Provided by: libbio-perl-perl_1.7.2-3_all bug

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, "\n";

          # 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://github.com/bioperl/bioperl-live/issues

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