NAME

       Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output

SYNOPSIS

          use Bio::Tools::tRNAscanSE;

          my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE');

          # parse the results
          while( my $gene = $parser->next_prediction ) {

              @exon_arr = $gene->get_SeqFeatures();

          }

DESCRIPTION

       This script will parse tRNAscan-SE output.  Just the tabular output of the tRNA locations
       in the genome for now.

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::tRNAscanSE->new();
        Function: Builds a new Bio::Tools::tRNAscanSE object
        Returns : an instance of Bio::Tools::tRNAscanSE
        Args    : -fh/-file for input filename
                  -genetag => primary tag used in gene features (default 'tRNA_gene')
                  -exontag => primary tag used in exon features (default 'tRNA_exon')
                  -srctag  => source tag used in all features (default 'tRNAscan-SE')

   gene_tag
        Title   : gene_tag
        Usage   : $obj->gene_tag($newval)
        Function: Get/Set the value used for the 'gene_tag' of genes
                  Default is 'tRNA_gene' as set by the global $GeneTag
        Returns : value of gene_tag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   source_tag
        Title   : source_tag
        Usage   : $obj->source_tag($newval)
        Function: Get/Set the value used for the 'source_tag' of exons and genes
                  Default is 'tRNAscan-SE' as set by the global $SrcTag
        Returns : value of source_tag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   exon_tag
        Title   : exon_tag
        Usage   : $obj->exon_tag($newval)
        Function: Get/Set the value used for the 'primary_tag' of exons
                  Default is 'tRNA_exon' as set by the global $ExonTag
        Returns : value of exon_tag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   analysis_method
        Usage     : $genscan->analysis_method();
        Purpose   : Inherited method. Overridden to ensure that the name matches
                    /tRNAscan-SE/i.
        Returns   : String
        Argument  : n/a

   next_feature
        Title   : next_feature
        Usage   : while($gene = $genscan->next_feature()) {
                         # do something
                  }
        Function: Returns the next gene structure prediction of the Genscan result
                  file. Call this method repeatedly until FALSE is returned.

                  The returned object is actually a SeqFeatureI implementing object.
                  This method is required for classes implementing the
                  SeqAnalysisParserI interface, and is merely an alias for
                  next_prediction() at present.

        Example :
        Returns : A Bio::SeqFeature::Generic object.
        Args    :
       See also : L<Bio::SeqFeature::Generic>

   next_prediction
        Title   : next_prediction
        Usage   : while($gene = $genscan->next_prediction()) {
                         # do something
                  }
        Function: Returns the next gene structure prediction of the Genscan result
                  file. Call this method repeatedly until FALSE is returned.

        Example :
        Returns : A Bio::SeqFeature::Generic object.
        Args    :
       See also : L<Bio::SeqFeature::Generic>