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Christopher Fields
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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 Guigó (IMIM-UPF). See http://www1.imim.es/software/geneid. 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 prediction.

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


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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.

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AUTHOR - Keith James

 Email: kdj@sanger.ac.uk


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