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.