#
# BioPerl module for Bio::CodonUsage::Table
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Richard Adams (richard.adams@ed.ac.uk)
#
# Copyright Richard Adams
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::CodonUsage::Table - for access to the Codon usage Database
at http://www.kazusa.or.jp/codon.
=head1 SYNOPSIS
use Bio::CodonUsage::Table;
use Bio::DB::CUTG;
use Bio::CodonUsage::IO;
use Bio::Tools::SeqStats;
# Get a codon usage table from web database
my $cdtable = Bio::DB::CUTG->new(-sp => 'Mus musculus',
-gc => 1);
# Or from local file
my $io = Bio::CodonUsage::IO->new(-file => "file");
my $cdtable = $io->next_data();
# Or create your own from a Bio::PrimarySeq compliant object,
# $codonstats is a ref to a hash of codon name /count key-value pairs
my $codonstats = Bio::Tools::SeqStats->count_codons($Seq_objct);
# '-data' must be specified, '-species' and 'genetic_code' are optional
my $CUT = Bio::CodonUsage::Table->new(-data => $codonstats,
-species => 'Hsapiens_kinase');
print "leu frequency is ", $cdtable->aa_frequency('LEU'), "\n";
print "freq of ATG is ", $cdtable->codon_rel_frequency('ttc'), "\n";
print "abs freq of ATG is ", $cdtable->codon_abs_frequency('ATG'), "\n";
print "number of ATG codons is ", $cdtable->codon_count('ATG'), "\n";
print "GC content at position 1 is ", $cdtable->get_coding_gc('1'), "\n";
print "total CDSs for Mus musculus is ", $cdtable->cds_count(), "\n";
=head1 DESCRIPTION
This class provides methods for accessing codon usage table data.
All of the methods at present are simple look-ups of the table or are
derived from simple calculations from the table. Future methods could
include measuring the codon usage of a sequence , for example, or
provide methods for examining codon usage in alignments.
=head1 SEE ALSO
L<Bio::Tools::CodonTable>,
L<Bio::WebAgent>,
L<Bio::CodonUsage::IO>,
L<Bio::DB::CUTG>
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::CodonUsage::Table;
use strict;
use vars qw(%STRICTAA @AA);
use Bio::SeqUtils;
use Bio::Tools::CodonTable;
use base qw(Bio::Root::Root);
BEGIN{
@AA = qw(A C D E F G H I K L M N P Q R S T V W Y *);
map {$STRICTAA{$_} = undef} @AA;
}
=head2 new
Title : new
Usage : my $cut = Bio::CodonUsage::Table->new(-data => $cut_hash_ref,
-species => 'H.sapiens_kinase'
-genetic_code =>1);
Returns : a reference to a new Bio::CodonUsage::Table object
Args : none or a reference to a hash of codon counts. This constructor is
designed to be compatible with the output of
Bio::Tools::SeqUtils::count_codons()
Species and genetic code parameters can be entered here or via the
species() and genetic_code() methods separately.
=cut
sub new {
my ($class, @args) = @_;
my $self= $class->SUPER::new(@args);
if (@args) {
$self->_rearrange([qw(DATA)], @args);
shift @args; # get rid of key
my $arg = shift @args;
$self->throw("need a hash reference, not a [" . ref($arg). "] reference") if ref($arg) ne 'HASH';
### flags to detect argument type, can be either to start with ##
my $is_codon_hash = 1;
my $is_Aa_hash = 1;
for my $k (keys %$arg) {
## convert to UC
$k =~ s/(\w+)/\U$1/;
if (!exists($STRICTAA{$k}) ){
$is_Aa_hash = 0;
}
elsif ($k =~ /[^ATCGatcg]/) {
$is_codon_hash = 0;
}
}
if (!$is_codon_hash && !$is_Aa_hash) {
$self->throw(" invalid key values in CUT hash - must be unique aa or nucleotide identifiers");
}
elsif ($is_Aa_hash) {
$self->_init_from_aa($arg);
}
elsif($is_codon_hash) {
$self->_init_from_cod($arg);
}
while (@args) {
my $key = shift @args;
$key =~ s/\-(\w+)/\L$1/;
$self->$key(shift @args);
}
}
return $self;
}
=head2 all_aa_frequencies
Title : all_aa_frequencies
Usage : my $freq = $cdtable->all_aa_frequencies();
Returns : a reference to a hash where each key is an amino acid
and each value is its frequency in all proteins in that
species.
