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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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t/SearchIO/Writer/HitTableWriter.t
 
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# -*-Perl-*- Test Harness script for Bioperl
 
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# $Id: SearchIO_HitTableWriter.t 14995 2008-11-16 06:20:00Z cjfields $
 
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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 => 8);
 
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    use_ok('Bio::SearchIO');
 
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    use_ok('Bio::SearchIO::Writer::HitTableWriter');
 
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}
 
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my ($searchio, $result, $hit, $hsp);
 
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$searchio = Bio::SearchIO->new('-format' => 'blast',
 
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    '-file'   => test_input_file('HUMBETGLOA.tblastx'));
 
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$result = $searchio->next_result;
 
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isa_ok($result,'Bio::Search::Result::ResultI');
 
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$hit = $result->next_hit;
 
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is($hit->accession, 'AE000479');
 
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is($hit->bits, 33.6);
 
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$hsp = $hit->next_hsp;
 
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is($hit->hsp->bits,$hsp->bits);
 
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isa_ok($hsp->get_aln,'Bio::Align::AlignI');
 
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my $writer = Bio::SearchIO::Writer::HitTableWriter->new( 
 
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    -columns => [qw(query_name
 
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                    query_length
 
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                    hit_name
 
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                    hit_length
 
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                    bits
 
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                    score
 
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                    frac_identical_query
 
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                    expect
 
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                    )]  );
 
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my $outfile = test_output_file();
 
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my $out = Bio::SearchIO->new(-writer => $writer,
 
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             -file   => ">$outfile");
 
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$out->write_result($result, 1);
 
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ok(-s $outfile);
 
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# tests checking file output?