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


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


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

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.

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:


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


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).


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


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


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.

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