Skip to content
Snippets Groups Projects
Commit 2fb78fe1 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Info:

    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
parent ba447552
No related branches found
No related tags found
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment