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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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   $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

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

FEEDBACK

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Mailing Lists

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl.org

APPENDIX

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

next_prediction

 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    :

_parse_predictions

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

_prediction

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

_add_prediction

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

_predictions_parsed

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

_has_cds

 Title   : _has_cds()
 Usage   : $obj->_has_cds()
 Function: Whether or not the result contains the predicted CDSs, too.
 Example :
 Returns : TRUE or FALSE
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::Grail
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


# Let the code begin...

package Bio::Tools::Grail;
use strict;

use Bio::Tools::Prediction::Gene;
use Bio::Tools::Prediction::Exon;
use Symbol;

use base qw(Bio::Root::IO Bio::Root::Root);

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;
}


sub _parse_predictions {
    my ($self) = @_;

    # code needs to go here
    
    $self->_predictions_parsed(1);
}


sub _prediction {
    my ($self) = @_;

    return 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'};
}


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;