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Summary

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

Package variables

Included modules

Inherit

Bio::Tools::AnalysisResult

Synopsis

   $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
   # filehandle:
   $mzef = Bio::Tools::MZEF->new( -fh  => \*INPUT );
   # to indicate that the sequence was reversed prior to feeding it to MZEF
   # and that you want to have this reflected in the strand() attribute of 
   # the exons, as well have the coordinates translated to the non-reversed
   # sequence
   $mzef = Bio::Tools::MZEF->new( -file   => 'result.mzef',
                                  -strand => -1 );

   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
   while($gene = $mzef->next_prediction()) {
       # $gene is an instance of Bio::Tools::Prediction::Gene

       # $gene->exons() returns an array of 
       # Bio::Tools::Prediction::Exon objects
       # all exons:
       @exon_arr = $gene->exons();

       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # note that presently MZEF predicts only internal exons!
   }

   # essential if you gave a filename at initialization (otherwise the file
   # will stay open)
   $mzef->close();

Description

The MZEF module provides a parser for MZEF gene structure prediction
output.
This module inherits off Bio::Tools::AnalysisResult and therefore
implements Bio::SeqAnalysisParserI.

Methods

Methods description

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

 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   : 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 _add_prediction {

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

    if(! exists($self->{'_preds'})) {
	$self->{'_preds'} = [];
    }
    push(@{$self->{'_preds'}}, $gene);

}

sub _initialize_state {

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

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

    # handle our own parameters
    my ($strand, $params) =
	$self->_rearrange([qw(STRAND
			      )],
			  @args);

    # our private state variables
    $strand = 1 unless defined($strand);
    $self->{'_strand'} = $strand;
    $self->{'_preds_parsed'} = 0;
    $self->{'_has_cds'} = 0;
    # array of pre-parsed predictions
    $self->{'_preds'} = [];

}

sub _parse_predictions {

    my ($self) = @_;
    my ($method); # set but not used presently
    my $exon_tag = "InternalExon";
    my $gene;
    # my $seqname; # name given in output is poorly formatted
    my $seqlen;
    my $prednr = 1;

    while(defined($_ = $self->_readline())) {
	if(/^\s*(\d+)\s*-\s*(\d+)\s+/) {
	    # exon or signal
	    if(! defined($gene)) {
		$gene = Bio::Tools::Prediction::Gene->new(
                                       '-primary' => "GenePrediction$prednr",
				       '-source' => 'MZEF');
	    }
	    # we handle start-end first because may not be space delimited
	    # for large numbers
	    my ($start,$end) = ($1,$2);
	    s/^\s*(\d+)\s*-\s*(\d+)\s+//;
	    # split the rest into fields
	    chomp();
	    # format: Coordinates P Fr1 Fr2 Fr3 Orf 3ss Cds 5ss
	    # index:              0   1   2   3   4   5   6   7
	    my @flds = split(' ', $_);
	    # create the feature object depending on the type of signal --
	    # which is always an (internal) exon for MZEF
	    my $predobj = Bio::Tools::Prediction::Exon->new();
	    # set common fields
	    $predobj->source_tag('MZEF');
	    $predobj->significance($flds[0]);
	    $predobj->score($flds[0]); # what shall we set as overall score?
	    $predobj->strand($self->{'_strand'}); # MZEF searches only one
	    if($predobj->strand() == 1) {
		$predobj->start($start);
		$predobj->end($end);
	    } else {
		$predobj->start($seqlen-$end+1);
		$predobj->end($seqlen-$start+1);
	    }
	    # set scores
	    $predobj->start_signal_score($flds[5]);
	    $predobj->end_signal_score($flds[7]);
	    $predobj->coding_signal_score($flds[6]);
	    # frame -- we simply extract the one with highest score from the
	    # orf field, and store the individual scores for now
	    my $frm = index($flds[4], "1");
	    $predobj->frame(($frm < 0) ? undef : $frm);
	    $predobj->primary_tag($exon_tag);
	    $predobj->is_coding(1);
	    # add to gene structure (should be done only when start and end
	    # are set, in order to allow for proper expansion of the range)
	    $gene->add_exon($predobj);		
	    next;
	}
	if(/^\s*Internal .*(MZEF)/) {
	    $self->analysis_method($1);
	    next;
	}
	if(/^\s*File_Name:\s+(\S+)\s+Sequence_length:\s+(\d+)/) {
	    # $seqname = $1; # this is too poor currently (file name truncated
                             # to 10 chars) in order to be sensible enough
	    $seqlen = $2;
	    next;
	}
    }
    # $gene->seq_id($seqname);
    $self->_add_prediction($gene) if defined($gene);
    $self->_predictions_parsed(1);

}

sub _prediction {

    my ($self) = @_;

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

}

sub _predictions_parsed {

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

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
	$self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}


1;

}

sub analysis_method {

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

}

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

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Describe contact details here

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