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

       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:

         http://bugzilla.open-bio.org/

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 = new Bio::Tools::tRNAscanSE();
        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>