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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/Amplicon.t
 
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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 => 21);
 
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    use_ok 'Bio::PrimarySeq';
 
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    use_ok 'Bio::SeqFeature::Primer';
 
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    use_ok 'Bio::SeqFeature::Amplicon';
 
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}
 
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my ($amplicon, $amplicon_seq, $fwd_primer, $rev_primer, $template);
 
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# Basic amplicon object
 
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$amplicon = Bio::SeqFeature::Amplicon->new();
 
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isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
 
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isa_ok $amplicon, 'Bio::SeqFeature::SubSeq';
 
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# Amplicon with explicit sequence (sequence string)
 
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ok $amplicon = Bio::SeqFeature::Amplicon->new(
 
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    -seq => 'CCCCCAAAAAGGGGGTTTTT',
 
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);
 
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ok $amplicon_seq = $amplicon->seq;
 
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isa_ok $amplicon_seq, 'Bio::PrimarySeq';
 
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is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
 
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# Amplicon with explicit sequence (sequence object)
 
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$fwd_primer = Bio::SeqFeature::Primer->new(
 
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    -start  => 1,
 
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    -end    => 4,
 
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    -strand => 1
 
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);
 
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$rev_primer = Bio::SeqFeature::Primer->new(
 
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    -seq    => 'GATTA',
 
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    -start  => 16,
 
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    -end    => 20,
 
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    -strand => -1
 
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);
 
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ok $amplicon = Bio::SeqFeature::Amplicon->new(
 
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    -start      => 1,
 
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    -end        => 20,
 
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    -seq        => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
 
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    -fwd_primer => $fwd_primer,
 
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);
 
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ok $amplicon->rev_primer($rev_primer);
 
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is_deeply $amplicon->fwd_primer(), $fwd_primer;
 
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is_deeply $amplicon->rev_primer(), $rev_primer;
 
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ok $amplicon_seq = $amplicon->seq;
 
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isa_ok $amplicon_seq, 'Bio::PrimarySeq';
 
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is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
 
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# Amplicon with implicit sequence
 
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$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');
 
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ok $amplicon = Bio::SeqFeature::Amplicon->new(
 
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    -start  => 11,
 
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    -end    => 30,
 
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    -strand => -1
 
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);
 
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ok $template->add_SeqFeature($amplicon);
 
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ok $amplicon_seq = $amplicon->seq;
 
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isa_ok $amplicon_seq, 'Bio::PrimarySeq';
 
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is $amplicon_seq->seq, 'AAAAACCCCCTTTTTGGGGG';