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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2011-06-17 13:51:18 UTC
  • mfrom: (3.1.6 sid)
  • Revision ID: james.westby@ubuntu.com-20110617135118-hncy38e0134j8oi5
Tags: 1.6.901-1
* New upstream release.
* Point debian/watch to search.cpan.org.
* Build using dh and overrides:
  - Use Debhelper 8 (debian/rules, debian/control).
  - Simplified debian/rules.
* Split into libbio-perl-perl, as discussed with the Debian Perl team.
  (debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
* debian/control:
  - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
    No other changes needed.
  - Vcs-Browser URL made redirectable to viewvc.
  - Removed useless ‘svn’ in the Vcs-Svn URL.

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t/Assembly/Assembly.t
1
 
# -*-Perl-*- Test Harness script for Bioperl
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# $Id: Assembly.t 15407 2009-01-20 05:18:29Z cjfields $
3
 
 
4
 
use strict;
5
 
 
6
 
BEGIN {
7
 
    use lib '.';
8
 
    use Bio::Root::Test;
9
 
    
10
 
    test_begin(-tests => 51,
11
 
        -requires_module => 'DB_File');
12
 
        
13
 
        use_ok('Bio::Assembly::IO');
14
 
}
15
 
 
16
 
#
17
 
# Testing IO
18
 
#
19
 
 
20
 
#
21
 
# Some PHRAP input
22
 
#
23
 
 
24
 
my $in = Bio::Assembly::IO->new
25
 
        (-file => test_input_file('consed_project','edit_dir','test_project.phrap.out'));
26
 
 
27
 
isa_ok($in, 'Bio::Assembly::IO');
28
 
 
29
 
my $sc;
30
 
 
31
 
TODO: {
32
 
        local $TODO = "phrap parser doesn't include the sequence string in the sequence objects.";
33
 
        $in->verbose(2);
34
 
        eval {$sc = $in->next_assembly};
35
 
        ok(!$@);
36
 
}
37
 
 
38
 
$in = Bio::Assembly::IO->new
39
 
        (-file => test_input_file('consed_project','edit_dir','test_project.phrap.out'));
40
 
 
41
 
$in->verbose(-1);
42
 
 
43
 
$sc = $in->next_assembly;
44
 
 
45
 
isa_ok($sc,
46
 
           'Bio::Assembly::Scaffold');
47
 
 
48
 
#
49
 
# Testing Scaffold
50
 
#
51
 
 
52
 
is $sc->id, "NoName";
53
 
is $sc->id('test'), "test";
54
 
 
55
 
isa_ok($sc->annotation, 'Bio::AnnotationCollectionI');
56
 
is $sc->annotation->get_all_annotation_keys, 0,"no annotations in Annotation collection?";
57
 
is $sc->get_nof_contigs, 1;
58
 
is $sc->get_nof_sequences_in_contigs, 2;
59
 
is($sc->get_nof_singlets, 2, "get_nof_singlets");
60
 
is($sc->get_contig_seq_ids, 2, "get_contig_seq_ids");
61
 
is($sc->get_contig_ids, 1, "get_contig_ids");
62
 
is($sc->get_singlet_ids, 2, "get_singlet_ids");
63
 
 
64
 
#
65
 
# Testing Contig
66
 
#
67
 
 
68
 
#
69
 
# Testing ContigAnalysis
70
 
#
71
 
 
72
 
#
73
 
# Testing Ace 
74
 
#
75
 
 
76
 
my $aio = Bio::Assembly::IO->new(
77
 
        -file=>test_input_file('consed_project','edit_dir','test_project.fasta.screen.ace.2'),
78
 
