Provided by: bioperl_1.6.901-2_all bug

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.