bp_biofetch_genbank_proxy.pl man page on Fedora

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BP_BIOFETCH_GENBANK_PRUser1Contributed Perl DocumeBP_BIOFETCH_GENBANK_PROXY(1)

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,"\n";

       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 v5.14.1			  2011-07-22	  BP_BIOFETCH_GENBANK_PROXY(1)
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