        -format=>'ace',
79
 
);
80
 
 
81
 
my $assembly = $aio->next_assembly();
82
 
 
83
 
my @contigs = $assembly->all_contigs();
84
 
 
85
 
my $direction = $contigs[0]->strand;
86
 
is $direction, 1;
87
 
 
88
 
my $features =  $contigs[0]->get_features_collection;
89
 
my @contig_features = $features->get_all_features;
90
 
is @contig_features, 8;
91
 
 
92
 
my @annotations = grep {$_->primary_tag eq 'Annotation'} @contig_features;
93
 
is @annotations, 2;
94
 
my $had_tag = 0;
95
 
foreach my $an (@annotations) {
96
 
        if ($an->has_tag('extra_info')) {
97
 
                $had_tag++;
98
 
                is (($an->get_tag_values('extra_info'))[0], "contig extra\ninfo\n");
99
 
        }
100
 
        elsif ($an->has_tag('comment')){
101
 
                $had_tag++;
102
 
                is (($an->get_tag_values('comment'))[0], "contig tag\ncomment\n");
103
 
        }
104
 
}
105
 
is $had_tag, 2;
106
 
 
107
 
is $assembly->get_nof_contigs, 1;
108
 
is $assembly->get_nof_sequences_in_contigs, 2;
109
 
is($assembly->get_nof_singlets, 0, "get_nof_singlets");
110
 
is($assembly->get_contig_seq_ids, 2, "get_contig_seq_ids");
111
 
is($assembly->get_contig_ids, 1, "get_contig_ids");
112
 
is($assembly->get_singlet_ids, 0, "get_singlet_ids");
113
 
 
114
 
 
115
 
$aio = Bio::Assembly::IO->new(
116
 
        -file=>test_input_file('assembly_with_singlets.ace'),
117
 
        -format=>'ace',
118
 
);
119
 
$assembly = $aio->next_assembly();
120
 
is $assembly->get_nof_contigs, 3;
121
 
my @ace_contigs = $assembly->all_contigs();
122
 
isa_ok $ace_contigs[0], "Bio::Assembly::Contig",'the contig is a Bio::Assembly::Contig';
123
 
is $assembly->get_nof_sequences_in_contigs, 6;
124
 
is($assembly->get_nof_singlets, 33, "get_nof_singlets");
125
 
my @ace_singlets = $assembly->all_singlets();
126
 
isa_ok $ace_singlets[0], "Bio::Assembly::Contig",'the singlet is a Bio::Assembly::Contig';
127
 
isa_ok $ace_singlets[0], "Bio::Assembly::Singlet",'the singlet is a Bio::Assembly::Singlet';
128
 
