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10 non-PAUSE users.

Christopher Fields
and 1 contributors


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


  use Bio::Tools::Genewise;
  my $gw = Bio::Tools::Genewise(-file=>"genewise.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";


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.


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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.

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


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:


AUTHOR - Fugu Team, Jason Stajich

 Email: fugui@worf.fugu-sg.org
 Email: jason-at-bioperl.org


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


 Title   : new
 Usage   : $obj->new(-file=>"genewise.out");
 Function: Constructor for genewise wrapper. Takes either a file or filehandle
 Example :
 Returns : Bio::Tools::Genewise object

See Bio::Tools::Genewise


 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


 Title   : _score
 Usage   : $obj->_score
 Function: get/set for score info
 Returns : a score value


 Title   : _prot_id
 Usage   : $obj->_prot_id
 Function: get/set for protein id 
 Returns :a protein id


 Title   : _target_id
 Usage   : $obj->_target_id
 Function: get/set for genomic sequence id
 Example :
 Returns :a target id


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

 Example :
 Returns : a Bio::SeqFeature::Gene::GeneStructure object
 Args    :

See Bio::SeqFeature::Gene::GeneStructure