Bio::Variation AAReverseMutate
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Summary
Bio::Variation::AAReverseMutate - point mutation and codon
information from single amino acid changes
Package variables
No package variables defined.
Included modules
Bio::Tools::CodonTable
Bio::Variation::Allele
Bio::Variation::RNAChange
Inherit
Bio::Root::Root
Synopsis
    $aamut = Bio::Variation::AAReverseMutate->new
(-aa_ori => 'F',
-aa_mut => 'S',
-codon_ori => 'ttc', # optional
-codon_table => '3' # 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, "\n"; } } else { print "No point mutations possible\n", }
Description
Bio::Variation::AAReverseMutate objects take in reference and mutated
amino acid information and deduces potential point mutations at RNA
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.
Methods
new
No description
Code
aa_oriDescriptionCode
aa_mutDescriptionCode
codon_oriDescriptionCode
codon_tableDescriptionCode
each_VariantDescriptionCode
Methods description
aa_oricode    nextTop
 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
aa_mutcodeprevnextTop
 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
codon_oricodeprevnextTop
 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 chracter content is not checked. Example : Returns : string Args : string
codon_tablecodeprevnextTop
 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
each_VariantcodeprevnextTop
 Title   : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants. Example : Returns : list of Variants Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($aa_ori, $aa_mut, $codon_ori, $codon_table) =
	$self->_rearrange([qw(AA_ORI
			      AA_MUT
			      CODON
			      CODON_TABLE
			      )],@args);

  $aa_ori && $self->aa_ori($aa_ori);
  $aa_mut  && $self->aa_mut($aa_mut);
  $codon_ori  && $self->codon_ori($codon_ori);
  $codon_table && $self->codon_table($codon_table);

  return $self; # success - we hope!
}
aa_oridescriptionprevnextTop
sub aa_ori {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) {
	    $self->throw("'$value' is not a valid one letter amino acid symbol\n");
	} else {
	    $self->{'aa_ori'} = uc $value;
	}
    }
    return $self->{'aa_ori'};
}
aa_mutdescriptionprevnextTop
sub aa_mut {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) {
	    $self->throw("'$value' is not a valid one letter amino acid symbol\n");
	} else {
	    $self->{'aa_mut'} = uc $value;
	}
    }
    return $self->{'aa_mut'};
}
codon_oridescriptionprevnextTop
sub codon_ori {
    my ($self,$value) = @_;
    if( defined $value) {
	if (length $value != 3 or lc $value =~ /[^atgc]/) {
	    $self->warn("Codon string\" $value\" is not valid unique codon");
	}
	$self->{'codon_ori'} = lc $value;
    }
    return $self->{'codon_ori'};
}
codon_tabledescriptionprevnextTop
sub codon_table {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d+$/ ) {
	    $self->throw("'$value' is not a valid codon table ID\n".
			"Has to be a positive integer. Defaulting to 1\n");
	} else {
	    $self->{'codon_table'} = $value;
	}
    }
    if( ! exists $self->{'codon_table'} ) {
	return 1;
    } else {
	return $self->{'codon_table'};
    }
}
each_VariantdescriptionprevnextTop
sub each_Variant {
   my ($self,@args) = @_;
   
   $self->throw("aa_ori is not defined\n") if not defined $self->aa_ori;
   $self->throw("aa_mut is not defined\n") if not defined $self->aa_mut;

   my (@points, $codon_pos, $allele_ori, $allele_mut);
   my $ct  = Bio::Tools::CodonTable->new( '-id' => $self->codon_table );
   foreach my $codon_ori ($ct->revtranslate($self->aa_ori)) {
       next if $self->codon_ori and $self->codon_ori ne $codon_ori;
       foreach my $codon_mut ($ct->revtranslate($self->aa_mut)) {
	   my $k = 0;
	   my $length = 0; 
	   $codon_pos = $allele_ori = $allele_mut = undef;
	   while ($k<3) {
	       my $nt_ori = substr ($codon_ori, $k, 1);
	       my $nt_mut = substr ($codon_mut, $k, 1);
	       if ($nt_ori ne $nt_mut) {
		   $length++;
		   $codon_pos = $k+1;
		   $allele_ori = $nt_ori;
		   $allele_mut = $nt_mut;
	       }
	       $k++;
	   }
	   if ($length == 1) {
	       my $rna = Bio::Variation::RNAChange->new 
		   ('-length'        => '1',     
		    '-codon_ori'     => $codon_ori,
		    '-codon_mut'     => $codon_mut,
		    '-codon_pos'     => $codon_pos,
		    '-isMutation'    => 1
		    );
	       my $all_ori = Bio::Variation::Allele->new('-seq'=>$allele_ori);
	       $rna->allele_ori($all_ori);
	       my $all_mut = Bio::Variation::Allele->new('-seq'=>$allele_mut);
	       $rna->allele_mut($all_mut);
	       push @points, $rna;
	   }
       }
   }
   return @points;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
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Support Top
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 BugsTop
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 LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _