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Summary

Bio::Tools::Eponine - Results of one Eponine run

Package variables

Included modules

Inherit

Bio::Tools::AnalysisResult

Synopsis

 use Bio::Tools::Run::Eponine;
 use strict;
    my $seq = "/data/seq.fa";
    my $threshold  = "0.999";
    my @params = ( '-seq' => $seq,
                 '-threshold' => $threshold);

   my $factory = Bio::Tools::Run::Eponine->new(@params);
     # run eponine against fasta 
        my $r = $factory->run_eponine($seq);
        my $parser = Bio::Tools::Eponine->new($r);

       while (my $feat = $parser->next_prediction){
                #$feat contains array of SeqFeature
               foreach my $orf($feat) {
                   print $orf->seq_id. "\n";
               }
       }

Description

Parser for Eponine, a probabilistic transcription start site detector
optimized for mammalian genomic sequence. This module inherits off
Bio::Tools::AnalysisResult and therefore implements
Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and
Bio::SeqAnalysisParserI).

Methods

Methods description

 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :

 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns :

 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE

 Usage     : $mzef->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /mzef/i.
 Returns   : String
 Argument  : n/a

    Title   :   create_feature
    Usage   :   obj->create_feature($feature)
    Function:   Returns an array of features
    Returns :   Returns an array of features
    Args    :   none

 Title   : next_feature
 Usage   : while($gene = $mzef->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the MZEF result
           file. Call this method repeatedly until FALSE is returned.

           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for 
           next_prediction() at present.

           Note that with the present version of MZEF there will only be one
           object returned, because MZEF does not predict individual genes
           but just potential internal exons.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

 Title   : next_prediction
 Usage   : while($gene = $mzef->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the MZEF result
           file. Call this method repeatedly until FALSE is returned.

           Note that with the present version of MZEF there will only be one
           object returned, because MZEF does not predict individual genes
           but just potential internal exons.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

Methods code

sub _initialize_state {

    my($self,@args) = @_;

    # first call the inherited method!
    my $make = $self->SUPER::_initialize_state(@args);

    # handle our own parameters

    # our private state variables
    $self->{'_preds_parsed'} = 0;
    #array of Bio::SeqFeatures
    $self->{'_flist'} =[];

}

sub _parse_predictions {

    my ($self) = @_;

    while(defined($_ = $self->_readline())) {
        if (! /^\#/){ #ignore introductory lines

	      my @element = split;
	      my (%feature);
	      $feature {name} = $element[0];
	      $feature {score} = $element[5];
	      $feature {start} = $element[3];
	      $feature {end} = $element[4];
	      $feature {strand} = $element[6];
	      $feature {source}= 'Eponine';
	      $feature {primary}= 'TSS';
	      $feature {program} = 'eponine-scan';
	      $feature {program_version} = '2';
            
	      $self->create_feature(\%feature);
	            next;

	}
    }
    $self->_predictions_parsed(1);

}

sub _prediction {

    my ($self) = @_;

    return undef unless(exists($self->{'_flist'}) && @{$self->{'_flist'}});
    return shift(@{$self->{'_flist'}});

}

sub _predictions_parsed {

    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    # array of pre-parsed predictions
    if(! exists($self->{'_preds_parsed'})) {
	$self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}


1;

}

sub analysis_method {

 #-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /epo/i)) {
	$self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);

}

sub create_feature {

    my ($self, $feat) = @_;
     #create and fill Bio::EnsEMBL::Seqfeature object

      my $tss = Bio::SeqFeature::Generic->new
                    (   -seq_id  => $feat->{'name'},
                        -start   => $feat->{'start'},
                        -end     => $feat->{'end'},
                        -strand  => $feat->{'strand'},
            		-score   => $feat->{'score'},
                        -source_tag  => $feat->{'source'},
		        -primary_tag => $feat->{'primary'});

		

  if ($tss) {
         # add to _flist
      push(@{$self->{'_flist'}}, $tss);
   }

   #print $tss->gff_string;

}

sub next_feature {

    my ($self,@args) = @_;
    # even though next_prediction doesn't expect any args (and this method
    # does neither), we pass on args in order to be prepared if this changes
    # ever
    return $self->next_prediction(@args);

}

sub next_prediction {

    my ($self) = @_;
    my $gene;

    # if the prediction section hasn't been parsed yet, we do this now
    $self->_parse_predictions() unless $self->_predictions_parsed();

    # return the next gene structure (transcript)
    return $self->_prediction();

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org          - General discussion
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Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Describe contact details here

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _