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.