Admin: 2 revisions

2011-10-26T06:16:41Z

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imported>AlexanderGoesmann at 18:00, 16 November 2004

2004-11-16T18:00:37Z

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Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

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__NOTOC__
= A simple GenDB Demo Script =

This simple demo script listed below fetches all contigs from a GenDB project database and prints out their names.

<pre><nowiki>

#!/usr/bin/env perl

# simple GenDB demo script that reads all contigs and writes their names

use strict;
use Carp;
use Getopt::Std;
use Term::ReadKey;
use IO::Handle;
use GPMS::Application_Frame::GENDB;

#
# this is necessary if the script is started via rsh(1)
# otherwise you won't see any output until the first <RETURN>
#
STDOUT->autoflush(1);

sub usage {
print "gendb_demo - get all contig sequences and write their names\n";
print "usage: gendb_demo -p <project>\n\n";
}

# global variables
our($opt_p);

getopts('p:');

# start sanity checks
if (!$opt_p) {
usage;
print "ERROR: Can't initialize GenDB: No project name given!\n";
exit 1;
};

# get the login name of the current user
my $user = defined( $ENV{'LOGNAME'} ) ? $ENV{'LOGNAME'} : (getpwuid( $> ))[0];

print "Enter your database password: ";
ReadMode('noecho');
my $password = ReadLine(0);
chomp $password;
print "\n";
ReadMode('normal');

# try to initialize GenDB project
# initialize an Application_Frame for the current project
my $gendbAppFrame = GPMS::Application_Frame::GENDB->new($user, $password);

# check if the initialization succeeded
die "Unable to initialize ApplicationFrame for GenDB project!" unless (ref $gendbAppFrame);

# try to initialize a project for the given name
$gendbAppFrame->project($opt_p);

# check a basic privilege
exit unless $gendbAppFrame->right("basic_access");

# get a global O2DBI-2 master object
my $master = $gendbAppFrame->application_master();

# fetchall contigs and print their names
print "Contigs in GenDB project $opt_p:\n\n";
my $contigs = $master->Region->Source->Contig->fetchall();
foreach my $contig (@$contigs) {
print $contig->name."\n";
}

print "\nDone.\n\n";

</nowiki></pre>

GenDBWiki/DeveloperDocumentation/GenDBDemoScript - Revision history

Admin: 2 revisions

imported>AlexanderGoesmann at 18:00, 16 November 2004

Unknown user at 00:00, 1 January 1970