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Merge branch 'master' of github.com:bioperl/bioperl-live

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commit 2cd1789795e49dbf34e91c40e42f00b35af6385e 2 parents 8a95e51 + 98053e9
bosborne authored March 28, 2013
4  t/Align/SimpleAlign.t
@@ -7,7 +7,7 @@ BEGIN {
7 7
     use lib '.';
8 8
     use Bio::Root::Test;
9 9
 
10  
-    test_begin( -tests => 205 );
  10
+    test_begin( -tests => 206 );
11 11
 
12 12
     use_ok('Bio::SimpleAlign');
13 13
     use_ok('Bio::AlignIO');
@@ -366,6 +366,8 @@ SKIP: {
366 366
 # Bio::FeatureHolder stuff
367 367
 
368 368
 $aln = Bio::SimpleAlign->new;
  369
+isa_ok($aln,"Bio::AnnotatableI");
  370
+
369 371
 for my $seqset ( [qw(one AGAGGAT)], [qw(two AGACGAT)], [qw(three AGAGGTT)] ) {
370 372
     $aln->add_seq(
371 373
         Bio::LocatableSeq->new(
54  t/AlignIO/AlignIO.t
@@ -4,12 +4,12 @@
4 4
 use strict;
5 5
 
6 6
 BEGIN {
7  
-	use lib '.';
  7
+    use lib '.';
8 8
     use Bio::Root::Test;
9  
-    
10  
-    test_begin(-tests => 28);
11  
-	
12  
-	use_ok('Bio::AlignIO');
  9
+
  10
+    test_begin(-tests => 29);
  11
+
  12
+    use_ok('Bio::AlignIO');
13 13
 }
14 14
 
15 15
 my $DEBUG = test_debug();
@@ -20,33 +20,39 @@ my ($str,$aln,$strout,$status);
20 20
 # not all parsers support output (noted as 0)
21 21
 my %files = (
22 22
     # file                   format       I  O
23  
-	'testaln.phylip' 	=> ['phylip',     1, 1],
24  
-	'testaln.psi'	 	=> ['psi',        1, 1],
25  
-	'testaln.arp'       => ['arp',        1, 0],
26  
-	'rfam_tests.stk'    => ['stockholm',  1, 1],
27  
-	'testaln.pfam'      => ['pfam',       1, 1],
28  
-	'testaln.msf'       => ['msf',        1, 1],
29  
-	'testaln.fasta'     => ['fasta',      1, 1],
30  
-	'testaln.selex'     => ['selex',      1, 1],
31  
-	'testaln.mase'      => ['mase',       1, 0],
32  
-	'testaln.prodom'    => ['prodom',     1, 0],
33  
-	'testaln.aln'       => ['clustalw',   1, 1],
34  
-	'testaln.metafasta' => ['metafasta',  1, 1],
35  
-	'testaln.nexus'     => ['nexus',      1, 1],
36  
-	'testaln.po'        => ['po',         1, 1],
37  
-	'testaln.xmfa'      => ['xmfa',       1, 1],
  23
+    'testaln.phylip'     => ['phylip',     1, 1],
  24
+    'testaln.psi'         => ['psi',        1, 1],
  25
+    'testaln.arp'       => ['arp',        1, 0],
  26
+    'rfam_tests.stk'    => ['stockholm',  1, 1],
  27
+    'testaln.pfam'      => ['pfam',       1, 1],
  28
+    'testaln.msf'       => ['msf',        1, 1],
  29
+    'testaln.fasta'     => ['fasta',      1, 1],
  30
+    'testaln.selex'     => ['selex',      1, 1],
  31
+    'testaln.mase'      => ['mase',       1, 0],
  32
+    'testaln.prodom'    => ['prodom',     1, 0],
  33
+    'testaln.aln'       => ['clustalw',   1, 1],
  34
+    'testaln.metafasta' => ['metafasta',  1, 1],
  35
+    'testaln.nexus'     => ['nexus',      1, 1],
  36
+    'testaln.po'        => ['po',         1, 1],
  37
+    'testaln.xmfa'      => ['xmfa',       1, 1],
38 38
  );
39 39
 
