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 --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
Scott Cain, firstname.lastname@example.org
Lincoln Stein, email@example.com
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.