This is a lazy-but-easy way to get the dbcontext arguments. All you need to do is to invoke get_dbcontext_from_argv before using the standard Getopt. The below options will be absorbed and removed from @ARGV.

db_file, host, dbname, dbuser, dbpass, driver

Now you can take the advantage of Perl's do method to execute a file as perl script and get returned the last line of it. For your most accessed dbcontext setting, you can have a filed named, say biosql.perlobj, with the content like

    use strict; # The ceiling line
    use Bio::DB::SimpleDBContext;
    use Bio::DB::BioDB;

    my $dbc = Bio::DB::SimpleDBContext->new(
        -driver => 'mysql',
        -dbname => 'ontology_biosql',
        -host => 'localhost',
        -user => 'root',
        -pass => ''
    my $adaptor = Bio::DB::BioDB->new(
        -database => 'biosql',
        -dbcontext => $dbc
    return $adaptor; # The floor line

In your command line, you just need to type like

perl --db_file ontology_biosql.perlobj --ontology_name InterPro

rather than the classic verbose one.


Juguang XIAO,