40 40
 # input file handles
41 41
 
  42
+my $aln = Bio::AlignIO->new(
  43
+    -file  => test_input_file('longnames.aln'),
  44
+    -format=>'clustalw',
  45
+)->next_aln();
  46
+isa_ok($aln, 'Bio::AnnotatableI');
  47
+
42 48
 while (my ($file, $fdata) = each %files) {
43 49
     my ($format, $in, $out) = @{$fdata};
44 50
     if ($in) {
45 51
         my $fhin = Bio::AlignIO->newFh(
46  
-           '-file'  => test_input_file($file), 
  52
+           '-file'  => test_input_file($file),
47 53
                            '-format' => $format);
48 54
         my $fhout = Bio::AlignIO->newFh(
49  
-           '-file' => ">".test_output_file(), 
  55
+           '-file' => ">".test_output_file(),
50 56
                         '-format' => 'clustalw');
51 57
         while ( $aln = <$fhin>) {
52 58
             cmp_ok($aln->num_sequences, '>=', 2, "input filehandle method test : $format");
@@ -62,10 +68,10 @@ while (my ($file, $fdata) = each %files) {
62 68
     if ($out) {
63 69
         my $status = 0;
64 70
         my $fhin = Bio::AlignIO->newFh(
65  
-           '-file' => test_input_file('testaln.aln'), 
  71
+           '-file' => test_input_file('testaln.aln'),
66 72
                         '-format' => 'clustalw');
67 73
         my $fhout = Bio::AlignIO->newFh(
68  
-           '-file'  => '>'.test_output_file(), 
  74
+           '-file'  => '>'.test_output_file(),
69 75
                            '-format' => $format);
70 76
         while ( $aln = <$fhin> ) {
71 77
             $status = print $fhout $aln;
117  t/Annotation/Annotation.t
@@ -7,7 +7,7 @@ BEGIN {
7 7
     use lib '.';
8 8
     use Bio::Root::Test;
9 9
 
10  
-    test_begin(-tests => 159);
  10
+    test_begin(-tests => 152);
11 11
 
12 12
     use_ok('Bio::Annotation::Collection');
13 13
     use_ok('Bio::Annotation::DBLink');
@@ -19,9 +19,6 @@ BEGIN {
19 19
     use_ok('Bio::Annotation::StructuredValue');
20 20
     use_ok('Bio::Annotation::TagTree');
21 21
     use_ok('Bio::Annotation::Tree');
22  
-    use_ok('Bio::Seq');
23  
-    use_ok('Bio::SimpleAlign');
24  
-    use_ok('Bio::Cluster::UniGene');
25 22
 }
26 23
 
27 24
 my $DEBUG = test_debug();
@@ -29,8 +26,8 @@ my $DEBUG = test_debug();
29 26
 #simple value
30 27
 
31 28
 my $simple = Bio::Annotation::SimpleValue->new(-tagname => 'colour',
32  
-					       -value   => '1',
33  
-					      );
  29
+                                               -value   => '1',
  30
+                                              );
34 31
 
35 32
 isa_ok($simple, 'Bio::AnnotationI');
36 33
 is $simple->display_text, 1;
@@ -44,8 +41,8 @@ is $simple->display_text, 0;
44 41
 # link
45 42
 
46 43
 my $link1 = Bio::Annotation::DBLink->new(-database => 'TSC',
47  
-					 -primary_id => 'TSC0000030',
48  
-					);
  44
+                                         -primary_id => 'TSC0000030',
  45
+                                        );
49 46
 isa_ok($link1,'Bio::AnnotationI');
50 47
 is $link1->database(), 'TSC';
51 48
 is $link1->primary_id(), 'TSC0000030';
@@ -55,8 +52,8 @@ isa_ok($ac,'Bio::AnnotationCollectionI');
55 52
 
56 53
 $ac->add_Annotation('dblink',$link1);
57 54
 $ac->add_Annotation('dblink',
58  
-		    Bio::Annotation::DBLink->new(-database => 'TSC',
59  
-						 -primary_id => 'HUM_FABV'));
  55
+                    Bio::Annotation::DBLink->new(-database => 'TSC',
  56
+                                                 -primary_id => 'HUM_FABV'));
60 57
 
61 58
 my $comment = Bio::Annotation::Comment->new( '-text' => 'sometext');
62 59
 is $comment->text, 'sometext';
@@ -66,18 +63,18 @@ $ac->add_Annotation('comment', $comment);
66 63
 
67 64
 
68 65
 my $target = Bio::Annotation::Target->new(-target_id  => 'F321966.1',
69  
-					  -start      => 1,
70  
-					  -end        => 200,
71  
-					  -strand     => 1,
72  
-					 );
  66
+                                          -start      => 1,
  67
+                                          -end        => 200,
  68
+                                          -strand     => 1,
  69
+                                         );
73 70
 isa_ok($target,'Bio::AnnotationI');
74 71
 ok $ac->add_Annotation('target', $target);
75 72
 
