2020-09-23bash脚本的模板开头

#!/bin/bash
 
######################################################
#参数传递
while getopts "l:m:s:h" opt; do
  case $opt in
    l)
      slist=$OPTARG
      ;;
    m)
      maxtseq=$OPTARG
      ;;
    s)
      matchsize=$OPTARG 
      ;;
    h)
     echo "" 
      ;;      
#    \?)
#     echo "Invalid option: -$OPTARG" 
#     ;;
  esac
done

######################################################
#帮助文档
display_usage() {
        echo -e "\nThis script is for identifing different modes of duplicated gene pairs and genes"
        echo -e "\n\tUsage:bash dupGenFinder.sh -l -m -s \n"
        echo -e "\t-l: The target species list file \n"
        echo -e "\t-m: parameter for blastp: -max_target_seqs, default is 5 \n"
        echo -e "\t-s: match_size (number of genes required to call a collinear block for MCScanX), default is 5 \n\n"
        }


# if less than one arguments supplied, display usage 
    if [  $# -le 0 ] 
    then 
        display_usage
        exit 1
    fi 
    
# check whether user had supplied -h or --help . If yes display usage 
    if [[ ( $* == "--help") ||  $* == "-h" ]] 
    then 
        display_usage
        exit 0
    fi 

######################################################
#变量判定

if [ ! $matchsize ];then
    matchsize=5
fi

if [ ! $maxtseq ];then
    maxtseq=5
fi

if [ ! $slist ];then
    echo -e "\tERROR: Lack of required list file of species names"
    echo -e '\tExample: echo -e "Arabidopsis_thaliana\\nLindera_megaphylla\\nGlycine_max" > SpeciesList'
    exit 1
fi