NAME

       bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.

SYNOPSIS

         % bp_genbank2gff.pl -d genbank -f localfile.gb
         % bp_genbank2gff.pl -d genbank --accession AP003256
         % bp_genbank2gff.pl --accession AP003256 --stdout

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.

       The database must already have been created and the current user must have appropriate
       INSERT and UPDATE privileges.  The --create option will initialize a new database with the
       appropriate schema, deleting any tables that were already there.

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
          --stdout                 direct output to STDOUT
          --adaptor   <adaptor>    adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)   --viral                  the genome you are loading is viral (changes tag
                                        choices)
          --source    <source>     source field for features ['genbank']
           EITHER --file           Arguments that follow are Genbank/EMBL file names
           OR --gb_folder          What follows is a folder full of gb files to process    OR --accession          Arguments that follow are genbank accession numbers
                                        (not gi!)
           OR --acc_file           Accession numbers (not gi!) in a file (one per line,                                 no punc.)
           OR --acc_pipe           Accession numbers (not gi!) from a STDIN pipe (one
                                        per line)

SEE ALSO

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

AUTHOR

       Scott Cain, cain@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.