76 73
 
77 74
 my $ref = Bio::Annotation::Reference->new( -authors  => 'author line',
78  
-					   -title    => 'title line',
79  
-					   -location => 'location line',
80  
-					   -start    => 12);
  75
+                                           -title    => 'title line',
  76
+                                           -location => 'location line',
  77
+                                           -start    => 12);
81 78
 isa_ok($ref,'Bio::AnnotationI');
82 79
 is $ref->authors, 'author line';
83 80
 is $ref->title,  'title line';
@@ -153,7 +150,7 @@ is (scalar($nested_ac->get_Annotations('dblink')), 0);
153 150
 my @anns = $nested_ac->get_Annotations('gene names');
154 151
 isa_ok($anns[0], "Bio::Annotation::StructuredValue");
155 152
 @anns = map { $_->get_Annotations('dblink');
156  
-	  } $nested_ac->get_Annotations('nested');
  153
+          } $nested_ac->get_Annotations('nested');
157 154
 is (scalar(@anns), 3);
158 155
 is (scalar($nested_ac->flatten_Annotations()), 2);
159 156
 is (scalar($nested_ac->get_Annotations()), 7);
@@ -164,8 +161,8 @@ SKIP: {
164 161
   use_ok('Bio::Annotation::OntologyTerm');
165 162
   # OntologyTerm annotation
166 163
   my $termann = Bio::Annotation::OntologyTerm->new(-label => 'test case',
167  
-						   -identifier => 'Ann:00001',
168  
-						   -ontology => 'dumpster');
  164
+                                                   -identifier => 'Ann:00001',
  165
+                                                   -ontology => 'dumpster');
169 166
   isa_ok($termann->term,'Bio::Ontology::Term');
170 167
   is ($termann->term->name, 'test case');
171 168
   is ($termann->term->identifier, 'Ann:00001');
@@ -175,22 +172,18 @@ SKIP: {
175 172
 }
176 173
 
177 174
 # AnnotatableI
  175
+use Bio::Seq;
178 176
 my $seq = Bio::Seq->new();
179  
-isa_ok($seq,"Bio::AnnotatableI");
180 177
 SKIP: {
181  
-	test_skip(-requires_modules => [qw(Bio::SeqFeature::Annotated URI::Escape)],
182  
-			  -tests => 4);
183  
-	my $fea = Bio::SeqFeature::Annotated->new();
184  
-	isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
185  
-	isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
186  
-	$fea = Bio::SeqFeature::Generic->new();
187  
-	isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
188  
-	isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
  178
+        test_skip(-requires_modules => [qw(Bio::SeqFeature::Annotated URI::Escape)],
  179
+                          -tests => 4);
  180
+        my $fea = Bio::SeqFeature::Annotated->new();
  181
+        isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
  182
+        isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
  183
+        $fea = Bio::SeqFeature::Generic->new();
  184
+        isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
  185
+        isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
189 186
 }
190  
-my $clu = Bio::Cluster::UniGene->new();
191  
-isa_ok($clu, "Bio::AnnotatableI");
192  
-my $aln = Bio::SimpleAlign->new();
193  
-isa_ok($aln,"Bio::AnnotatableI");
194 187
 
195 188
 # tests for Bio::Annotation::AnnotationFactory
196 189
 
@@ -199,13 +192,13 @@ isa_ok($factory, 'Bio::Factory::ObjectFactoryI');
199 192
 
200 193
 # defaults to SimpleValue
201 194
 $ann = $factory->create_object(-value => 'peroxisome',
202  
-			       -tagname => 'cellular component');
  195
+                               -tagname => 'cellular component');
203 196
 isa_ok($ann, 'Bio::Annotation::SimpleValue');
204 197
 
205 198
 $factory->type('Bio::Annotation::OntologyTerm');
206 199
 
207 200
 $ann = $factory->create_object(-name => 'peroxisome',
208  
-			       -tagname => 'cellular component');
  201
+                               -tagname => 'cellular component');
209 202
 ok(defined $ann);
210 203
 isa_ok($ann, 'Bio::Annotation::OntologyTerm');
211 204
 
@@ -230,43 +223,41 @@ isa_ok($ann,'Bio::Annotation::Comment');
230 223
 # factory guessing the type: Target
231 224
 $factory = Bio::Annotation::AnnotationFactory->new();
232 225
 $ann = $factory->create_object(-target_id => 'F1234',
233  
-			       -start     => 1,
234  
-			       -end       => 10 );
  226
+                               -start     => 1,
  227
+                               -end       => 10 );
235 228
 ok defined $ann;
236 229
 isa_ok($ann,'Bio::Annotation::Target');
237 230
 
