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.\" ========================================================================
.\"
.IX Title "Bio::Variation::AAReverseMutate 3pm"
.TH Bio::Variation::AAReverseMutate 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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.SH "NAME"
Bio::Variation::AAReverseMutate \- point mutation and codon
  information from single amino acid changes
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    $aamut = Bio::Variation::AAReverseMutate\->new
\&                 (\-aa_ori => \*(AqF\*(Aq, 
\&                  \-aa_mut => \*(AqS\*(Aq,
\&                  \-codon_ori => \*(Aqttc\*(Aq, # optional
\&                  \-codon_table => \*(Aq3\*(Aq  # defaults to 1
\&                  );
\&
\&   @points = $aamut\->each_Variant;
\&
\&   if (scalar @points > 0 ) {
\&       foreach $rnachange ( @points ) {
\&           # $rnachange is a Bio::Variation::RNAChange object
\&           print " ", $rnachange\->allele_ori\->seq, ">", 
\&           $rnachange\->allele_mut\->seq, " in ",
\&           $rnachange\->codon_ori, ">", $rnachange\->codon_mut,
\&           " at position ", $rnachange\->codon_pos, "\en";
\&       }
\&   } else  {
\&       print "No point mutations possible\en",
\&   }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::Variation::AAReverseMutate objects take in reference and mutated
amino acid information and deduces potential point mutations at \s-1RNA\s0
level leading to this change. The choice can be further limited by
letting the object know what is the the codon in the reference
sequence. The results are returned as Bio::Variation::RNAChange
objects.
.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 "aa_ori"
.IX Subsection "aa_ori"
.Vb 3
\& Title   : aa_ori
\& Usage   : $obj\->aa_ori();
\& Function: 
\&
\&            Sets and returns original aa sequence.  If value is not
\&            set, returns false. 
\&
\&            Amino acid sequences are stored in upper case characters,
\&            others in lower case.
\&
\& Example : 
\& Returns : string
\& Args    : single character amino acid code
.Ve
.SS "aa_mut"
.IX Subsection "aa_mut"
.Vb 3
\& Title   : aa_mut
\& Usage   : $obj\->aa_mut();
\& Function: 
\&
\&            Sets and returns the mutated allele sequence.  If value is not
\&            set, returns false. 
\&
\& Example : 
\& Returns : string
\& Args    : single character amino acid code
.Ve
.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,
\&            returns false.  The string has to be three characters
\&            long. The character content is not checked.
\&
\& Example : 
\& Returns : string
\& Args    : string
.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 "each_Variant"
.IX Subsection "each_Variant"
.Vb 3
\& Title   : each_Variant
\& Usage   : $obj\->each_Variant();
\& Function: 
\&
\&            Returns a list of Variants.
\&
\& Example : 
\& Returns : list of Variants
\& Args    : none
.Ve