bp_biofetch_genbank_proxy(1p) [debian man page]

BP_BIOFETCH_GENBANK_PROXY(1p)				User Contributed Perl Documentation			     BP_BIOFETCH_GENBANK_PROXY(1p)

NAME

       biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank

SYNOPSIS

	 Install in cgi-bin directory of a Web server.	Stand back.

DESCRIPTION

       This CGI script acts as the server side of the BioFetch protocol as described in http://obda.open-bio.org/Specs/.  It provides two database
       access services, one for data source "genbank" (nucleotide entries) and the other for data source "genpep" (protein entries).

       This script works by forwarding its requests to NCBI's eutils script, which lives at http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi.
       It then reformats the output according to the BioFetch format so the sequences can be processed and returned by the Bio::DB::BioFetch
       module.	Returned entries are temporarily cached on the Web server's file system, allowing frequently-accessed entries to be retrieved
       without another round trip to NCBI.

   INSTALLATION
       You must have the following installed in order to run this script:

	  1) perl
	  2) the perl modules LWP and Cache::FileCache
	  3) a web server (Apache recommended)

       To install this script, copy it into the web server's cgi-bin directory.  You might want to shorten its name; "dbfetch" is recommended.

       There are several constants located at the top of the script that you may want to adjust.  These are:

       CACHE_LOCATION

       This is the location on the filesystem where the cached files will be located.  The default is /usr/tmp/dbfetch_cache.

       MAX_SIZE

       This is the maximum size that the cache can grow to.  When the cache exceeds this size older entries will be deleted automatically.  The
       default setting is 100,000,000 bytes (100 MB).

       EXPIRATION

       Entries that haven't been accessed in this length of time will be removed from the cache.  The default is 1 week.

       PURGE

       This constant specifies how often the cache will be purged for older entries.  The default is 1 hour.

TESTING

       To see if this script is performing as expected, you may test it with this script:

	use Bio::DB::BioFetch;
	my $db = Bio::DB::BioFetch->new(-baseaddress=>'http://localhost/cgi-bin/dbfetch',
					-format     =>'genbank',
					-db	    =>'genbank');
	my $seq = $db->get_Seq_by_id('DDU63596');
	print $seq->seq,"
";

       This should print out a DNA sequence.

SEE ALSO

       Bio::DB::BioFetch, Bio::DB::Registry

AUTHOR

       Lincoln Stein, <lstein-at-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_BIOFETCH_GENBANK_PROXY(1p)

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Bio::Graphics::Glyph::two_bolts(3pm)			User Contributed Perl Documentation		      Bio::Graphics::Glyph::two_bolts(3pm)

NAME

       Bio::Graphics::Glyph::two_bolts - The "two bolts" glyph

SYNOPSIS

	 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph draws two "bolts" on a line. They look like this;

       --------///-- --///--------

   OPTIONS
       In addition to the common options, the following glyph-specific options are recognized:

	 Option      Description		  Default
	 ------      -----------		  -------

	 -bolt_height  Height of the bolt	   10

	 -bolt_length  Length of the bolt	   20

	 -bolt_color   Color of the bolt	   red

	 -remainder_length
		       Length of the short line    10

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::two_bolts(3pm)

Linux and UNIX Man Pages

bp_biofetch_genbank_proxy(1p) [debian man page]

Check Out this Related Man Page