/
TribeMCL.t
84 lines (69 loc) · 2.54 KB
/
TribeMCL.t
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
81
82
83
84
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 24,
-requires_module => 'Algorithm::Diff');
use_ok('Bio::Tools::Run::TribeMCL');
use_ok('Bio::SearchIO');
}
my $blast_out = test_input_file("TribeMCL.bls");
#do from raw blast output
my @params=('inputtype'=>'blastfile',I=>'3.0');
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
SKIP : {
unless ($fact){
skip("Couldn't create a TribeMCL wrapper",22);
}
my $desc = test_input_file("TribeMCL.desc");
$fact->description_file($desc);
isa_ok $fact,'Bio::Tools::Run::TribeMCL';
unless ($fact->matrix_executable){
skip("Tribe Matrix program not found. Skipping tests...", 21);
}
unless ($fact->mcl_executable){
skip("Markov Clustering program not found. Skipping tests...",21);
}
my $bequiet = 1 ;
$fact->quiet($bequiet);
my ($fam) = $fact->run($blast_out);
my @members = $fam->get_members;
isa_ok $fam,"Bio::Cluster::SequenceFamily";
isa_ok $members[0],"Bio::Seq";
is ($members[0]->id, 'ENSANGP00000008485');
is ($members[1]->id, 'ENSDRMP3263');
is ($members[2]->id, 'ENSMUSP00000026170');
is ($fam->description,'ubiquitin');
is ($fam->annotation_score,45.0549450549451);
is ($fam->size,91);
#do from searchio
my $sio = Bio::SearchIO->new(-format=>'blast',
-file=>$blast_out);
@params=('inputtype'=>'searchio',I=>'3.0');
$fact = Bio::Tools::Run::TribeMCL->new(@params);
$fact->description_file($desc);
isa_ok $fact,'Bio::Tools::Run::TribeMCL';
$bequiet =1 ;
$fact->quiet($bequiet);
($fam) = $fact->run($sio);
isa_ok $fam,"Bio::Cluster::SequenceFamily";
isa_ok $members[0],"Bio::Seq";
is ($members[0]->id, 'ENSANGP00000008485');
is ($members[1]->id, 'ENSDRMP3263');
is ($members[2]->id, 'ENSMUSP00000026170');
is ($fam->description,'ubiquitin');
is ($fam->annotation_score,45.0549450549451);
is ($fam->size,91);
@params=('inputtype'=>'pairs',I=>'3.0');
$fact = Bio::Tools::Run::TribeMCL->new(@params);
isa_ok $fact,'Bio::Tools::Run::TribeMCL';
$bequiet =1 ;
$fact->quiet($bequiet);
($fam) = $fact->run( [[qw(ENSP00000257547 ENSP00000261659 1 50)],
[qw(O42187 ENSP00000257547 1 119)]]);
@members = $fam->get_members;
is ($members[0]->id, 'ENSP00000257547');
is ($members[1]->id, 'ENSP00000261659');
is ($members[2]->id, 'O42187');
}