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
79
80
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: Domcut.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 26,
-requires_modules => [qw(IO::String
LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::PrimarySeq');
use_ok('Bio::Tools::Analysis::Protein::Domcut');
}
my $verbose = test_debug();
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
SKIP: {
######## test using PrimarySeq object ##############
my $seq = Bio::PrimarySeq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS',
-display_id => 'test2');
ok $tool = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$seq);
ok $tool->run ();
if ($tool->status eq 'TERMINATED_BY_ERROR') {
skip('Problem with DomCut run, check status', 21);
}
ok my $raw = $tool->result('');
ok my $parsed = $tool->result('parsed');
is ($parsed->[23]{'score'}, '-0.209');
my @res = $tool->result('Bio::SeqFeatureI');
if (scalar @res > 0) {
ok 1;
} else {
skip('No network access - could not connect to Domcut server', 18);
}
ok my $meta = $tool->result('meta');
SKIP: {
test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
is($meta->named_submeta_text('Domcut', 1,2), "0.068 0.053");
is ($meta->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS");
}
########## test using Bio::Seq object ##############
ok my $tool2 = Bio::WebAgent->new(-verbose =>$verbose);
ok my $seq2 = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
-display_id => 'test2');
ok $tool2 = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$seq2->primary_seq);
ok $tool2->run ();
@res = $tool2->result('Bio::SeqFeatureI');
if (scalar @res > 0) {
ok 1;
} else {
skip('No network access - could not connect to Domcut server', 10);
}
ok my $parsed2 = $tool2->result('parsed');
is ($parsed2->[23]{'score'}, '-0.209');
ok my $meta2 = $tool2->result('meta');
is($meta2->named_submeta_text('Domcut', 1,2), "0.068 0.053");
is ($meta2->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS");
ok my $seq4 = Bio::Seq->new();
ok $seq2->primary_seq($meta2);
ok $seq2->add_SeqFeature(@res);
ok $seq2->primary_seq->named_submeta_text('Domcut', 1,2);
}
|
