Bio::Tools::tRNAscanSE(3pm)				User Contributed Perl Documentation			       Bio::Tools::tRNAscanSE(3pm)

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://redmine.open-bio.org/projects/bioperl/

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>

perl v5.14.2							    2012-03-02					       Bio::Tools::tRNAscanSE(3pm)