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Man Pages


Manual Reference Pages  -  BIO::TOOLS::GENEWISE (3)

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NAME

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

CONTENTS

SYNOPSIS



  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";
        }
      }
  }



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.

FEEDBACK

    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.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

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 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:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Fugu Team, Jason Stajich



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



APPENDIX

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

    new



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



See Bio::Tools::Genewise

    _get_strand



 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



    _score



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



    _prot_id



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



    _target_id



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



    next_prediction



 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

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