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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Scansite.t,v 1.1 2003/11/18
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $ERROR);
$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;
};
if( $@ ) {
warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests");
$ERROR = 1;
}
}
END {
if ($DEBUG) {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the tests depending on web access',1);
}
} else {
foreach ( $Test::ntest..$NUMTESTS) {
skip('set env BIOPERLDEBUG to run tests over web ',1);
}
}
}
exit 0 if $ERROR == 1;
use Data::Dumper;
require Bio::Tools::Analysis::Protein::Scansite;
use Bio::SeqIO;
use Bio::PrimarySeq;
require Bio::WebAgent;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
my $seqio=new Bio::SeqIO( -verbose => $verbose,
-format => 'swiss',
-file => Bio::Root::IO->catfile('t','data', 'swiss.dat'));
my $seq = $seqio->next_seq();
ok $tool = Bio::Tools::Analysis::Protein::Scansite->new(
-seq=>$seq->primary_seq);
ok $tool->stringency('Low');
ok $tool->stringency(), 'Low';
ok $tool->protein_id(), $tool->seq->display_id();
exit unless $DEBUG;
ok $tool->run ();
exit if $tool->status eq 'TERMINATED_BY_ERROR';
ok my $raw = $tool->result('');
print $raw if $verbose;
ok my $parsed = $tool->result('parsed');
ok $parsed->[0]{'percentile'}, '0.230';
ok my @res = $tool->result('Bio::SeqFeatureI');
ok $res[0]->start, 101;
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