BP_GENBANK2GFF(1p) User Contributed Perl Documentation BP_GENBANK2GFF(1p)NAME
bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
SYNOPSIS
% bp_genbank2gff.pl -d genbank -f localfile.gb
% bp_genbank2gff.pl -d genbank --accession AP003256
% bp_genbank2gff.pl --accession AP003256 --stdout
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.
The database must already have been created and the current user must have appropriate INSERT and UPDATE privileges. The --create option
will initialize a new database with the appropriate schema, deleting any tables that were already there.
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
--stdout direct output to STDOUT
--adaptor <adaptor> adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle) --viral the genome you are loading is viral (changes tag
choices)
--source <source> source field for features ['genbank']
EITHER --file Arguments that follow are Genbank/EMBL file names
OR --gb_folder What follows is a folder full of gb files to process OR --accession Arguments that follow are genbank accession numbers
(not gi!)
OR --acc_file Accession numbers (not gi!) in a file (one per line, no punc.)
OR --acc_pipe Accession numbers (not gi!) from a STDIN pipe (one
per line)
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Scott Cain, cain@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.
perl v5.14.2 2012-03-02 BP_GENBANK2GFF(1p)
Check Out this Related Man Page
Bio::Graphics::Glyph::three_letters(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::three_letters(3pm)NAME
Bio::Graphics::Glyph::three_letters - DAS-compatible package to use for drawing a line of groups of three letters
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph draws groups of three letters separated by horizontal lines.
OPTIONS
In addition to the common options, the following glyph-specific options are recognized:
Option Description Default
------------------------
-text The three letters to show "CAG"
-width Width of one letter group 20
-interval Interval between 10
letter groups
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Vsevolod (Simon) Ilyushchenko <simonf@cshl.edu>.
Copyright (c) 2004 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.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::three_letters(3pm)