Raw content of Bio::Variation::AAReverseMutate
<![CDATA[# $Id: AAReverseMutate.pm,v 1.6 2002/10/22 07:38:49 lapp Exp $
#
# BioPerl module for Bio::Variation::AAReverseMutate
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Variation::AAReverseMutate - point mutation and codon
information from single amino acid changes
=head1 SYNOPSIS
$aamut = new Bio::Variation::AAReverseMutate
(-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",
}
=head1 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 L<Bio::Variation::RNAChange>
objects.
=head1 FEEDBACK
=head2 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://bio.perl.org/MailList.html - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Variation::AAReverseMutate;
my $VERSION=1.0;
use vars qw(@ISA);
use strict;
# Object preamble - inheritance
use Bio::Tools::CodonTable;
use Bio::Variation::RNAChange;
use Bio::Variation::Allele;
@ISA = qw( Bio::Root::Root);
sub new {
my($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!
}
=head2 aa_ori
Title : aa_ori
Usage : $obj->aa_ori();
Function:
Sets and returns original aa sequence. If value is not
set, returns false.
Amino acid sequences are stored in upper case characters,
others in lower case.
Example :
Returns : string
Args : single character amino acid code
=cut
sub aa_ori {
my ($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'};
}
=head2 aa_mut
Title : aa_mut
Usage : $obj->aa_mut();
Function:
Sets and returns the mutated allele sequence. If value is not
set, returns false.
Example :
Returns : string
Args : single character amino acid code
=cut
sub aa_mut {
my ($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'};
}
=head2 codon_ori
Title : codon_ori
Usage : $obj->codon_ori();
Function:
Sets and returns codon_ori triplet. If value is not set,
returns false. The string has to be three characters
long. The chracter content is not checked.
Example :
Returns : string
Args : string
=cut
sub codon_ori {
my ($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'};
}
=head2 codon_table
Title : codon_table
Usage : $obj->codon_table();
Function:
Sets and returns the codon table id of the RNA
If value is not set, returns 1, 'universal' code, as the default.
Example :
Returns : integer
Args : none if get, the new value if set
=cut
sub codon_table {
my ($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'};
}
}
=head2 each_Variant
Title : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants.
Example :
Returns : list of Variants
Args : none
=cut
sub each_Variant{
my ($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;
]]>