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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqFeatAnnotated.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 34,
-requires_modules => [qw(URI::Escape Graph::Directed)],
-requires_networking => 1
);
use_ok('Bio::SeqFeature::Generic');
use_ok('Bio::SeqFeature::Annotated');
}
my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
-end => 5,
-strand => "+",
-frame => 2,
-type => 'nucleotide_motif',
-phase => 2,
-score => 12,
-source => 'program_b',
-display_name => 'test.annot',
-seq_id => 'test.displayname' );
ok (defined $sfa);
my $loc = $sfa->location;
ok $loc->isa("Bio::Location::Simple");
ok $sfa->display_name eq 'test.annot';
#test bsfa::from_feature
my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
-end => 440,
-strand => 1,
-primary => 'nucleotide_motif',
-source => 'program_a',
-tag => {
silly => 20,
new => 1
}
);
my $sfa2;
$sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
is $sfa2->type->name,'nucleotide_motif';
is $sfa2->primary_tag, 'nucleotide_motif';
is $sfa2->source->display_text,'program_a';
is $sfa2->source_tag,'program_a';
is $sfa2->strand,1;
is $sfa2->start,400;
is $sfa2->end,440;
is $sfa2->get_Annotations('silly')->value,20;
is $sfa2->get_Annotations('new')->value,1;
my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
is $sfaa->type->name,'nucleotide_motif';
is $sfaa->primary_tag, 'nucleotide_motif';
is $sfaa->source->display_text,'program_b';
is $sfaa->source_tag,'program_b';
is $sfaa->strand,1;
is $sfaa->start,1;
is $sfaa->end,5;
is $sfaa->score,12;
my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
-end => 5,
-strand => "+",
-frame => 2,
-phase => 2,
-score => 12,
-display_name => 'test.annot',
-seq_id => 'test.displayname' );
$sfa3->from_feature($sfg);
is $sfa3->type->name,'nucleotide_motif', 'type->name';
is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
is $sfa3->source->display_text,'program_a';
is $sfa3->source_tag,'program_a';
is $sfa3->strand,1;
is $sfa3->start,400;
is $sfa3->end,440;
is $sfa3->get_Annotations('silly')->value,20;
is $sfa3->get_Annotations('new')->value,1;
# Note there is an API conflict with SeqFeature::Generic, where score is a
# simple scalar, and here it is a Bio::Annotation::SimpleValue
# By popular vote there is no operator overloading, so this needs to be
# resolved
is $sfa3->score(), 12;
$sfa3->score(11);
is $sfa3->score(), 11;
$sfa3->score(0);
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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