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lib/Bio/Tools/Run/Infernal.pm  view on Meta::CPAN

                            # output to outfile_name/STDOUT.
  $factory->cmbuild($aln); # builds covariance model based on alignment
                           # CM to outfile_name or model_file (one is required
                           # here), output to STDOUT.
  $factory->cmemit();      # emits sequence from specified cov. model;
                           # set one if no file specified. output to
                           # outfile_name, returns Bio::SeqIO or (if -a is set)
                           # Bio::AlignIO
  $factory->cmcalibrate($file); # calibrates specified cov. model; output to
                                # STDOUT
  $factory->cmstat($file); # summary stats for cov. model; set one if no file
                           # specified; output to STDOUT

  # run based on the setting of the program parameter

  my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
                                                @params);
  my $search = $factory->run($seq);

  # using cmsearch returns a Bio::SearchIO object

lib/Bio/Tools/Run/Infernal.pm  view on Meta::CPAN

sub cmcalibrate {
    my ($self,@seq) = @_;
    $self->program('cmcalibrate');
    return  $self->_run();
}

=head2 cmstat

 Title   :   cmstat
 Usage   :   $obj->cmstat($seq)
 Function:   Runs Infernal cmstat and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model

=cut

sub cmstat {
    my ($self,@seq) = @_;
    $self->program('cmstat');
    return  $self->_run();

t/Infernal.t  view on Meta::CPAN

sub cmstat {
    my ($cm, $outfile) = (test_input_file('purine.c.cm'), test_output_file());
    my $factory = Bio::Tools::Run::Infernal->new(-model_file    => $cm,
                                                 -outfile_name  => $outfile,
                                                 -program       => 'cmstat',  
                                                 -verbose       => test_debug());
    SKIP: {
    test_skip(-requires_executable => $factory,
             -tests => 2);
    
    my $success = $factory->cmstat();
    ok($success, 'cmstat works');
    ok (-e $outfile, 'cmstat outfile created');
    }    
}

sub cmscore {
    my ($cm, $outfile) = (test_input_file('purine.c.cm'), test_output_file());
    my $factory = Bio::Tools::Run::Infernal->new(-model_file    => $cm,
                                                 -outfile_name  => $outfile,
                                                 -program       => 'cmscore',