Mercurial > repos > kkonganti > hfp_nowayout

annotate 0.5.0/dbcheck @ 10:74ac6f6a9526 tip

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planemo upload
author kkonganti
date Tue, 01 Apr 2025 11:08:01 -0400
parents 97cd2f532efe
children
rev   line source
kkonganti@0 1 #!/usr/bin/env bash
kkonganti@0 2
kkonganti@0 3 ##########################################################
kkonganti@0 4 # Constants
kkonganti@0 5 ##########################################################
kkonganti@0 6 GREEN=$(tput setaf 2)
kkonganti@0 7 RED=$(tput setaf 1)
kkonganti@0 8 CYAN=$(tput setaf 6)
kkonganti@0 9 CLRESET=$(tput sgr0)
kkonganti@0 10 prog_name="nowayout"
kkonganti@0 11 dbBuild="03182024"
kkonganti@0 12 dbPath="/hpc/db/${prog_name}/$dbBuild"
kkonganti@0 13 taxonomyPath="$dbPath/taxonomy"
kkonganti@0 14
kkonganti@0 15 usage()
kkonganti@0 16 {
kkonganti@0 17 echo
kkonganti@0 18 echo usage: "$0" [-h]
kkonganti@0 19 echo
kkonganti@0 20 echo "Check for species presence in ${prog_name} database(s)."
kkonganti@0 21 echo
kkonganti@0 22 echo 'Example usage:'
kkonganti@0 23 echo
kkonganti@0 24 echo 'dbcheck -l'
kkonganti@0 25 echo 'dbcheck -g Cathartus'
kkonganti@0 26 echo 'dbcheck -d mitomine -g Cathartus'
kkonganti@0 27 echo 'dbcheck -d mitomine -s "Cathartus quadriculus"'
kkonganti@0 28 echo
kkonganti@0 29 echo 'Options:'
kkonganti@0 30 echo " -l : List ${prog_name} databases"
kkonganti@0 31 echo ' -d : Search this database. Default: mitomine.'
kkonganti@0 32 echo ' -g : Genus to search for.'
kkonganti@0 33 echo ' -s : "Genus Species" to search for.'
kkonganti@0 34 echo ' -h : Show this help message and exit'
kkonganti@0 35 echo
kkonganti@0 36 echo "$1"
kkonganti@0 37 }
kkonganti@0 38
kkonganti@0 39 while getopts ":d:g:s:l" OPT; do
kkonganti@0 40 case "${OPT}" in
kkonganti@0 41 l)
kkonganti@0 42 listdb="list"
kkonganti@0 43 ;;
kkonganti@0 44 d)
kkonganti@0 45 dbname=${OPTARG}
kkonganti@0 46 ;;
kkonganti@0 47 g)
kkonganti@0 48 genus=${OPTARG}
kkonganti@0 49 ;;
kkonganti@0 50 s)
kkonganti@0 51 species=${OPTARG}
kkonganti@0 52 ;;
kkonganti@0 53 ?)
kkonganti@0 54 usage
kkonganti@0 55 exit 0
kkonganti@0 56 ;;
kkonganti@0 57 esac
kkonganti@0 58 done
kkonganti@0 59
kkonganti@0 60
kkonganti@0 61
kkonganti@0 62 if [ -n "$listdb" ]; then
kkonganti@0 63 num_dbs=$(find "$taxonomyPath" -type d | tail -n+2 | wc -l)
kkonganti@0 64 echo "=============================================="
kkonganti@0 65
kkonganti@0 66 db_num="1"
kkonganti@0 67 find $taxonomyPath -type d | tail -n+2 | while read -r db; do
kkonganti@0 68 dbName=$(basename "$db")
kkonganti@0 69 echo "${db_num}. $dbName"
kkonganti@0 70 db_num=$(( db_num + 1 ))
kkonganti@0 71 done
kkonganti@0 72 echo "=============================================="
kkonganti@0 73 echo "Number of ${prog_name} databases: $num_dbs"
kkonganti@0 74 echo "=============================================="
kkonganti@0 75
kkonganti@0 76 exit 0
kkonganti@0 77 fi
kkonganti@0 78
kkonganti@0 79
kkonganti@0 80
kkonganti@0 81 if [ -z "$dbname" ]; then
kkonganti@0 82 dbname="mitomine"
kkonganti@0 83 fi
kkonganti@0 84
kkonganti@0 85 if [[ -n "$genus" && -n "$species" ]]; then
kkonganti@0 86 usage "ERROR: Only one of -g or -s needs to be defined!"
kkonganti@0 87 exit 1
kkonganti@0 88 elif [ -n "$genus" ]; then
kkonganti@0 89 check="$genus"
kkonganti@0 90 elif [ -n "$species" ]; then
kkonganti@0 91 check="$species"
kkonganti@0 92 else
kkonganti@0 93 check=""
kkonganti@0 94 fi
kkonganti@0 95
kkonganti@0 96 if [ -z "$check" ]; then
kkonganti@0 97 usage "ERROR: -g or -s is required! check:$check"
kkonganti@0 98 exit 1
kkonganti@0 99 fi
kkonganti@0 100
kkonganti@0 101 lineages="$taxonomyPath/$dbname/lineages.csv"
kkonganti@0 102
kkonganti@0 103 echo
kkonganti@0 104 echo -e "Checking ${dbname} for ${CYAN}${check}${CLRESET}...\nPlease wait..."
kkonganti@0 105 echo
kkonganti@0 106
kkonganti@0 107 num=$(grep -F ",$check," "$lineages" | cut -f1 -d, | sort -u | wc -l)
kkonganti@0 108 num_species=$(tail -n+2 "$lineages" | cut -f8 -d, | sort -u | wc -l)
kkonganti@0 109 num_entries=$(tail -n+2 "$lineages" | wc -l)
kkonganti@0 110
kkonganti@0 111 echo "$dbname brief stats"
kkonganti@0 112 echo "=============================================="
kkonganti@0 113 echo "DB Build: $dbBuild"
kkonganti@0 114 echo "Number of unique species: $num_species"
kkonganti@0 115 echo "Number of accessions in database: $num_entries"
kkonganti@0 116 echo "=============================================="
kkonganti@0 117
kkonganti@0 118
kkonganti@0 119 if [ "$num" -gt 0 ]; then
kkonganti@0 120 echo
kkonganti@0 121 echo "${GREEN}$check is present in ${dbname}${CLRESET}."
kkonganti@0 122 echo "Number of accessions representing $check: $num"
kkonganti@0 123 echo "=============================================="
kkonganti@0 124 else
kkonganti@0 125 echo "${RED}$check is absent in ${dbname}${CLRESET}."
kkonganti@0 126 echo -e "No worries. Please request the developer of\n${prog_name} to augment the database!"
kkonganti@0 127 echo "=============================================="
kkonganti@0 128 fi