NAME

       load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files.

SYNOPSIS

         % load_genbank.pl -d genbank -f localfile.gb
         % load_genbank.pl -d genbank -a AP003256

       NOTE: The script bp_genbank2gff.pl in the BioPerl distribution is the same as this script.

DESCRIPTION

       This script loads a Bio::DB::GFF database with the features contained in a either a local
       genbank file or an accession that is fetched from genbank.  Various command-line options
       allow you to control which database to load and whether to allow an existing database to
       be overwritten.

       This script currently only uses MySQL, though it is a proof-of- principle and could easily
       be extended to work with other RDMS that are supported by GFF through adaptors.

COMMAND-LINE OPTIONS

       Command-line options can be abbreviated to single-letter options.  e.g. -d instead of
       --database.

          --create                  Force creation and initialization of database
          --dsn       <dsn>         Data source (default dbi:mysql:test)
          --user      <user>        Username for mysql authentication
          --pass      <password>    Password for mysql authentication
          --proxy     <proxy>       Proxy server to use for remote access
          --file                    Arguments that follow are Genbank/EMBL file names (default)
          --accession               Arguments that follow are genbank accession numbers
          --stdout                  Write converted GFF file to stdout rather than loading

SEE ALSO

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

AUTHOR

       Scott Cain, cain@cshl.org

       Lincoln Stein, lstein@cshl.org

       Copyright (c) 2003 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.  See DISCLAIMER.txt for disclaimers of warranty.