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1 #!/usr/bin/env bash
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2
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3 ##########################################################
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4 # Constants
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5 ##########################################################
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6 GREEN=$(tput setaf 2)
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7 RED=$(tput setaf 1)
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8 CYAN=$(tput setaf 6)
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9 CLRESET=$(tput sgr0)
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10 prog_name="nowayout"
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11 dbBuild="03062025"
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12 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
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13 dbPath="${SCRIPT_DIR}/assets/dbfiles"
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14 taxonomyPath="$dbPath/taxonomy"
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15
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16 usage()
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17 {
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18 echo
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19 echo usage: "$0" [-h]
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20 echo
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21 echo "Check for species presence in ${prog_name} database(s)."
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22 echo
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23 echo 'Example usage:'
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24 echo
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25 echo 'dbcheck -l'
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26 echo 'dbcheck -g Cathartus'
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27 echo 'dbcheck -d mitomine -g Cathartus'
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28 echo 'dbcheck -d mitomine -s "Cathartus quadriculus"'
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29 echo
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30 echo 'Options:'
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31 echo " -l : List ${prog_name} databases"
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32 echo ' -d : Search this database. Default: mitomine.'
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33 echo ' -g : Genus to search for.'
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34 echo ' -s : "Genus Species" to search for.'
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35 echo ' -h : Show this help message and exit'
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36 echo
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37 echo "$1"
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38 }
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39
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40 while getopts ":d:g:s:l" OPT; do
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41 case "${OPT}" in
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42 l)
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43 listdb="list"
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44 ;;
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45 d)
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46 dbname=${OPTARG}
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47 ;;
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48 g)
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49 genus=${OPTARG}
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50 ;;
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51 s)
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52 species=${OPTARG}
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53 ;;
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54 ?)
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55 usage
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56 exit 0
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57 ;;
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58 esac
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59 done
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60
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61
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62
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63 if [ -n "$listdb" ]; then
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64 num_dbs=$(find -L "$taxonomyPath" -type d | tail -n+2 | wc -l)
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65 echo "=============================================="
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66
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67 db_num="1"
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68 find -L "$taxonomyPath" -type d | tail -n+2 | while read -r db; do
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69 dbName=$(basename "$db")
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70 echo "${db_num}. $dbName"
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71 db_num=$(( db_num + 1 ))
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72 done
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73 echo "=============================================="
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74 echo "Number of ${prog_name} databases: $num_dbs"
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75 echo "=============================================="
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76
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77 exit 0
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78 fi
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79
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80
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81
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82 if [ -z "$dbname" ]; then
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83 dbname="mitomine2"
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84 fi
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85
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86 if [[ -n "$genus" && -n "$species" ]]; then
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87 usage "ERROR: Only one of -g or -s needs to be defined!"
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88 exit 1
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89 elif [ -n "$genus" ]; then
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90 check="$genus"
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91 elif [ -n "$species" ]; then
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92 check="$species"
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93 else
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94 check=""
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95 fi
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96
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97 if [ -z "$check" ]; then
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98 usage "ERROR: -g or -s is required! check:$check"
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99 exit 1
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100 fi
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101
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102 lineages="$taxonomyPath/$dbname/lineages.csv"
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103
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104 echo
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105 echo -e "Checking ${dbname} for ${CYAN}${check}${CLRESET}...\nPlease wait..."
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106 echo
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107
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108 num=$(grep -F ",$check," "$lineages" | cut -f1 -d, | sort -u | wc -l)
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109 num_species=$(tail -n+2 "$lineages" | cut -f8 -d, | sort -u | wc -l)
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110 num_entries=$(tail -n+2 "$lineages" | wc -l)
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111
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112 echo "$dbname brief stats"
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113 echo "=============================================="
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114 echo "DB Build: $dbBuild"
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115 echo "Number of unique species: $num_species"
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116 echo "Number of accessions in database: $num_entries"
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117 echo "=============================================="
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118
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119
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120 if [ "$num" -gt 0 ]; then
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121 echo
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122 echo "${GREEN}$check is present in ${dbname}${CLRESET}."
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123 echo "Number of accessions representing $check: $num"
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124 echo "=============================================="
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125 else
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126 echo "${RED}$check is absent in ${dbname}${CLRESET}."
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127 echo -e "No worries. Please request the developer of\n${prog_name} to augment the database!"
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128 echo "=============================================="
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129 fi |
