oracular (3) Bio::Tools::Geneid.3pm.gz

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