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Summary

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

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

   $grail = Bio::Tools::Grail->new(-file => 'result.grail');
   # filehandle:
   $grail = Bio::Tools::Grail->new( -fh  => \*INPUT );

   # parse the results
   while($gene = $grail->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();

       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
       # singleton exons only -- should be same as $gene->exons() because
       # there are no other exons supposed to exist in this structure
       @single_exons = $gene->exons('Single');
   }

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

Description

The Grail module provides a parser for Grail gene structure prediction
output.

Methods

Methods description

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

 Title   : _has_cds()
 Usage   : $obj->_has_cds()
 Function: Whether or not the result contains the predicted CDSs, too.
 Example :
 Returns : TRUE or FALSE

 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

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

 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 _has_cds {

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

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

1;

}

sub _parse_predictions {

    my ($self) = @_;

    # code needs to go here
    
    $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'};

}

sub new {

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

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

  return $self;

}

sub next_prediction {

    my ($self) = @_;
    
    # get next gene structure
    my $gene = $self->_prediction();

    if($gene) {
	# fill in predicted protein, and if available the predicted CDS
	#
	my ($id, $seq);
	# use the seq stack if there's a seq on it
	my $seqobj = pop(@{$self->{'_seqstack'}});
	if(! $seqobj) {
	    # otherwise read from input stream
	    ($id, $seq) = $self->_read_fasta_seq();
	    $seqobj = Bio::PrimarySeq->new('-seq' => $seq,
					   '-display_id' => $id,
					   '-alphabet' => "protein");
	}
	# check that prediction number matches the prediction number
	# indicated in the sequence id (there may be incomplete gene
	# predictions that contain only signals with no associated protein
	# and CDS, like promoters, poly-A sites etc)
	$gene->primary_tag() =~ /[^0-9]([0-9]+)$/;
	my $prednr = $1;
	if($seqobj->display_id() !~ /_predicted_\w+_$prednr\|/) {
	    # this is not our sequence, so push back for the next prediction
	    push(@{$self->{'_seqstack'}}, $seqobj);
	} else {
	    $gene->predicted_protein($seqobj);
	    # CDS prediction, too?
	    if($self->_has_cds()) {
		($id, $seq) = $self->_read_fasta_seq();
		$seqobj = Bio::PrimarySeq->new('-seq' => $seq,
					       '-display_id' => $id,
					       '-alphabet' => "dna");
		$gene->predicted_cds($seqobj);
	    }
	}
    }
    return $gene;

}

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
  http://bio.perl.org/MailList.html             - About the mailing lists

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/

Email jason@bioperl.org
Describe contact details here

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