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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: GDB.t,v 1.13 2002/05/31 18:51:02 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
my $error;
my $SKIPTEST = 1; # set this to 0 if you want to run the GDB test
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
$error = 0;
use Test;
use vars qw($NUMTESTS);
$NUMTESTS = 11;
plan tests => $NUMTESTS;
unless( $SKIPTEST ) {
foreach ( $Test::ntest..$NUMTESTS ) {
skip('GDB test skipped to avoid timeouts',1);
$error = 1;
}
}
eval { require ('LWP/UserAgent.pm'); require('HTML/Parser.pm');
require ('HTTP/Request/Common.pm');
};
if( $@ ) {
print STDERR "Cannot load LWP::UserAgent or HTML::Parser, skipping tests\n";
foreach ( $Test::ntest..$NUMTESTS) { skip('LWP::UserAgent or HTML::Parser not installed',1); }
$error = 1;
}
if( $] < 5.005 ) {
print STDERR "GDB parsing does not work with 5.005 or lower Perl versions.\n";
foreach ( $Test::ntest..$NUMTESTS) { skip('need perl > 5.005',1); }
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::DB::GDB;
my $verbose = -1;
my ($gdb, $marker, $info);
# get a single seq
$marker = 'D1S234';
eval {
ok defined ( $gdb = new Bio::DB::GDB(-verbose=>$verbose) );
ok($info = $gdb->get_info(-type=>'marker',
-id => $marker));
};
if( $@ || ! defined $info) {
warn "Warning: Couldn't connect to GDB website with Bio::DB::GDB.pm!\nError: Do you have network access? Skipping all other tests";
foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access',1); }
exit(0);
}
ok $info->{gdbid}, 'GDB:188296', 'value was ' . $info->{gdbid};
ok $info->{primers}->[0], 'GCCCAGGAGGTTGAGG', 'value was ' . $info->{primers}->[0];
ok $info->{primers}->[1], 'AAGGCAGGCTTGAATTACAG', 'value was ' . $info->{primers}->[1];
ok $info->{'length'}, 226, 'value was '. $info->{'length'};
$marker = 'UT497';
$info = undef;
eval {
ok ($info = $gdb->get_info(-type=>'marker',
-id => $marker));
};
if( $@ || ! defined $info ) {
warn "Warning: Couldn't connect to GDB website with Bio::DB::GDB.pm!\nError: Do you have network access? Skipping all other tests";
foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access',1); }
exit(0);
}
ok $info->{gdbid}, 'GDB:198271', 'value was ' . $info->{gdbid};
ok $info->{primers}->[0], 'GGGTGACAGAACAAGACCT', 'value was ' . $info->{primers}->[0];
ok $info->{primers}->[1], 'ACCCATTAGCCTTGAACTGA', 'value was ' . $info->{primers}->[1];
ok $info->{'length'}, 155, 'value was '. $info->{'length'};
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