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Viewing changes to t/AlignIO/clustalw.t

  • 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/AlignIO/clustalw.t
 
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# -*-Perl-*- Test Harness script for Bioperl
 
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# $Id: clustalw.t 14971 2008-10-28 16:08:52Z 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 => 6);
 
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        use_ok('Bio::AlignIO::clustalw');
 
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}
 
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my $DEBUG = test_debug();
 
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my ($str,$aln,$strout,$status);
 
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# CLUSTAL
 
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my $io = Bio::AlignIO->new(
 
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   -file => test_input_file("testaln.aln") );
 
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$aln = $io->next_aln();
 
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isa_ok($aln,'Bio::Align::AlignI');
 
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is $aln->consensus_string, "MNEGEHQIKLDELFEKLLRARKIFKNKDVLRHSWEPKDLPHRHEQIEA".
 
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"LAQILVPVLRGETMKIIFCGHHACELGEDRGTKGFVIDELKDVDEDRNGKVDVIEINCEHMDTHYRVLPNIAKLF".
 
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"DDCTGIGVPMHGGPTDEVTAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTRINTELKRAKVSVIGISND".
 
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"LKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAFYPGVLDEGVIPLCAALAAREHGDARKALDLLRV".
 
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"AGEIAEREGASKVTEKHVWKAQEKIEQDMMEEVIKTLPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYI".
 
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"DLEPLTQRRISDLINELDMLGIINAKVVSKGRYGRTKEIRLMVTSYKIRNVLRYDYSIQPLLTISLKSEQRRLI",
 
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"clustalw consensus_string test";
 
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my $outfile = test_output_file();
 
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$strout = Bio::AlignIO->new(
 
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   '-file' => ">$outfile", 
 
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                              '-format' => 'clustalw');
 
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$status = $strout->write_aln($aln);
 
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is $status, 1, "clustalw (.aln) output test";
 
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undef $strout;
 
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$str = Bio::AlignIO->new(
 
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   '-file'=> $outfile, 
 
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                           '-format' => 'clustalw');
 
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$aln = $str->next_aln($aln);
 
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isa_ok($aln,'Bio::Align::AlignI');
 
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is $aln->get_seq_by_pos(1)->get_nse, 'P84139/1-420', "clustalw (.aln) input test";