1BP_BIOFETCH_GENBANK_PROUXsYe(r1)Contributed Perl DocumenBtPa_tBiIoOnFETCH_GENBANK_PROXY(1)
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6 biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for
7 GenBank
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10 Install in cgi-bin directory of a Web server. Stand back.
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13 This CGI script acts as the server side of the BioFetch protocol as
14 described in http://obda.open-bio.org/Specs/. It provides two database
15 access services, one for data source "genbank" (nucleotide entries) and
16 the other for data source "genpep" (protein entries).
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18 This script works by forwarding its requests to NCBI's eutils script,
19 which lives at http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi.
20 It then reformats the output according to the BioFetch format so the
21 sequences can be processed and returned by the Bio::DB::BioFetch mod‐
22 ule. Returned entries are temporarily cached on the Web server's file
23 system, allowing frequently-accessed entries to be retrieved without
24 another round trip to NCBI.
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26 INSTALLATION
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28 You must have the following installed in order to run this script:
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30 1) perl
31 2) the perl modules LWP and Cache::FileCache
32 3) a web server (Apache recommended)
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34 To install this script, copy it into the web server's cgi-bin direc‐
35 tory. You might want to shorten its name; "dbfetch" is recommended.
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37 There are several constants located at the top of the script that you
38 may want to adjust. These are:
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40 CACHE_LOCATION
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42 This is the location on the filesystem where the cached files will be
43 located. The default is /usr/tmp/dbfetch_cache.
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45 MAX_SIZE
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47 This is the maximum size that the cache can grow to. When the cache
48 exceeds this size older entries will be deleted automatically. The
49 default setting is 100,000,000 bytes (100 MB).
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51 EXPIRATION
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53 Entries that haven't been accessed in this length of time will be
54 removed from the cache. The default is 1 week.
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56 PURGE
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58 This constant specifies how often the cache will be purged for older
59 entries. The default is 1 hour.
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62 To see if this script is performing as expected, you may test it with
63 this script:
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65 use Bio::DB::BioFetch;
66 my $db = Bio::DB::BioFetch->new(-baseaddress=>'http://localhost/cgi-bin/dbfetch',
67 -format =>'genbank',
68 -db =>'genbank');
69 my $seq = $db->get_Seq_by_id('DDU63596');
70 print $seq->seq,"\n";
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72 This should print out a DNA sequence.
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75 Bio::DB::BioFetch, Bio::DB::Registry
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78 Lincoln Stein, <lstein-at-cshl.org>
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80 Copyright (c) 2003 Cold Spring Harbor Laboratory
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82 This library is free software; you can redistribute it and/or modify it
83 under the same terms as Perl itself. See DISCLAIMER.txt for dis‐
84 claimers of warranty.
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88perl v5.8.8 2007-05-07 BP_BIOFETCH_GENBANK_PROXY(1)