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BP_GENBANK2GFF(1)     User Contributed Perl Documentation    BP_GENBANK2GFF(1)


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.

perl v5.20.2                      2015-09-15                 BP_GENBANK2GFF(1)

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