238 231
 # factory guessing the type: OntologyTerm
239 232
 $factory = Bio::Annotation::AnnotationFactory->new();
240 233
 ok(defined ($ann = $factory->create_object(-name => 'peroxisome',
241  
-					   -tagname => 'cellular component')));
  234
+                                           -tagname => 'cellular component')));
242 235
 like(ref $ann, qr(Bio::Annotation::OntologyTerm));
243 236
 
244 237
 # tree
245 238
 my $tree_filename = test_input_file('longnames.dnd');
246 239
 my $tree = Bio::TreeIO->new(-file=>$tree_filename)->next_tree();
247 240
 my $ann_tree = Bio::Annotation::Tree->new(
248  
-					  -tagname  => 'tree',
249  
-					  -tree_obj => $tree,
250  
-					 );
  241
+                                          -tagname  => 'tree',
  242
+                                          -tree_obj => $tree,
  243
+                                         );
251 244
 
252 245
 isa_ok($ann_tree, 'Bio::AnnotationI');
253 246
 $ann_tree->tree_id('test');
254 247
 is $ann_tree->tree_id(), 'test', "tree_id()";
255 248
 $ann_tree->tagname('tree');
256 249
 is $ann_tree->tagname(), 'tree', "tagname()";
257  
-my $aln_filename = test_input_file('longnames.aln');
258 250
 use Bio::AlignIO;
259  
-$aln = Bio::AlignIO->new(-file  => $aln_filename,
260  
-			 -format=>'clustalw')->next_aln();
261  
-isa_ok($aln, 'Bio::AnnotatableI');
  251
+my $aln = Bio::AlignIO->new(-file  => test_input_file('longnames.aln'),
  252
+                         -format=>'clustalw')->next_aln();
262 253
 $ac = Bio::Annotation::Collection->new();
263 254
 $ac->add_Annotation('tree',$ann_tree);
264 255
 $aln->annotation($ac);
265 256
 for my $treeblock ( $aln->annotation->get_Annotations('tree') ) {
266 257
   my $treeref = $treeblock->tree();
267 258
   my @nodes = sort { defined $a->id &&
268  
-		       defined $b->id &&
269  
-			 $a->id cmp $b->id } $treeref->get_nodes();
  259
+                       defined $b->id &&
  260
+                         $a->id cmp $b->id } $treeref->get_nodes();
270 261
   is(@nodes, 26);
271 262
   is $nodes[12]->id, 'Skud_Contig1703.7', "add tree to AlignI";
272 263
   my $str;
@@ -284,23 +275,23 @@ isa_ok($ann,'Bio::Annotation::Tree');
284 275
 
285 276
 #tagtree
286 277
 my $struct = [ 'genenames' => [
287  
-			       ['genename' => [
288  
-					       [ 'Name' => 'CALM1' ],
289  
-					       ['Synonyms'=> 'CAM1'],
290  
-					       ['Synonyms'=> 'CALM'],
291  
-					       ['Synonyms'=> 'CAM' ] ] ],
292  
-			       ['genename'=> [
293  
-					      [ 'Name'=> 'CALM2' ],
294  
-					      [ 'Synonyms'=> 'CAM2'],
295  
-					      [ 'Synonyms'=> 'CAMB'] ] ],
296  
-			       [ 'genename'=> [
297  
-					       [ 'Name'=> 'CALM3' ],
298  
-					       [ 'Synonyms'=> 'CAM3' ],
299  
-					       [ 'Synonyms'=> 'CAMC' ] ] ]
300  
-			      ] ];
  278
+                               ['genename' => [
  279
+                                               [ 'Name' => 'CALM1' ],
  280
+                                               ['Synonyms'=> 'CAM1'],
  281
+                                               ['Synonyms'=> 'CALM'],
  282
+                                               ['Synonyms'=> 'CAM' ] ] ],
  283
+                               ['genename'=> [
  284
+                                              [ 'Name'=> 'CALM2' ],
  285
+                                              [ 'Synonyms'=> 'CAM2'],
  286
+                                              [ 'Synonyms'=> 'CAMB'] ] ],
  287
+                               [ 'genename'=> [
  288
+                                               [ 'Name'=> 'CALM3' ],
  289
+                                               [ 'Synonyms'=> 'CAM3' ],
  290
+                                               [ 'Synonyms'=> 'CAMC' ] ] ]
  291
+                              ] ];
301 292
 
