Bio::Tools Grail
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Summary
Bio::Tools::Grail - Results of one Grail run
Package variables
No package variables defined.
Included modules
Bio::Tools::Prediction::Exon
Bio::Tools::Prediction::Gene
Symbol
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) $genscan->close();
Description
The Grail module provides a parser for Grail gene structure prediction
output.
Methods
new
No description
Code
next_predictionDescriptionCode
_parse_predictionsDescriptionCode
_predictionDescriptionCode
_add_predictionDescriptionCode
_predictions_parsedDescriptionCode
_has_cdsDescriptionCode
Methods description
next_predictioncode    nextTop
 Title   : next_prediction
Usage : while($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_predictionscodeprevnextTop
 Title   : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_predictioncodeprevnextTop
 Title   : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_predictioncodeprevnextTop
 Title   : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cdscodeprevnextTop
 Title   : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

  return $self;
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($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 $gene;
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
    my ($self) = @_;

    # code needs to go here
$self->_predictions_parsed(1);
}
_predictiondescriptionprevnextTop
sub _prediction {
    my ($self) = @_;

    return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
    return shift(@{$self->{'_preds'}});
}
_add_predictiondescriptionprevnextTop
sub _add_prediction {
    my ($self, $gene) = @_;

    if(! exists($self->{'_preds'})) {
	$self->{'_preds'} = [];
    }
    push(@{$self->{'_preds'}}, $gene);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
	$self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}
_has_cdsdescriptionprevnextTop
sub _has_cds {
    my ($self, $val) = @_;

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

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _