Bio::Tools Genomewise
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Summary
Bio::Tools::Genomewise - Results of one Genomewise run
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Gene::Exon
Bio::SeqFeature::Gene::GeneStructure
Bio::SeqFeature::Gene::Transcript
Bio::SeqFeature::Generic
Bio::Tools::AnalysisResult
Inherit
Bio::Tools::Genewise
Synopsis
  use Bio::Tools::Genomewise;
my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out");
while (my $gene = $gw->next_prediction){ my @transcripts = $gene->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start." ".$e->end."\n"; } } }
Description
This is the parser for the output of Genewise. It takes either a file
handle or a file name and returns a
Bio::SeqFeature::Gene::GeneStructure object. You will need to specify
the proper target sequence id on the object with the
$feature->seq_id($seqid).
Methods
newDescriptionCode
next_predictionDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);
Function: Constructor for genomewise wrapper. Takes either a file or filehandle
Example :
Returns : Bio::Tools::Genomewise
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $genewise->next_prediction()) {
# do something
}
Function: Returns the gene structure prediction of the Genomewise result
file. Call this method repeatedly until FALSE is returned.
Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($self) = @_;

    my $genes;
    while ($_ = $self->_readline) {
	$self->debug( $_ );
	last if m{^//};

	if( /^Gene\s+\d+\s*$/ ) {
	    $genes = Bio::SeqFeature::Gene::GeneStructure->new
		(-source => $Srctag,
		 -seq_id => $self->_target_id, # if this had been specified
); $_ = $self->_readline; $self->debug( $_ ); unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) { $self->warn("Unparseable genomewise output"); last; } my $transcript = Bio::SeqFeature::Gene::Transcript->new (-source => $Srctag, -seq_id => $self->_target_id, # if this had been specified
-start => $1, -end => $2, ); my $nbr = 1; while( $_ = $self->_readline ) { $self->debug( $_ ); unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){
$self->_pushback($_);
last; } my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3); ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start, $e_end); $transcript->strand($e_strand) unless $transcript->strand != 0; my $exon = Bio::SeqFeature::Gene::Exon->new (-seq_id=>$self->_target_id, -source => $Srctag, -start=>$e_start, -end=>$e_end, -frame => $phase, -strand=>$e_strand); $exon->add_tag_value("Exon",$nbr++); $exon->add_tag_value('phase',$phase); $transcript->add_exon($exon); } $genes->add_transcript($transcript); last; # only process a single gene at a time
} } return $genes; } 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 - Fugu Team, Jason Stajich Top
 Email: fugui-at-worf.fugu-sg.org
jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_get_strandTop
 Title   : _get_strand
Usage : $obj->_get_strand
Function: takes start and end values, swap them if start>end and returns end
Example :
Returns :$start,$end,$strand
scoreTop
 Title   : score
Usage : $obj->score
Function: get/set for score info
Example :
Returns : a score value
_prot_idTop
 Title   : _prot_id
Usage : $obj->_prot_id
Function: get/set for protein id
Example :
Returns :a protein id
_target_idTop
 Title   : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id