302 293
 my $ann_struct = Bio::Annotation::TagTree->new(-tagname => 'gn',
303  
-					       -value => $struct);
  294
+                                               -value => $struct);
304 295
 
305 296
 isa_ok($ann_struct, 'Bio::AnnotationI');
306 297
 my $val = $ann_struct->value;
@@ -308,7 +299,7 @@ like($val, qr/Name: CALM1/,'default itext');
308 299
 
309 300
 # roundtrip
310 301
 my $ann_struct2 = Bio::Annotation::TagTree->new(-tagname => 'gn',
311  
-						-value => $val);
  302
+                                                -value => $val);
312 303
 is($ann_struct2->value, $val,'roundtrip');
313 304
 
314 305
 # formats
16  t/Cluster/UniGene.t
... ...
@@ -0,0 +1,16 @@
  1
+# -*-Perl-*- Test Harness script for Bioperl
  2
+# $Id$
  3
+
  4
+use strict;
  5
+
  6
+BEGIN {
  7
+    use lib '.';
  8
+    use Bio::Root::Test;
  9
+
  10
+    test_begin(-tests => 2);
  11
+
  12
+    use_ok('Bio::Cluster::UniGene');
  13
+}
  14
+
  15
+my $clu = Bio::Cluster::UniGene->new();
  16
+isa_ok($clu, "Bio::AnnotatableI");
73  t/Seq/Seq.t
@@ -3,24 +3,25 @@
3 3
 
4 4
 use strict;
5 5
 
6  
-BEGIN { 
  6
+BEGIN {
7 7
     use lib '.';
8 8
     use Bio::Root::Test;
9  
-    
10  
-    test_begin(-tests => 72);
11  
-	
12  
-	use_ok('Bio::Seq');
13  
-	use_ok('Bio::Seq::RichSeq');
14  
-	use_ok('Bio::SeqFeature::Generic');
15  
-	use_ok('Bio::Species');
16  
-	use_ok('Bio::Annotation::SimpleValue');
  9
+
  10
+    test_begin(-tests => 73);
  11
+
  12
+    use_ok('Bio::Seq');
  13
+    use_ok('Bio::Seq::RichSeq');
  14
+    use_ok('Bio::SeqFeature::Generic');
  15
+    use_ok('Bio::Species');
  16
+    use_ok('Bio::Annotation::SimpleValue');
17 17
 }
18 18
 
19 19
 ok my $seq = Bio::Seq->new(-seq=>'ACTGTGGCGTCAACT',
20 20
                         -desc=>'Sample Bio::Seq object',
21  
-			-alphabet => 'dna',
  21
+                        -alphabet => 'dna',
22 22
                         -is_circular => 1
23 23
                        );
  24
+isa_ok($seq,"Bio::AnnotatableI");
24 25
 
25 26
 ok $seq->is_circular;
26 27
 ok not $seq->is_circular(0);
@@ -35,10 +36,10 @@ is $trunc->seq, 'ACTG', 'truncated sequence string';
35 36
 is $seq->seq(),  'ACTGTGGCGTCAACT' ;
36 37
 
37 38
 ok $seq = Bio::Seq->new(-seq=>'actgtggcgtcaact',
38  
-		     -desc=>'Sample Bio::Seq object',
39  
-		     -display_id => 'something',
40  
-		     -accession_number => 'accnum',
41  
-		     -alphabet => 'dna' );
  39
+                        -desc=>'Sample Bio::Seq object',
  40
+                        -display_id => 'something',
  41
+                        -accession_number => 'accnum',
  42
+                        -alphabet => 'dna' );
42 43
 
43 44
 is uc $seq->alphabet, 'DNA' , 'alphabet';
44 45
 
@@ -65,24 +66,24 @@ is scalar($seq->top_SeqFeatures()), 0;
65 66
 is scalar($seq->flush_SeqFeatures()), 0;
66 67
 
67 68
 my $newfeat = Bio::SeqFeature::Generic->new( -start => 10,
68  
-					     -end => 12,
69  
-					     -primary => 'silly',
70  
-					     -source => 'stuff');
  69
+                                             -end => 12,
  70
+                                             -primary => 'silly',
  71
+                                             -source => 'stuff');
71 72
 
72 73
 
73 74
 $seq->add_SeqFeature($newfeat);
74 75
 is $seq->feature_count, 1;
75 76
 
76 77
 my $species = Bio::Species->new
77  
-    (-verbose => 1, 
  78
+    (-verbose => 1,
78 79
      -classification => [ qw( sapiens Homo Hominidae
79  
-			      Catarrhini Primates Eutheria
80  
-			      Mammalia Vertebrata Chordata
81  
-			      Metazoa Eukaryota )]);
  80
+                              Catarrhini Primates Eutheria
  81
+                              Mammalia Vertebrata Chordata
  82
+                              Metazoa Eukaryota )]);
82 83
 $seq->species($species);
83 84
 is $seq->species->binomial, 'Homo sapiens';
84 85
 $seq->annotation->add_Annotation('description',
85  
-		 Bio::Annotation::SimpleValue->new(-value => 'desc-here'));
  86
+                 Bio::Annotation::SimpleValue->new(-value => 'desc-here'));
86 87
 my ($descr) = $seq->annotation->get_Annotations('description');
87 88
 is $descr->value(), 'desc-here';
88 89
 is $descr->tagname(), 'description';
@@ -98,15 +99,15 @@ is  $trans->seq(), 'TVAST' , 'translated sequence';
98 99
 # acid ...with the addendum that there should be no assumption by the method
99 100
 # to complete the codon unless specified, using the -complete_codons flag.
100 101
 
101  
-$seq->seq('ACTGTGGCGTCAACN'); 
  102
+$seq->seq('ACTGTGGCGTCAACN');
102 103
 $trans = $seq->translate();
103 104
 is $trans->seq(), 'TVAST', 'translated sequence with explicit unambiguous codons';
104 105
 
105  
-$seq->seq('ACTGTGGCGTCAAC'); 
  106
+$seq->seq('ACTGTGGCGTCAAC');
106 107
 $trans = $seq->translate();
107 108
 is $trans->seq(), 'TVAS', 'translated sequence with unknown unambiguous codons';
108 109
 
109  
-$seq->seq('ACTGTGGCGTCAAC'); 
  110
+$seq->seq('ACTGTGGCGTCAAC');
110 111
 $trans = $seq->translate(-complete_codons => 1);
111 112
 is $trans->seq(), 'TVAST', 'translated sequence with unknown unambiguous codons, completed';
112 113
 
@@ -139,7 +140,7 @@ $seq->seq('atgtggtaa');
139 140
 $trans = $seq->translate(undef,undef,undef,undef,1);
140 141
 is $trans->seq(), 'MW', 'translated sequence';
141 142
 
142  
-#frame 
  143
+#frame
143 144
 my $string;
144 145
 my @frames = (0, 1, 2);
145 146
 foreach my $frame (@frames) {
@@ -168,15 +169,15 @@ is( $seq->translate('J', '-',)->seq, 'MWJJ');
168 169
 
169 170
 # tests for RichSeq
170 171
 ok my $richseq = Bio::Seq::RichSeq->new( -seq => 'atgtggtaataa',
171  
-				      -accession_number => 'AC123',
172  
-				      -alphabet => 'rna',
173  
-				      -molecule => 'mRNA',		
174  
-				      -id => 'id1',
175  
-				      -dates => [ '2001/1/1' ],
176  
-				      -pid => '887821',
177  
-				      -keywords => 'JUNK1;JUNK2',
178  
-				      -division => 'Fungi',
179  
-				      -secondary_accessions => 'AC1152' );
  172
+                                      -accession_number => 'AC123',
  173
+                                      -alphabet => 'rna',
  174
+                                      -molecule => 'mRNA',
  175
+                                      -id => 'id1',
  176
+                                      -dates => [ '2001/1/1' ],
  177
+                                      -pid => '887821',
  178
+                                      -keywords => 'JUNK1;JUNK2',
  179
+                                      -division => 'Fungi',
  180
+                                      -secondary_accessions => 'AC1152' );
180 181
 
181 182
 is ($richseq->seq, 'atgtggtaataa');
182 183
 is ($richseq->display_id, 'id1');
@@ -210,7 +211,7 @@ is $seq->display_id, 0, "Bug #2864";
210 211
 # transcribe/rev_transcribe
211 212
 
212 213
 $seq = Bio::Seq->new( -id => 'seq1', -alphabet=>'dna',
213  
-		      -seq=> 'attTcgcatgT' );
  214
+                      -seq=> 'attTcgcatgT' );
214 215
 ok my $xseq = $seq->transcribe;
215 216
 is $xseq->alphabet, 'rna';
216 217
 ok !($xseq->seq =~ /[tT]/);

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