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

       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>

perl v5.32.1                                       2021-08-15                        Bio::Tools::tRNAscanSE(3pm)

       Email jason-at-bioperl.org

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

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

          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();

          }