Summary

Bio::Tools::Glimmer - A parser for GLIMMER gene predictions

Package variables

Included modules

Inherit

Bio::Tools::AnalysisResult

Synopsis

   use Bio::Tools::Glimmer;
   my $parser = new Bio::Tools::Glimmer(-file => $file);
     # filehandle:
   $parser = Bio::Tools::Glimmer->new( -fh  => \*INPUT );

   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same
   while(my $gene = $parser->next_prediction()) {
       # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
       # off Bio::SeqFeature::Gene::Transcript.
       #
       # $gene->exons() returns an array of 
       # Bio::Tools::Prediction::Exon objects
       # all exons:
       @exon_arr = $gene->exons();

       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
   }

Description

This is a module for parsing Glimmer predictions (currently GlimmerM
3.0 is all that has been tested). It will create gene objects from
the prediction report which can be attached to a sequence using
Bioperl objects, or output as GFF suitable for loading into
Bio::DB::GFF for use with Gbrowse.
GlimmerM is open source and available at:
http://www.tigr.org/software/glimmerm/

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::Glimmer();
 Function: Builds a new Bio::Tools::Glimmer object 
 Returns : an instance of Bio::Tools::Glimmer
 Args    :

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

 Title   : next_feature
 Usage   : while($gene = $glimmer->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Glimmer 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.

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

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

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

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

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

Methods code

sub _initialize_state {

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

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

    $self->{'_preds_parsed'} = 0;
    # array of pre-parsed predictions
    $self->{'_preds'} = [];

}

sub new {

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

  my $self = $class->SUPER::new(@args);
  return $self;

}

sub analysis_method {

 #-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /glimmer/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();

    # get next gene structure
    $gene = $self->_prediction();
    return $gene;

}

sub _parse_predictions {

    my ($self) = @_;

    my ($gene,$seqname,$seqlen,$method,$version,$lastgenenum);
    
    while(defined($_ = $self->_readline())) {
	if( /^(Glimmer\S*)\s+\((.+)\)/ ) {
	    $method = $1;
	    $version = $2;
	    $version =~ s/[\(\)]//g;
	    $version =~ s/Version\s*//g;
	    
	    next;
	} elsif(/^Sequence name:\s+(.+)$/ ) {
	    $seqname = $1;

	    next;
	} elsif( /^Sequence length:\s+(\S+)/ ) {
	    $seqlen = $1;
	    next;
	} elsif( /^(Predicted genes)|(Gene)|\s+\#/ ||
		 /^\s+$/ ) { 
	    next;
	    
	} elsif( # glimmer 3.0 output
		 /^\s+(\d+)\s+ # gene num
		 (\d+)\s+      # exon num
		 ([\+\-])\s+   # strand
		 (\S+)\s+      # exon type
		 (\d+)\s+(\d+) # exon start, end
		 \s+(\d+)      # exon length		 
		 /ox ) {
	    my ($genenum,$exonnum,$strand,$type,$start,$end,$len) = 
		( $1,$2,$3,$4,$5,$6,$7);
	    if( ! $lastgenenum ||
		$lastgenenum != $genenum) {		
		$self->_add_prediction($gene) if( $gene );
		$gene = Bio::Tools::Prediction::Gene->new
		    (
		     '-seq_id'      => $seqname,
		     '-primary_tag' => "gene",
		     '-source_tag'  => "$method\_$version",
		     '-tag'         => { 'Group' => "GenePrediction$genenum"},
		     );
	    }
	    my $exon = new Bio::Tools::Prediction::Exon
		('-seq_id'     => $seqname,
		 '-start'      => $start,
		 '-end'        => $end,
		 '-strand'     => $strand eq '-' ? '-1' : '1',
		 '-source_tag' => "$method\_$version",
		 '-primary_tag'=> 'exon',
		 '-tag'         => { 'Group' => "GenePrediction$genenum"},
		 );
	    $gene->add_exon($exon,lc($type));
	    $lastgenenum = $genenum;
	}

}

sub _prediction {

    my ($self) = @_;

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

}

sub _add_prediction {

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

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

}

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'};

}

General documentation

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