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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: HNN.t,v 1.1 2003/07/23
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($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 = 13;
plan tests => $NUMTESTS;
eval {
require IO::String;
require LWP::UserAgent;
};
if( $@ ) {
warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests");
$ERROR = 1;
}
#check this is available, set error flag if not.
eval {
require Bio::Seq::Meta::Array;
};
if ($@) {
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::PrimarySeq;
use Bio::Seq;
require Bio::Tools::Analysis::Protein::HNN;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
my $seq = Bio::PrimarySeq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
-display_id => 'test2',
);
ok $tool = Bio::Tools::Analysis::Protein::HNN->new( -seq=>$seq,
);
if( $DEBUG ) {
ok $tool->run ();
exit if $tool->status eq 'TERMINATED_BY_ERROR';
ok my $raw = $tool->result('');
ok my $parsed = $tool->result('parsed');
ok ($parsed->[0]{'coil'}, '1000');
my @res = $tool->result('Bio::SeqFeatureI');
if (scalar @res > 0) {
ok 1;
} else {
skip('No network access - could not connect to HNN server', 1);
}
ok my $meta = $tool->result('meta');
ok my $seqobj = Bio::Seq->new(-primary_seq => $meta, display_id=>"a");
ok $seqobj->add_SeqFeature($tool->result('Bio::SeqFeatureI'));
if (!$METAERROR) { #if Bio::Seq::Meta::Array available
ok ( $meta->named_submeta_text('HNN_helix',1,2), '0 111');
ok ( $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS');
}
} else {
for ( $Test::ntest..$NUMTESTS) {
skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
}
}
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