is($assembly->get_contig_seq_ids, 6, "get_contig_seq_ids");
129
 
is($assembly->get_contig_ids, 3, "get_contig_ids");
130
 
is($assembly->get_singlet_ids, 33, "get_singlet_ids");
131
 
 
132
 
 
133
 
 
134
 
 
135
 
#
136
 
# Testing TIGR format
137
 
#
138
 
 
139
 
# Importing an assembly
140
 
 
141
 
my $asm_in = Bio::Assembly::IO->new(
142
 
    -file => test_input_file("sample_dataset.tasm "),
143
 
    -format=>'tigr'
144
 
);
145
 
my $scaf_in = $asm_in->next_assembly;
146
 
 
147
 
isa_ok($scaf_in, 'Bio::Assembly::Scaffold');
148
 
is($scaf_in->id, 'NoName');
149
 
is($scaf_in->get_nof_contigs, 13);
150
 
is($scaf_in->get_nof_sequences_in_contigs, 36);
151
 
is($scaf_in->get_nof_singlets, 0);
152
 
my @seqids = sort qw(sdsu|SDSU1_RFPERU_001_A09.x01.phd.1
153
 
sdsu|SDSU1_RFPERU_001_B03.x01.phd.1 sdsu|SDSU1_RFPERU_001_B04.x01.phd.1
154
 
sdsu|SDSU1_RFPERU_001_E04.x01.phd.1 sdsu|SDSU_RFPERU_002_A01.x01.phd.1
155
 
sdsu|SDSU_RFPERU_002_B07.x01.phd.1 sdsu|SDSU_RFPERU_002_C12.x01.phd.1
156
 
sdsu|SDSU_RFPERU_002_D08.x01.phd.1 sdsu|SDSU_RFPERU_002_H12.x01.phd.1
157
 
sdsu|SDSU_RFPERU_003_G09.x01.phd.1 sdsu|SDSU_RFPERU_004_H12.x01.phd.1
158
 
sdsu|SDSU_RFPERU_005_F02.x01.phd.1 sdsu|SDSU_RFPERU_006_D03.x01.phd.1
159
 
sdsu|SDSU_RFPERU_006_E04.x01.phd.1 sdsu|SDSU_RFPERU_006_E05.x01.phd.1
160
 
sdsu|SDSU_RFPERU_006_H08.x01.phd.1 sdsu|SDSU_RFPERU_007_E09.x01.phd.1
161
 
sdsu|SDSU_RFPERU_007_F06.x01.phd.1 sdsu|SDSU_RFPERU_008_B02.x01.phd.1
162
 
sdsu|SDSU_RFPERU_009_E07.x01.phd.1 sdsu|SDSU_RFPERU_010_B05.x01.phd.1
163
 
sdsu|SDSU_RFPERU_010_B06.x01.phd.1 sdsu|SDSU_RFPERU_010_C09.x01.phd.1
164
 
sdsu|SDSU_RFPERU_010_D10.x01.phd.1 sdsu|SDSU_RFPERU_012_H02.x01.phd.1
165
 
sdsu|SDSU_RFPERU_013_B05.x01.phd.1 sdsu|SDSU_RFPERU_013_C07.x01.phd.1
166
 
sdsu|SDSU_RFPERU_013_C08.x01.phd.1 sdsu|SDSU_RFPERU_013_G10.x01.phd.1
167
 
sdsu|SDSU_RFPERU_013_H05.x01.phd.1 sdsu|SDSU_RFPERU_014_H06.x01.phd.1
168
 
sdsu|SDSU_RFPERU_015_A05.x01.phd.1 sdsu|SDSU_RFPERU_015_C06.x01.phd.1
169
 
sdsu|SDSU_RFPERU_015_E04.x01.phd.1 sdsu|SDSU_RFPERU_015_G04.x01.phd.1
170
 
sdsu|SDSU_RFPERU_015_H03.x01.phd.1);
171
 
my @contigids = sort qw(106 144 148 17 185 2 210 36 453 500 613 668 93);
172
 
is_deeply([sort $scaf_in->get_contig_seq_ids], \@seqids);
173
 
is_deeply([sort $scaf_in->get_contig_ids], \@contigids);
174
 
is_deeply([$scaf_in->get_singlet_ids], []);
175
 
isa_ok($scaf_in->get_seq_by_id('sdsu|SDSU1_RFPERU_001_A09.x01.phd.1'),'Bio::LocatableSeq');
176
 
my $contig = $scaf_in->get_contig_by_id('106');
177
 
isa_ok($contig,'Bio::Assembly::Contig');
178
 
# check Contig object SeqFeature::Collection
179
 
# should add more specific Contig tests...
180
 
my @sfs = $contig->get_features_collection->get_all_features;
181
 
is(scalar(@sfs), 5);
182
 
my %primary_tags = map { $_->primary_tag => 1 } @sfs;
183
 
ok exists $primary_tags{'_aligned_coord:sdsu|SDSU_RFPERU_006_E04.x01.phd.1'};
184
 
is($sfs[1]->seq_id(), undef); # should this be undef?
185
 
 
186
 
isa_ok($scaf_in->annotation, 'Bio::AnnotationCollectionI');
187
 
is($scaf_in->annotation->get_all_annotation_keys, 0,"no annotations in Annotation collection?");
188
 
 
189
 
# Exporting an assembly
190
 
 
191
 
my $asm_outfile = test_output_file();
192
 
my $asm_out = Bio::Assembly::IO->new(
193
 
    -file=> ">$asm_outfile",
194
 
    -format=>'tigr'
195
 
);
196
 
 
197
 
ok $asm_out->write_assembly( -scaffold => $scaf_in);
198