Args : none
=cut
sub all_aa_frequencies {
my $self = shift;
my %aa_freqs =();
for my $aa (keys %STRICTAA) {
my $freq = $self->aa_frequency($aa);
$aa_freqs{$aa} = $freq;
}
return \%aa_freqs;
}
=head2 codon_abs_frequency
Title : codon_abs_frequency
Usage : my $freq = $cdtable->codon_abs_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
of all codons in the organism.
Returns : a percentage frequency
Args : a non-ambiguous codon string
=cut
sub codon_abs_frequency {
my ($self, $a) = @_;
my $cod = uc $a;
if ($self->_check_codon($cod)) {
my $ctable = Bio::Tools::CodonTable->new;
$ctable->id($self->genetic_code() );
my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)};
return $self->{'_table'}{$aa}{$cod}{'per1000'}/10 ;
}
else {return 0;}
}
=head2 codon_rel_frequency
Title : codon_rel_frequency
Usage : my $freq = $cdtable->codon_rel_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
of codons coding for the same amino acid. E.g., ATG and TGG
would return 100 as those codons are unique.
Returns : a percentage frequency
Args : a non-ambiguous codon string
=cut
sub codon_rel_frequency {
my ($self, $a) = @_;
my $cod = uc $a;
if ($self->_check_codon($cod)) {
my $ctable = Bio::Tools::CodonTable->new;
$ctable->id($self->genetic_code () );
my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)};
return $self->{'_table'}{$aa}{$cod}{'rel_freq'};
}
else {
return 0;
}
}
=head2 probable_codons
Title : probable_codons
Usage : my $prob_codons = $cd_table->probable_codons(10);
Purpose : to obtain a list of codons for the amino acid above a given
threshold % relative frequency
Returns : A reference to a hash where keys are 1 letter amino acid codes
and values are references to arrays of codons whose frequency
is above the threshold.
Arguments: a minimum threshold frequency
=cut
sub probable_codons {
my ($self, $threshold) = @_;
if (!$threshold || $threshold < 0 || $threshold > 100) {
$self->throw(" I need a threshold percentage ");
}
my %return_hash;
for my $a(keys %STRICTAA) {
my @common_codons;
my $aa =$Bio::SeqUtils::THREECODE{$a};
for my $codon (keys %{ $self->{'_table'}{$aa}}) {
if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $threshold/100){
push @common_codons, $codon;
}
}
$return_hash{$a} = \@common_codons;
}
## check to make sure that all codons are populated ##
if (grep{scalar @{$return_hash{$_}} == 0} keys %return_hash) {
$self->warn("Threshold is too high, some amino acids do not" .
" have any codon above the threshold!");
}
return \%return_hash;
}
=head2 most_common_codons
Title : most_common_codons
Usage : my $common_codons = $cd_table->most_common_codons();
Purpose : To obtain the most common codon for a given amino acid
Returns : A reference to a hash where keys are 1 letter amino acid codes
and the values are the single most common codons for those amino acids
Arguments: None
=cut
sub most_common_codons {
my $self = shift;
my %return_hash;
for my $a ( keys %STRICTAA ) {
my $common_codon = '';
my $rel_freq = 0;
my $aa = $Bio::SeqUtils::THREECODE{$a};
if ( ! defined $self->{'_table'}{$aa} ) {
$self->warn("Amino acid $aa ($a) does not have any codons!");
next;
}
for my $codon ( keys %{ $self->{'_table'}{$aa}} ) {
if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $rel_freq ){
$common_codon = $codon;
$rel_freq = $self->{'_table'}{$aa}{$codon}{'rel_freq'};
}
}
$return_hash{$a} = $common_codon;
}
return \%return_hash;
}
=head2 codon_count
Title : codon_count
Usage : my $count = $cdtable->codon_count('CTG');
Purpose : To obtain the absolute number of the codons in the
organism.
Returns : an integer
Args : a non-ambiguous codon string
=cut
sub codon_count {
my $self = shift;
if (@_) {
my $a = shift;
my $cod = uc $a;
if ($self->_check_codon($cod)) {
my $ctable = Bio::Tools::CodonTable->new;
$ctable->id($self->genetic_code());
my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)};
return $self->{'_table'}{$aa}{$cod}{'abs_count'};
}
else {return 0;}
}
else {
$self->warn(" need to give a codon sequence as a parameter ");
return 0;
}
}
=head2 get_coding_gc
Title : get_coding_gc
Usage : my $count = $cdtable->get_coding_gc(1);
Purpose : To return the percentage GC composition for the organism at
codon positions 1,2 or 3, or an average for all coding sequence
('all').
