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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

--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)

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