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#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Keith James
#
# Copyright Genome Research Ltd.
#
# You may distribute this module under the same terms as Perl itself

# POD documentation - main docs before the code


=encoding utf-8

=head1 NAME

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

=head1 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);
        }
      }
  }

=head1 DESCRIPTION

This is the parser for the output of geneid by Enrique Blanco and
Roderic GuigE<243> (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.

=head1 FEEDBACK

=head2 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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 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

=head1 AUTHOR - Keith James

 Email: kdj@sanger.ac.uk

=head1 APPENDIX