EnglishFrenchSpanish

Ad


OnWorks favicon

bp_biofetch_genbank_proxyp - Online in the Cloud

Run bp_biofetch_genbank_proxyp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_biofetch_genbank_proxyp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


bp_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.

Use bp_biofetch_genbank_proxyp online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    USBLoaderGX
    USBLoaderGX
    USBLoaderGX is a GUI for
    Waninkoko's USB Loader, based on
    libwiigui. It allows listing and
    launching Wii games, Gamecube games and
    homebrew on Wii and WiiU...
    Download USBLoaderGX
  • 2
    Firebird
    Firebird
    Firebird RDBMS offers ANSI SQL features
    & runs on Linux, Windows &
    several Unix platforms. Features
    excellent concurrency & performance
    & power...
    Download Firebird
  • 3
    KompoZer
    KompoZer
    KompoZer is a wysiwyg HTML editor using
    the Mozilla Composer codebase. As
    Nvu's development has been stopped
    in 2005, KompoZer fixes many bugs and
    adds a f...
    Download KompoZer
  • 4
    Free Manga Downloader
    Free Manga Downloader
    The Free Manga Downloader (FMD) is an
    open source application written in
    Object-Pascal for managing and
    downloading manga from various websites.
    This is a mirr...
    Download Free Manga Downloader
  • 5
    UNetbootin
    UNetbootin
    UNetbootin allows you to create bootable
    Live USB drives for Ubuntu, Fedora, and
    other Linux distributions without
    burning a CD. It runs on Windows, Linux,
    and ...
    Download UNetbootin
  • 6
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM is an easy to use
    ERP and CRM open source software package
    (run with a web php server or as
    standalone software) for businesses,
    foundations...
    Download Dolibarr ERP - CRM
  • More »

Linux commands

Ad