1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: ELM.t,v 1.1 2003/11/18
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($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 = 14;
plan tests => $NUMTESTS;
eval {
require IO::String;
require LWP::UserAgent;
require HTML::HeadParser
};
if( $@ ) {
warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests");
$ERROR = 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;
require Bio::Tools::Analysis::Protein::ELM;
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 $tool = Bio::Tools::Analysis::Protein::ELM->new(
-seq=>$seq->primary_seq);
ok $tool->compartment(['golgi', 'er']);
ok my $cmp = $tool->compartment();
ok $cmp->[1], 'GO:0005783';
ok $tool->species, 9606;
ok $tool->species(8355);
ok $tool->species, 8355;
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->{'CLV_NDR_NDR_1'}{'locus'}[0], '54-56';
ok my @res = $tool->result('Bio::SeqFeatureI');
|