Returns : a number (%-age GC content) or 0 if these fields are undefined
Args : 1,2,3 or 'all'.
=cut
sub get_coding_gc {
my $self = shift;
if (! @_) {
$self->warn(" no parameters supplied must be a codon position (1,2,3) or 'all'");
return 0;
}
else{
my $n = shift;
##return request if valid ##
if ( exists($self->{'_coding_gc'}{$n} ) ) {
return sprintf("%.2f", $self->{'_coding_gc'}{$n});
}
##else return 'all' value if exists
elsif (exists($self->{'_coding_gc'}{'all'} )) {
$self->warn("coding gc doesn't have value for [$n], returning gc content for all CDSs");
return sprintf("%.2f", $self->{'_coding_gc'}{'all'});
}
### else return 0,
else {
$self->warn("coding gc values aren't defined, returning 0");
return 0;
}
}#end of outer else
}
=head2 set_coding_gc
Title : set_coding_gc
Usage : my $count = $cdtable->set_coding_gc(-1=>55.78);
Purpose : To set the percentage GC composition for the organism at
codon positions 1,2 or 3, or an average for all coding sequence
('all').
Returns : void
Args : a hash where the key must be 1,2,3 or 'all' and the value the %age GC
at that codon position..
=cut
sub set_coding_gc {
my ($self, $key, $value) = @_;
my @allowed = qw(1 2 3 all);
$key =~ s/\-//;
if (!grep {$key eq $_} @allowed ) {
$self->warn ("invalid key! - must be one of [ ". (join " ", @allowed) . "]");
return;
}
$self->{'_coding_gc'}{$key} = $value;
}
=head2 species
Title : species
Usage : my $sp = $cut->species();
Purpose : Get/setter for species name of codon table
Returns : Void or species name string
Args : None or species name string
=cut
sub species {
my $self = shift;
if (@_ ){
$self->{'_species'} = shift;
}
return $self->{'_species'} || "unknown";
}
=head2 genetic_code
Title : genetic_code
Usage : my $sp = $cut->genetic_code();
Purpose : Get/setter for genetic_code name of codon table
Returns : Void or genetic_code id, 1 by default
Args : None or genetic_code id, 1 by default if invalid argument.
=cut
sub genetic_code {
my $self = shift;
if (@_ ){
my $val = shift;
if ($val < 0 || $val >16 || $val =~ /[^\d]/
|| $val ==7 || $val ==8) {
$self->warn ("invalid genetic code - must be 1-16 but not 7 or 8,setting to default [1]");
$self->{'_genetic_code'} = 1;
}
else {
$self->{'_genetic_code'} = shift;
}
}
return $self->{'_genetic_code'} || 1;
}
=head2 cds_count
Title : cds_count
Usage : my $count = $cdtable->cds_count();
Purpose : To retrieve the total number of CDSs used to generate the Codon Table
for that organism.
Returns : an integer
Args : none (if retrieving the value) or an integer( if setting ).
=cut
sub cds_count {
my $self= shift;
if (@_) {
my $val = shift;
if ($val < 0) {
$self->warn("can't have negative count initializing to 1");
$self->{'_cds_count'} = 0.00;
}
else{
$self->{'_cds_count'} = $val;
}
}
$self->warn("cds_count value is undefined, returning 0")
if !exists($self->{'_cds_count'});
return $self->{'_cds_count'} || 0.00;
}
=head2 aa_frequency
Title : aa_frequency
Usage : my $freq = $cdtable->aa_frequency('Leu');
Purpose : To retrieve the frequency of an amino acid in the organism
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid
=cut
sub aa_frequency {
my ($self, $a) = @_;
## process args ##
## deal with cases ##
my $aa = lc $a;
$aa =~ s/^(\w)/\U$1/;
if (!exists($STRICTAA{$aa}) && !exists($Bio::SeqUtils::ONECODE{$aa}) ) {
$self->warn("Invalid amino acid! must be a unique 1 letter or 3 letter identifier");
return;
}
#translate to 3 letter code for Ctable #
my $aa3 = $Bio::SeqUtils::THREECODE{$aa} || $aa;
## return % of all amino acids in organism ##
my $freq = 0;
map {$freq += $self->{'_table'}{$aa3}{$_}{'per1000'} } keys %{$self->{'_table'}{$aa3}};
return sprintf("%.2f", $freq/10);
}
=head2 common_codon
Title : common_codon
Usage : my $freq = $cdtable->common_codon('Leu');
Purpose : To retrieve the frequency of the most common codon of that aa
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid
=cut
sub common_codon{
my ($self, $a) = @_;
my $aa = lc $a;
$aa =~ s/^(\w)/\U$1/;
if ($self->_check_aa($aa)) {
my $aa3 = $Bio::SeqUtils::THREECODE{$aa} ;
$aa3 ||= $aa;
my $max = 0;
for my $cod (keys %{$self->{'_table'}{$aa3}}) {
$max = ($self->{'_table'}{$aa3}{$cod}{'rel_freq'} > $max) ?
