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load_genbankp - Online in the Cloud

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


% 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.


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 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
--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

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