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.\"
.IX Title "LOAD_GENBANK 1p"
.TH LOAD_GENBANK 1p "2018-10-03" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
load_genbank.pl \- Load a Bio::DB::GFF database from GENBANK files.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  % load_genbank.pl \-d genbank \-f localfile.gb
\&  % load_genbank.pl \-d genbank \-a AP003256
.Ve
.PP
\&\s-1NOTE:\s0 The script bp_genbank2gff.pl in the BioPerl distribution is the
same as this script.
.SH "DESCRIPTION"
.IX Header "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.
.PP
This script currently only uses MySQL, though it is a proof\-of\-
principle and could easily be extended to work with other \s-1RDMS\s0
that are supported by \s-1GFF\s0 through adaptors.
.SH "COMMAND-LINE OPTIONS"
.IX Header "COMMAND-LINE OPTIONS"
Command-line options can be abbreviated to single-letter options.
e.g. \-d instead of \-\-database.
.PP
.Vb 8
\&   \-\-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
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
.SH "AUTHOR"
.IX Header "AUTHOR"
Scott Cain, cain@cshl.org
.PP
Lincoln Stein, lstein@cshl.org
.PP
Copyright (c) 2003 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.