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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +17 -0 lines
Add license words.

# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
# This file is part of the SEED Toolkit.
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.

# Simple script to test the local DAS server.

use LWP::UserAgent;
use Data::Dumper;

use Bio::Das;

use XML::Simple;
use FIG;
my $fig = new FIG();

my $url = $fig->cgi_url() . "/das.cgi/das";

my $genome = "160490.1";


my $das = new Bio::Das(-source => $url,
		       -dsn => $genome);
print "das=$das\n";
print Dumper($das);
my $s = $das->segment('160490.1--NC_002737',1,5000);
print "types ", Dumper($das->types());
print Dumper($s);
my @f = $s->features('CDS:curated');
print Dumper(@f);

# Retrieve types

my $types = das_get($url,  $genome, "types");
print Dumper($types);

# Entry points on the genome.

das_get($url, $genome, 'entry_points');

my $f = das_get($url, $genome, 'features',
		segment => '160490.1--NC_002737:1,3000',
		type => 'CDS:curated');

sub das_get
    my($url, $genome, $cmd, @params) = @_;

    my @pairs;
    while (@params)
	my($name, $val) = splice(@params, 0, 2);
	push(@pairs, "$name=$val");
    my $params = join("&", @pairs);
    my $req_url = "$url/das/$genome/$cmd?$params";

    my $agent = new LWP::UserAgent();

    print "Request: genome=$genome cmd=$cmd $params\n";
    print "Url: $req_url\n";
    my $resp = $agent->get($req_url);

    if ($resp->is_success())
	print "Success:\n";
	print $resp->content;
	my $xml = XMLin($resp->content);
	return $xml;
	print "Error: ", $response->status_line, "\n";

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