Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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


   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";


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).


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.                  - General discussion  - About the mailing lists


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



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 genomewise wrapper. Takes either a file or filehandle
  Example :
  Returns : L<Bio::Tools::Genomewise>


  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
  Example :
  Returns : a score value


  Title   : _prot_id
  Usage   : $obj->_prot_id
  Function: get/set for protein id 
  Example :
  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 Genomewise result
            file. Call this method repeatedly until FALSE is returned.
  Example :
  Returns : a Bio::SeqFeature::Gene::GeneStructure object
  Args    :