi
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}
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if [ "$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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