NAME

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

SYNOPSIS

  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);
        }
      }
  }

DESCRIPTION

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.

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 - Keith James

 Email: kdj@sanger.ac.uk

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

next_prediction

 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

_add_exon

 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

_set_strand

 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

_target_id

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