Bio::Variation::RNAChange(3pm)				User Contributed Perl Documentation			    Bio::Variation::RNAChange(3pm)

NAME

       Bio::Variation::RNAChange - Sequence change class for RNA level

SYNOPSIS

	  $rnachange = Bio::Variation::RNAChange->new
	      ('-start' 	=> $start,
	       '-end'		=> $end,
	       '-length'	=> $len,
	       '-codon_pos'	=> $cp,
	       '-upStreamSeq'	=> $upflank,
	       '-dnStreamSeq'	=> $dnflank,
	       '-proof' 	=> $proof,
	       '-isMutation'	=> 1,
	       '-mut_number'	=> $mut_number
	      );
	  $a1 = Bio::Variation::Allele->new;
	  $a1->seq('a');
	  $rnachange->allele_ori($a1);
	  my $a2 = Bio::Variation::Allele->new;
	  $a2->seq('t');
	  $rnachange->add_Allele($a2);
	  $rnachange->allele_mut($a2);

	  print "The codon change is ", $rnachange->codon_ori,
	      ">", $rnachange->codon_mut, "
";

	  # add it to a SeqDiff container object
	  $seqdiff->add_Variant($rnachange);

	  # and create links to and from DNA level mutation objects
	  $rnachange->DNAMutation($dnamut);
	  $dnamut->RNAChange($rnachange);

DESCRIPTION

       The instantiable class Bio::Variation::DNAMutation describes basic sequence changes at RNA molecule level. It uses methods defined in
       superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details.

       You are normally expected to create a corresponding Bio::Variation::DNAMutation object even if mutation is defined at RNA level. The
       numbering follows then cDNA numbering.  Link the DNAMutation object to the RNAChange object using the method DNAMutation(). If the
       variation described by a RNAChange object is translated, link the corresponding Bio::Variation::AAChange object to it using method
       AAChange(). See Bio::Variation::DNAMutation and Bio::Variation::AAChange for more information.

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 lists  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   codon_ori
	Title	: codon_ori
	Usage	: $obj->codon_ori();
	Function:

		   Sets and returns codon_ori triplet.	If value is not set,
		   creates the codon triplet from the codon position and
		   flanking sequences.	The string has to be three characters
		   long. The character content is not checked.

	Example :
	Returns : string
	Args	: string

   codon_mut
	Title	: codon_mut
	Usage	: $obj->codon_mut();
	Function:

		   Sets and returns codon_mut triplet.	If value is not
		   set, creates the codon triplet from the codon position and
		   flanking sequences. Return undef for other than point mutations.

	Example :
	Returns : string
	Args	: string

   codon_pos
	Title	: codon_pos
	Usage	: $obj->codon_pos();
	Function:

		   Sets and returns the position of the mutation start in the
		   codon. If value is not set, returns false.

	Example :
	Returns : 1,2,3
	Args	: none if get, the new value if set

   codon_table
	Title	: codon_table
	Usage	: $obj->codon_table();
	Function:

		   Sets and returns the codon table id of the RNA
		   If value is not set, returns 1, 'universal' code, as the default.

	Example :
	Returns : integer
	Args	: none if get, the new value if set

   DNAMutation
	Title	: DNAMutation
	Usage	: $mutobj = $obj->DNAMutation;
		: $mutobj = $obj->DNAMutation($objref);
	Function: Returns or sets the link-reference to a mutation/change object.
		  If there is no link, it will return undef
	Returns : an obj_ref or undef

   AAChange
	Title	: AAChange
	Usage	: $mutobj = $obj->AAChange;
		: $mutobj = $obj->AAChange($objref);
	Function: Returns or sets the link-reference to a mutation/change object.
		  If there is no link, it will return undef
	Returns : an obj_ref or undef

   exons_modified
	Title	: exons_modified
	Usage	: $modified = $obj->exons_modified;
		: $modified = $obj->exons_modified(1);
	Function: Returns or sets information (example: a simple boolean flag) about
		  the modification of exons as a result of a mutation.

   region
	Title	: region
	Usage	: $obj->region();
	Function:

		   Sets and returns the name of the sequence region type or
		   protein domain at this location.  If value is not set,
		   returns false.

	Example :
	Returns : string
	Args	: string

   cds_end
	Title	: cds_end
	Usage	: $cds_end = $obj->get_cds_end();
	Function:

		  Sets or returns the cds_end from the beginning of the DNA sequence
		  to the coordinate start used to describe variants.
		  Should be the location of the last nucleotide of the
		  terminator codon of the gene.

	Example :
	Returns : value of cds_end, a scalar
	Args	:

   label
	Title	: label
	Usage	: $obj->label();
	Function:

		   Sets and returns mutation event label(s).  If value is not
		   set, or no argument is given returns false.	Each
		   instantiable subclass of L<Bio::Variation::VariantI> needs
		   to implement this method. Valid values are listed in
		   'Mutation event controlled vocabulary' in
		   http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

	Example :
	Returns : string
	Args	: string

   _change_codon_pos
	Title	: _change_codon_pos
	Usage	: $newCodonPos = _change_codon_pos($myCodonPos, 5)
	Function:

		  Keeps track of the codon position in a changeing sequence

	Returns : codon_pos = integer 1, 2 or 3
	Args	: valid codon position
		  signed integer offset to a new location in sequence

perl v5.14.2							    2012-03-02					    Bio::Variation::RNAChange(3pm)