Provided by: libbio-perl-perl_1.6.923-1_all bug


       Bio::Tools::Geneid - Results of one geneid run


         use Bio::Tools::Geneid;
         my $gid = Bio::Tools::Geneid(-file => "geneid.out");

         while (my $gene = $gid->next_prediction)
           my @transcripts = $gene->transcripts;
             foreach my $t (@transcripts)
               my @exons = $t->exons;
               foreach my $e (@exons)
                 printf("Exon %d..%d\n", $e->start, $e->end);


       This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-
       UPF). See It relies on native geneid output format
       internally and will work with geneid versions 1.0 and 1.1. Currently this module supports
       only the default mode of operation which is to predict exons and assemble an optimal gene

       It takes either a file handle or a file name and returns a
       Bio::SeqFeature::Gene::GeneStructure object.


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AUTHOR - Keith James



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

        Title   : new
        Usage   : $obj->new(-file = "<geneid.out");
                  $obj->new(-fh => \*GI);
        Function: Constructor for geneid wrapper. Takes either a file
                : or filehandle
        Returns : L<Bio::Tools::Geneid>

        Title   : next_prediction
        Usage   : while($gene = $geneid->next_prediction)
                      # do something
        Function: Returns the gene structure prediction of the geneid result
                  file. Call this method repeatedly until FALSE is returned.
        Returns : A Bio::SeqFeature::Gene::GeneStructure object
        Args    : None

        Title   : _add_exon
        Usage   : $obj->_add_exon($gene, $transcript, ... exon data ...)
        Function: Adds a new exon to both gene and transcript from the data
                : supplied as args
        Example :
        Returns : Nothing

        Title   : _set_strand
        Usage   : $obj->_set_strand($gene)
        Function: Sets the overall gene strand to the same strand as all
                : the exons if they are all on the same strand, or to strand 0
                : if the exons are on different strands.
        Example :
        Returns : Nothing

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