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Bio::Tools::tRNAscanSEUser Contributed Perl DocumentaBio::Tools::tRNAscanSE(3)

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>

perl v5.32.1			  2019-12-07	     Bio::Tools::tRNAscanSE(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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