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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/masta.t
1
 
# -*-Perl-*-
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#Some simple tests for meme and transfac parsers
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use strict;
5
 
 
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BEGIN {
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    # to handle systems with no installed Test module
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    # we include the t dir (where a copy of Test.pm is located)
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    # as a fallback
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    eval { require Test; };
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    if( $@ ) {
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        use lib 't';
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    }
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    use Test;
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    plan tests => 16;
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}
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use Bio::Matrix::PSM::IO;
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use Bio::Root::IO;
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ok(1);
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END {
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 unlink(Bio::Root::IO->catfile(qw(t data masta_w.dat)));
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}
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#Let's try masta formats here
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my $mio =  new Bio::Matrix::PSM::IO(-format=>'masta', 
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                                      -file=>Bio::Root::IO->catfile(qw(t data masta.dat)));
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my $wmio=new Bio::Matrix::PSM::IO(-format=>'masta', 
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                                      -file=>">".Bio::Root::IO->catfile(qw(t data masta_w.dat)));
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$wmio->_flush_on_write(1);
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ok $mio;
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ok $wmio;
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my @cons;
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my $carry;
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while (my $site=$mio->next_matrix) {
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        ok $site;
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        push @cons,$site->consensus;    
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        $carry=$site if ($site->id eq 'm1logs');
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} 
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ok $cons[0],'CAGAAAAATNGAATNCCCACCCCCC';
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ok $cons[1],'CAGAAAAATAGAATCCCCACCCCCC';
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ok $cons[2],'CAGAAAAATNNAATNCCCACCNCCC';
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$wmio->write_psm($carry,'PWM');
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$carry->id('m1freq');
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$wmio->write_psm($carry,'PFM');
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$carry->id('m1seq');
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$wmio->write_psm($carry,'SEQ');
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$wmio->DESTROY;
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my $chio=new Bio::Matrix::PSM::IO(-format=>'masta', 
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                                      -file=>Bio::Root::IO->catfile(qw(t data masta_w.dat)));
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ok $chio;
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my $site=$chio->next_matrix;
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ok $site->id,'m1logs';
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ok $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';        
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$site=$chio->next_matrix;
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ok $site->id,'m1freq';
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ok $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';  
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$site=$chio->next_matrix;
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ok $site->id,'m1seq';
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ok $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';