Bio::Tools Grail
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Tools::Grail - Results of one Grail run
Package variables
No package variables defined.
Included modules
Bio::Root::IO Bio::Root::Root
   $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) $genscan->close();
The Grail module provides a parser for Grail gene structure prediction
No description
Methods description
next_predictioncode    nextTop
 Title   : next_prediction
Usage : while($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 :
 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
 Title   : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
Methods code
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@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
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'};

General documentation
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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
AUTHOR - Jason StajichTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _