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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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t/SeqFeature/SeqFeatAnnotated.t
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# -*-Perl-*- Test Harness script for Bioperl
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# $Id$
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use strict;
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BEGIN { 
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    use lib '.';
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    use Bio::Root::Test;
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    test_begin(-tests => 34, 
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               -requires_modules => [qw(URI::Escape Graph::Directed)],
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               -requires_networking => 1
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        );
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        use_ok('Bio::SeqFeature::Generic');
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        use_ok('Bio::SeqFeature::Annotated');
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}
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my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
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                                          -end => 5,
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                                          -strand => "+",
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                                          -frame => 2,
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                                          -type => 'nucleotide_motif',
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                                          -phase => 2,
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                                          -score => 12,
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                                          -source => 'program_b',
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                                          -display_name => 'test.annot',
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                                          -seq_id => 'test.displayname' );
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ok (defined $sfa);
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my $loc = $sfa->location;
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ok $loc->isa("Bio::Location::Simple");    
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ok $sfa->display_name eq 'test.annot';
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#test bsfa::from_feature
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my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
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                                          -end => 440,
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                                          -strand => 1,
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                                          -primary => 'nucleotide_motif',
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                                          -source  => 'program_a',
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                                          -tag => {
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                                          silly => 20,
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                                          new => 1
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                                          }
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                                          );
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my $sfa2;
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$sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
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is $sfa2->type->name,'nucleotide_motif';
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is $sfa2->primary_tag, 'nucleotide_motif';
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is $sfa2->source->display_text,'program_a';
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is $sfa2->source_tag,'program_a';
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is $sfa2->strand,1;
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is $sfa2->start,400;
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is $sfa2->end,440;
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is $sfa2->get_Annotations('silly')->value,20;
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is $sfa2->get_Annotations('new')->value,1;
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my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
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is $sfaa->type->name,'nucleotide_motif';
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is $sfaa->primary_tag, 'nucleotide_motif';
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is $sfaa->source->display_text,'program_b';
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is $sfaa->source_tag,'program_b';
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is $sfaa->strand,1;
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is $sfaa->start,1;
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is $sfaa->end,5;
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is $sfaa->score,12;
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my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
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                                        -end => 5,
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                                        -strand => "+",
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                                        -frame => 2,
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                                        -phase => 2,
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                                        -score => 12,
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                                        -display_name => 'test.annot',
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                                        -seq_id => 'test.displayname' );
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$sfa3->from_feature($sfg);
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is $sfa3->type->name,'nucleotide_motif', 'type->name';
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is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
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is $sfa3->source->display_text,'program_a';
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is $sfa3->source_tag,'program_a';
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is $sfa3->strand,1;
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is $sfa3->start,400;
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is $sfa3->end,440;
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is $sfa3->get_Annotations('silly')->value,20;
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is $sfa3->get_Annotations('new')->value,1;
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# Note there is an API conflict with SeqFeature::Generic, where score is a
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# simple scalar, and here it is a Bio::Annotation::SimpleValue
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# By popular vote there is no operator overloading, so this needs to be
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# resolved
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is $sfa3->score(), 12; 
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$sfa3->score(11);
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is $sfa3->score(), 11; 
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$sfa3->score(0);
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is $sfa3->score(), 0;   # test that setting to 0 no longer is overriddent to set score to '.' (fixed in Bio::SeqFeature::Annotated version 1.3.7)
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