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


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


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 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
   --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)


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


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.