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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: embl.t 15635 2009-04-14 19:11:13Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 69);
use_ok('Bio::SeqIO::embl');
}
my $verbose = test_debug();
my $ast = Bio::SeqIO->new( -format => 'embl',
-verbose => $verbose,
-file => test_input_file('roa1.dat'));
$ast->verbose($verbose);
my $as = $ast->next_seq();
ok defined $as->seq;
is($as->display_id, 'HSHNCPA1');
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
is($as->molecule, 'RNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');
# EMBL Release 87 changes (8-17-06)
$ast = Bio::SeqIO->new( -format => 'embl',
-verbose => $verbose,
-file => test_input_file('roa1_v2.dat'));
$ast->verbose($verbose);
$as = $ast->next_seq();
ok defined $as->seq;
# accession # same as display name now
is($as->display_id, 'X79536');
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
# mRNA instead of RNA
is($as->molecule, 'mRNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');
my $ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
-format => 'embl');
my $seq = $ent->next_seq();
is(defined $seq->seq(), 1,
'success reading Embl with ^ location and badly split double quotes');
is(scalar $seq->annotation->get_Annotations('reference'), 3);
my $out_file = test_output_file();
my $out = Bio::SeqIO->new(-file=> ">$out_file",
-format => 'embl');
is($out->write_seq($seq),1,
'success writing Embl format with ^ < and > locations');
# embl with no FT
$ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
-format => 'embl');
$seq = $ent->next_seq();
ok($seq);
is(lc($seq->subseq(1,10)),'gatcagtaga');
is($seq->length, 4870);
# embl with no FH
my $noFH = Bio::SeqIO->new(-file => test_input_file('no_FH.embl'),
-format => 'embl');
is(scalar($noFH->next_seq->get_SeqFeatures), 4);
# bug 1571
$ent = Bio::SeqIO->new(-format => 'embl',
-file => test_input_file('test.embl2sq'));
is($ent->next_seq->length,4877);
# embl repbase
$ent = Bio::SeqIO->new(-file => test_input_file('BEL16-LTR_AG.embl'), -format => 'embl');
$seq = $ent->next_seq;
is($seq->display_id,'BEL16-LTR_AG');
# test secondary accessions in EMBL (bug #1332)
my $seqio = Bio::SeqIO->new(-format => 'embl',
-file => test_input_file('ECAPAH02.embl'));
$seq = $seqio->next_seq;
is($seq->accession_number, 'D10483');
is($seq->seq_version, 2);
my @accs = $seq->get_secondary_accessions();
is($accs[0], 'J01597');
is($accs[-1], 'X56742');
### TPA TESTS - Thanks to Richard Adams ###
# test Third Party Annotation entries in EMBL/Gb format
# to ensure compatability with parsers.
my $str = Bio::SeqIO->new(-format =>'embl',
-file => test_input_file('BN000066-tpa.embl'));
$seq = $str->next_seq;
ok(defined $seq);
is($seq->accession_number, 'BN000066');
is($seq->alphabet, 'dna');
is($seq->display_id, 'AGA000066');
is($seq->length, 5195);
is($seq->division, 'INV');
is($seq->get_dates, 2);
is($seq->keywords, 'acetylcholinesterase; achE1 gene; Third Party Annotation; TPA.');
is($seq->seq_version, 1);
is($seq->feature_count, 15);
my $spec_obj = $seq->species;
is ($spec_obj->common_name, 'African malaria mosquito');
is ($spec_obj->species, 'gambiae');
is ($spec_obj->genus, 'Anopheles');
is ($spec_obj->binomial, 'Anopheles gambiae');
my $ac = $seq->annotation;
my $reference = ($ac->get_Annotations('reference') )[1];
is ($reference->title,'"A novel acetylcholinesterase gene in mosquitoes codes for the insecticide target and is non-homologous to the ace gene in Drosophila"');
is ($reference->authors,'Weill M., Fort P., Berthomi eu A., Dubois M.P., Pasteur N., Raymond M.');
my $cmmnt = ($ac->get_Annotations('comment') )[0];
is($cmmnt->text, 'see also AJ488492 for achE-1 from Kisumu strain Third Party Annotation Database: This TPA record uses Anopheles gambiae trace archive data (http://trace.ensembl.org) ');
$ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
-format => 'embl');
$ent->verbose($verbose);
$seq = $ent->next_seq();
my $species = $seq->species();
my @cl = $species->classification();
is( $cl[3] ne $species->genus(), 1, 'genus duplication test');
$ent->close();
#
## read-write - test embl writing of a PrimarySeq
#
my $primaryseq = Bio::PrimarySeq->new( -seq => 'AGAGAGAGATA',
-id => 'myid',
-desc => 'mydescr',
-alphabet => 'DNA',
-accession_number => 'myaccession');
$verbose = -1 unless $ENV{'BIOPERLDEBUG'}; # silence warnings unless we are debuggin
my $embl = Bio::SeqIO->new(-format => 'embl',
-verbose => $verbose,
-file => ">$out_file");
ok($embl->write_seq($primaryseq));
# this should generate a warning
my $scalar = "test";
eval {
$embl->write_seq($scalar);
};
ok ($@);
# CDS records
# (which have nonstandard 'PA' and 'OX' tags)
# see http://bioperl.org/pipermail/bioperl-l/2009-February/029252.html
# and the rest of that thread
my $cds_file = Bio::SeqIO->new(-format =>'embl',
-file => test_input_file('cds_sample.embl'));
my $cds_seq = $cds_file->next_seq;
ok(defined $cds_seq);
is($cds_seq->display_id, 'EAL24309');
is($cds_seq->accession_number, 'CH236947.1', 'CDS - accession on PA line');
is($cds_seq->alphabet, 'dna');
is($cds_seq->length, 192);
is($cds_seq->species->binomial(), 'Homo sapiens');
is($cds_seq->seq_version, 1);
is($cds_seq->feature_count, 2);
my $cds_annot = $cds_seq->annotation;
ok(defined $cds_annot);
my $cds_dblink = ($cds_annot->get_Annotations('dblink'))[0];
ok(defined $cds_dblink);
is($cds_dblink->tagname, 'dblink', 'CDS - OX tagname');
is($cds_dblink->database, 'NCBI_TaxID', 'CDS - OX database');
is($cds_dblink->primary_id, '9606', 'CDS - OX primary_id');
|
