kkonganti@0: #!/usr/bin/env bash
kkonganti@0: 
kkonganti@0: ##########################################################
kkonganti@0: # Constants
kkonganti@0: ##########################################################
kkonganti@0: GREEN=$(tput setaf 2)
kkonganti@0: RED=$(tput setaf 1)
kkonganti@0: CYAN=$(tput setaf 6)
kkonganti@0: CLRESET=$(tput sgr0)
kkonganti@0: prog_name="nowayout"
kkonganti@0: dbBuild="03182024"
kkonganti@0: dbPath="/hpc/db/${prog_name}/$dbBuild"
kkonganti@0: taxonomyPath="$dbPath/taxonomy"
kkonganti@0: 
kkonganti@0: usage()
kkonganti@0: {
kkonganti@0:     echo
kkonganti@0:     echo usage: "$0" [-h] 
kkonganti@0:     echo
kkonganti@0:     echo "Check for species presence in ${prog_name} database(s)."
kkonganti@0:     echo
kkonganti@0:     echo 'Example usage:'
kkonganti@0:     echo
kkonganti@0:     echo 'dbcheck -l'
kkonganti@0:     echo 'dbcheck -g Cathartus'
kkonganti@0:     echo 'dbcheck -d mitomine -g Cathartus'
kkonganti@0:     echo 'dbcheck -d mitomine -s "Cathartus quadriculus"'
kkonganti@0:     echo
kkonganti@0:     echo 'Options:'
kkonganti@0:     echo " -l        : List ${prog_name} databases"
kkonganti@0:     echo ' -d        : Search this database. Default: mitomine.'
kkonganti@0:     echo ' -g        : Genus to search for.'
kkonganti@0:     echo ' -s        : "Genus Species" to search for.'
kkonganti@0:     echo ' -h        : Show this help message and exit'
kkonganti@0:     echo
kkonganti@0:     echo "$1"
kkonganti@0: }
kkonganti@0: 
kkonganti@0: while getopts ":d:g:s:l" OPT; do
kkonganti@0:     case "${OPT}" in
kkonganti@0:         l)
kkonganti@0:             listdb="list"
kkonganti@0:             ;;
kkonganti@0:         d)
kkonganti@0:             dbname=${OPTARG}
kkonganti@0:             ;;
kkonganti@0:         g)
kkonganti@0:             genus=${OPTARG}
kkonganti@0:             ;;
kkonganti@0:         s)
kkonganti@0:             species=${OPTARG}
kkonganti@0:             ;;
kkonganti@0:         ?)
kkonganti@0:             usage
kkonganti@0:             exit 0
kkonganti@0:             ;;
kkonganti@0:     esac
kkonganti@0: done
kkonganti@0: 
kkonganti@0: 
kkonganti@0: 
kkonganti@0: if [ -n "$listdb" ]; then
kkonganti@0:     num_dbs=$(find "$taxonomyPath" -type d | tail -n+2 | wc -l)
kkonganti@0:     echo "=============================================="
kkonganti@0:     
kkonganti@0:     db_num="1"
kkonganti@0:     find $taxonomyPath -type d | tail -n+2 | while read -r db; do
kkonganti@0:         dbName=$(basename "$db")
kkonganti@0:         echo "${db_num}. $dbName"
kkonganti@0:         db_num=$(( db_num + 1 ))
kkonganti@0:     done
kkonganti@0:     echo "=============================================="
kkonganti@0:     echo "Number of ${prog_name} databases: $num_dbs"
kkonganti@0:     echo "=============================================="
kkonganti@0: 
kkonganti@0:     exit 0
kkonganti@0: fi
kkonganti@0: 
kkonganti@0: 
kkonganti@0: 
kkonganti@0: if [ -z "$dbname" ]; then
kkonganti@0:     dbname="mitomine"
kkonganti@0: fi
kkonganti@0: 
kkonganti@0: if [[ -n "$genus" && -n "$species" ]]; then
kkonganti@0:     usage "ERROR: Only one of -g or -s needs to be defined!"
kkonganti@0:     exit 1
kkonganti@0: elif [ -n "$genus" ]; then
kkonganti@0:     check="$genus"
kkonganti@0: elif [ -n "$species" ]; then
kkonganti@0:     check="$species"
kkonganti@0: else 
kkonganti@0:     check=""
kkonganti@0: fi
kkonganti@0: 
kkonganti@0: if [ -z "$check" ]; then
kkonganti@0:     usage "ERROR: -g or -s is required! check:$check"
kkonganti@0:     exit 1
kkonganti@0: fi
kkonganti@0: 
kkonganti@0: lineages="$taxonomyPath/$dbname/lineages.csv"
kkonganti@0: 
kkonganti@0: echo
kkonganti@0: echo -e "Checking ${dbname} for ${CYAN}${check}${CLRESET}...\nPlease wait..."
kkonganti@0: echo
kkonganti@0: 
kkonganti@0: num=$(grep -F ",$check," "$lineages" | cut -f1 -d, | sort -u | wc -l)
kkonganti@0: num_species=$(tail -n+2 "$lineages" | cut -f8 -d, | sort -u | wc -l)
kkonganti@0: num_entries=$(tail -n+2 "$lineages" | wc -l)
kkonganti@0: 
kkonganti@0: echo "$dbname brief stats"
kkonganti@0: echo "=============================================="
kkonganti@0: echo "DB Build: $dbBuild"
kkonganti@0: echo "Number of unique species: $num_species"
kkonganti@0: echo "Number of accessions in database: $num_entries"
kkonganti@0: echo "=============================================="
kkonganti@0: 
kkonganti@0: 
kkonganti@0: if [ "$num" -gt 0 ]; then
kkonganti@0:     echo
kkonganti@0:     echo "${GREEN}$check is present in ${dbname}${CLRESET}."
kkonganti@0:     echo "Number of accessions representing $check: $num"
kkonganti@0:     echo "=============================================="
kkonganti@0: else
kkonganti@0:     echo "${RED}$check is absent in ${dbname}${CLRESET}."
kkonganti@0:     echo -e "No worries. Please request the developer of\n${prog_name} to augment the database!"
kkonganti@0:     echo "=============================================="
kkonganti@0: fi