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  • Andreas Kusalananda Kähäri's avatar
    Info: · 2fb78fe1
    Andreas Kusalananda Kähäri authored
        Script to populate the meta table with species aliases.
    
        The script reads the already existing aliases from the
        meta table (meta_key 'species.alias') and adds to this
        aliases computed from the species name.  It also uses the
        information stored for the meta_keys species.taxonomy_id,
        species.common_name, species.ensembl_common_name, and
        species.ensembl_alias_name as aliases.
    
        If the -n or --dryrun options are *not* specified, the existing
        list of aliases is deleted from the meta table and the new list
        is inserted.  In any case, the list of aliases will be displayed
        on the console.
    
        If the -d or --dbname options are *not* used, the script will
        iterate over all Core databases.  If the -d or --dbname option
        *is* used, only that Core database will be examined.
    
        This script assumes that the database is a single-species
        database.
    
        This script does not check for alias duplications between
        species.
    
    
    Usage:
            ./add_species_aliases.pl        [-n] -h dbhost [-P dbport] \
                                            -u dbuser [-p dbpass] \
                                            [-d dbname]
    
            ./add_species_aliases.pl        -?
    
    Arguments:
            -n/--dryrun             Dry run, don't write to database
            -h/--host dbhost        Database server host name
            -P/--port dbport        Database server port (optional)
            -u/--user dbuser        Database user name
            -p/--pass dbpass        User password (optional)
            -d/--name dbname        Database name (optional)
            -?/--help               Displays this information
    2fb78fe1
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