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# -*-Perl-*- Test Harness script for Bioperl
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# $Id: SiteMatrix.t 15112 2008-12-08 18:12:38Z sendu $
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test_begin(-tests => 14);
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use_ok('Bio::Matrix::PSM::SiteMatrix');
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my %param=(pA=>$A,pC=>$C,pG=>$G,pT=>$T,e_val=>$eval, correction =>0);
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ok my $matrix=Bio::Matrix::PSM::SiteMatrix->new(%param);
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is $matrix->IUPAC,'ABVCD';
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is $matrix->consensus,'ATACT';
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is $matrix->get_string('A'),$A;
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my %x= (base=>'A',pA=>1,pC=>0,pG=>0,pT=>0,prob=>10,rel=>0,
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lA=>undef,lC=>undef,lG=>undef,lT=>undef);
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my %pos = $matrix->next_pos;
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while(my ($k,$v) = each %x ) {
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if( ! defined $v && ! defined $r) {
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} elsif($pos{$k} ne $v ) {
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ok $matrix->e_val(0.0001);
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is $matrix->e_val,0.0001;
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#Now some PSM specific methods like regexp and matrix info
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is $matrix->regexp,'[Aa][CcGgTtBb][AaCcGgVv][Cc][AaGgTtDd]';
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my @x=(1,0,0.5,0,0.1);
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is_deeply [$matrix->get_array('A')], \@x;
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@x=qw([Aa] [CcGgTtBb] [AaCcGgVv] [Cc] [AaGgTtDd]);
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is_deeply [$matrix->regexp_array], \@x;