$self->{'_table'}{$aa3}{$cod}{'rel_freq'}:$max;
}
return $max;
}else {return 0;}
}
=head2 rare_codon
Title : rare_codon
Usage : my $freq = $cdtable->rare_codon('Leu');
Purpose : To retrieve the frequency of the least common codon of that aa
Returns : a percentage
Args : a 1 letter or 3 letter string representing the amino acid
=cut
sub rare_codon {
my ($self, $a) = @_;
my $aa = lc $a;
$aa =~ s/^(\w)/\U$1/;
if ($self->_check_aa($aa)) {
my $aa3 = $Bio::SeqUtils::THREECODE{$aa};
$aa3 ||= $aa;
my $min = 1;
for my $cod (keys %{$self->{'_table'}{$aa3}}) {
$min = ($self->{'_table'}{$aa3}{$cod}{'rel_freq'} < $min) ?
$self->{'_table'}{$aa3}{$cod}{'rel_freq'}:$min;
}
return $min;
}else {return 0;}
}
## internal sub that checks a codon is correct format
sub _check_aa {
my ($self, $aa ) = @_;
if (!exists($STRICTAA{$aa}) && !exists($Bio::SeqUtils::ONECODE{$aa}) ) {
$self->warn("Invalid amino acid! must be a unique 1 letter or 3 letter identifier");
return 0;
}else {return 1;}
}
sub _check_codon {
my ($self, $cod) = @_;
if ($cod =~ /[^ATCG]/ || $cod !~ /\w\w\w/) {
$self->warn(" impossible codon - must be 3 letters and just containing ATCG");
return 0;
}
else {return 1;}
}
sub _init_from_cod {
## make hash based on aa and then send to _init_from_aa
my ($self, $ref) = @_;
my $ct = Bio::Tools::CodonTable->new();
my %aa_hash;
for my $codon(keys %$ref ) {
my $aa = $ct->translate($codon);
$aa_hash{$aa}{$codon} = $ref->{$codon};
}
$self->_init_from_aa(\%aa_hash);
}
sub _init_from_aa {
my ($self, $ref) = @_;
## abs counts and count codons
my $total_codons = 0;
my %threeletter;
map{$threeletter{$Bio::SeqUtils::THREECODE{$_}} = $ref->{$_} } keys %$ref;
$ref = \%threeletter;
for my $aa (keys %$ref) {
for my $cod(keys %{$ref->{$aa}} ) {
$self->{'_table'}{$aa}{$cod}{'abs_count'} = $ref->{$aa}{$cod};
$total_codons += $ref->{$aa}{$cod};
}
}
## now calculate abs codon frequencies
for my $aa (keys %$ref) {
for my $cod(keys %{$ref->{$aa}} ) {
$self->{'_table'}{$aa}{$cod}{'per1000'} =
sprintf("%.2f",$ref->{$aa}{$cod} /$total_codons * 1000) ;
}
}
## now calculate rel codon_frequencies
for my $aa (keys %$ref) {
my $aa_freq = 0;
map{$aa_freq += $ref->{$aa}{$_} }
keys %{$ref->{$aa}};
for my $cod(keys %{$ref->{$aa}} ) {
$self->{'_table'}{$aa}{$cod}{'rel_freq'}=
sprintf("%.2f",$ref->{$aa}{$cod}/ $aa_freq );
}
}
## now calculate gc fields
my %GC;
for my $aa (keys %$ref) {
for my $cod(keys %{$ref->{$aa}} ) {
for my $index (qw(1 2 3) ) {
if (substr ($cod, $index -1, 1) =~ /g|c/oi) {
$GC{$index} += $ref->{$aa}{$cod};
}
}
}
}
my $tot = 0;
map{$tot += $GC{$_}} qw(1 2 3);
$self->set_coding_gc('all', $tot/(3 *$total_codons) * 100);
map{$self->set_coding_gc($_,$GC{$_}/$total_codons * 100)} qw(1 2 3);
##
return $self;
}
sub _gb_db {
my $self = shift;
return $self->{'_gd_db'} || "unknown";
}
1;