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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: ESEfinder.t,v 1.9 2003/12/18 03:03:26 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;
use vars qw($NUMTESTS $DEBUG $ERROR $METAERROR);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
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; };
$ERROR = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 12;
plan tests => $NUMTESTS;
eval {
require IO::String;
require LWP::UserAgent;
require Bio::WebAgent;
require HTML::HeadParser;
};
if( $@ ) {
warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests");
$ERROR = 1;
}
eval {
require Bio::Seq::Meta::Array;
};
if ($@) {
warn ("Bio::Seq::Meta::Array not installed - will skip tests using meta sequences");
$METAERROR = 1;
}
}
END {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the tests depending on web access',1);
}
}
exit 0 if $ERROR == 1;
use Data::Dumper;
use Bio::Tools::Analysis::DNA::ESEfinder;
use Bio::PrimarySeq;
use Bio::Seq;
use Bio::WebAgent;
ok 1;
my $verbose = $DEBUG;
my $tool;
#######all these tests work with 1ary seq########
my $seq = Bio::PrimarySeq->new(-id=>'bioperl',
-seq=>'atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt');
ok $tool = Bio::Tools::Analysis::DNA::ESEfinder->new(-verbose =>$verbose, -seq => $seq);
if( $DEBUG ) {
ok $tool->run ( );
ok my @res = $tool->result('Bio::SeqFeatureI');
ok my $raw = $tool->result('');
ok my $parsed = $tool->result('parsed');
ok my $meta = $tool->result('all');
ok ($parsed->[0][1], 41);
if (scalar @res > 0) {
ok 1;
} else {
skip('No network access - could not connect to ESEfinder server', 1);
}
if (!$METAERROR) { #if Bio::Seq::Meta::Array available
ok($meta->{'seq'}, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt" );
ok( $meta->named_submeta_text('ESEfinder_SRp55', 1,2), "-3.221149 -1.602223");
ok ($meta->seq, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt" );
}
} else {
for ( $Test::ntest..$NUMTESTS) {
skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
}
}
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