NAME

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

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).

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-at-worf.fugu-sg.org
               jason-at-bioperl-dot-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 genomewise wrapper. Takes either a file or filehandle
        Example :
        Returns : L<Bio::Tools::Genomewise>

   _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
        Example :
        Returns : a score value

   _prot_id
        Title   : _prot_id
        Usage   : $obj->_prot_id
        Function: get/set for protein id
        Example :
        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 Genomewise result
                  file. Call this method repeatedly until FALSE is returned.

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