Man page - load_genbank(1)
Packages contains this manual
- gbrowse_import_ucsc_db(1)
- gbrowse_clean(1)
- gbrowse_aws_balancer(1)
- gbrowse_syn_load_alignments_msa(1)
- ucsc_genes2gff(1)
- gbrowse_metadb_config(1)
- load_genbank(1)
- make_das_conf(1)
- bed2gff3(1)
- gbrowse_grow_cloud_vol(1)
- wiggle2gff3(1)
- scan_gbrowse(1)
- gbrowse_sync_aws_slave(1)
- gbrowse_slave(1)
- gbrowse_change_passwd(1)
- gbrowse_syn_load_alignment_database(1)
- gbrowse_create_account(1)
- gtf2gff3(1)
- gbrowse(1)
- gbrowse_set_admin_passwd(1)
apt-get install gbrowse
Manual
LOAD_GENBANK
NAMESYNOPSIS
DESCRIPTION
COMMAND-LINE OPTIONS
SEE ALSO
AUTHOR
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.