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/
        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>