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.\" ========================================================================
.\"
.IX Title "Bio::Variation::RNAChange 3pm"
.TH Bio::Variation::RNAChange 3pm "2021-03-04" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Variation::RNAChange \- Sequence change class for RNA level
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&   $rnachange = Bio::Variation::RNAChange\->new
\&       (\*(Aq\-start\*(Aq         => $start,
\&        \*(Aq\-end\*(Aq           => $end,
\&        \*(Aq\-length\*(Aq        => $len,
\&        \*(Aq\-codon_pos\*(Aq     => $cp,
\&        \*(Aq\-upStreamSeq\*(Aq   => $upflank,
\&        \*(Aq\-dnStreamSeq\*(Aq   => $dnflank,
\&        \*(Aq\-proof\*(Aq         => $proof,
\&        \*(Aq\-isMutation\*(Aq    => 1,
\&        \*(Aq\-mut_number\*(Aq    => $mut_number
\&       );
\&   $a1 = Bio::Variation::Allele\->new;
\&   $a1\->seq(\*(Aqa\*(Aq);
\&   $rnachange\->allele_ori($a1);
\&   my $a2 = Bio::Variation::Allele\->new;
\&   $a2\->seq(\*(Aqt\*(Aq);
\&   $rnachange\->add_Allele($a2);
\&   $rnachange\->allele_mut($a2);
\&
\&   print "The codon change is ", $rnachange\->codon_ori,
\&       ">", $rnachange\->codon_mut, "\en";
\&
\&   # 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);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The instantiable class Bio::Variation::DNAMutation describes basic
sequence changes at \s-1RNA\s0 molecule level. It uses methods defined in
superclass Bio::Variation::VariantI. See Bio::Variation::VariantI
for details.
.PP
You are normally expected to create a corresponding
Bio::Variation::DNAMutation object even if mutation is defined at
\&\s-1RNA\s0 level. The numbering follows then cDNA numbering.  Link the
DNAMutation object to the RNAChange object using the method
\&\fBDNAMutation()\fR. If the variation described by a RNAChange object is
translated, link the corresponding Bio::Variation::AAChange object
to it using method \fBAAChange()\fR. See Bio::Variation::DNAMutation and
Bio::Variation::AAChange for more information.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "codon_ori"
.IX Subsection "codon_ori"
.Vb 3
\& 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
.Ve
.SS "codon_mut"
.IX Subsection "codon_mut"
.Vb 3
\& 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
.Ve
.SS "codon_pos"
.IX Subsection "codon_pos"
.Vb 3
\& 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
.Ve
.SS "codon_table"
.IX Subsection "codon_table"
.Vb 3
\& 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, \*(Aquniversal\*(Aq code, as the default.
\&
\& Example :
\& Returns : integer
\& Args    : none if get, the new value if set
.Ve
.SS "DNAMutation"
.IX Subsection "DNAMutation"
.Vb 6
\& 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
.Ve
.SS "AAChange"
.IX Subsection "AAChange"
.Vb 6
\& 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
.Ve
.SS "exons_modified"
.IX Subsection "exons_modified"
.Vb 5
\& 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.
.Ve
.SS "region"
.IX Subsection "region"
.Vb 3
\& 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
.Ve
.SS "cds_end"
.IX Subsection "cds_end"
.Vb 3
\& 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    :
.Ve
.SS "label"
.IX Subsection "label"
.Vb 3
\& 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
\&            \*(AqMutation event controlled vocabulary\*(Aq in
\&            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
\&
\& Example :
\& Returns : string
\& Args    : string
.Ve
.SS "_change_codon_pos"
.IX Subsection "_change_codon_pos"
.Vb 3
\& 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
.Ve