Bio::CodonUsage IO
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Summary
Bio::CodonUsage::IO - for reading and writing codon usage tables to file
Package variables
No package variables defined.
Included modules
Bio::CodonUsage::Table
Inherit
Bio::Root::IO
Synopsis
  use Bio::CodonUsage::IO;
## read in a codon usage file my $io = Bio::CodonUsage::IO->new(-file => "in"); my $cut = $io->next_data(); ## write it out again my $out = Bio::CodonUsage::IO->new(-file => ">out"); $out->write_data($cut);
Description
This class provides standard IO methods for reading and writing text files
of codon usage tables. These tables can initially be retrieved using
Bio::DB::CUTG. At present only this format is supported for read/write.
Reading a CUTG will return a Bio::CodonUsage::Table object.
Methods
newDescriptionCode
next_dataDescriptionCode
write_dataDescriptionCode
_parse
No description
Code
Methods description
newcode    nextTop
 Title  : new
Usage : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile");
Purpose: To read/write a Bio:CodonUsage::Table object
Returns: A Bio:CodonUsage::IO object
Args : a file or file handle
next_datacodeprevnextTop
 Title  : next_data
Usage : my $cut = $io->next_data();
Purpose: To obtain a Bio:CodonUsage::Table object
Returns: A Bio:CodonUsage::Table object
Args : none
write_datacodeprevnextTop
 Title  : write_data
Usage : $io->write_data($cut);
Purpose: To write a CUT to file
Returns: void
Args : a Bio::CodonUsage::Table object reference
Methods code
newdescriptionprevnextTop
sub new {
	my ($class , @args) = @_;
	my $self = $class->SUPER::new(@args);
}
next_datadescriptionprevnextTop
sub next_data {
	my $self = shift;
	my $cut = $self->_parse;
	return $cut;
}
write_datadescriptionprevnextTop
sub write_data {
	my ($self, $cut) = @_;
	if (!$cut || ! $cut->isa(Bio::CodonUsage::Table)) {
		$self->throw("must supply a Bio::CodonUsage::Table object for writing\n");
			}
	my $outstring = "Codon usage table\n\n";

	my $sp_string = $cut->species . "[" . $cut->_gb_db . "]  " .
					$cut->cds_count . "  CDS's\n\n";
	$outstring .= $sp_string;
	my $colhead = sprintf("%-9s%-9s%15s%12s%12s\n\n", "AmAcid",
							 "Codon", "Number", "/1000", "Fraction");
	$outstring .= $colhead;

	### now write bulk of codon data  ##
my $ctable = Bio::Tools::CodonTable->new; for my $f (qw(G A T C)) { for my $s (qw(G A T C)) { for my $t (qw(G A T C)) { $cod = $f . $s . $t; my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)}; my $codstr = sprintf("%-9s%-9s%15.2f%12.2f%12.2f\n", $aa, $cod, my $tt = $cut->codon_count($cod)|| 0.00, my $ll =$cut->{'_table'}{$aa}{$cod}{'per1000'}|| 0.00, my $ss = $cut->codon_rel_frequency($cod) || 0.00); $outstring .= $codstr; } $outstring .= "\n"; } } $outstring .= "\n\n"; ## now append GC data
$outstring .= "Coding GC ". $cut->get_coding_gc('all'). "%\n"; $outstring .= "1st letter GC ". $cut->get_coding_gc(1). "%\n"; $outstring .= "2nd letter GC ". $cut->get_coding_gc(2). "%\n"; $outstring .= "3rd letter GC ". $cut->get_coding_gc(3). "%\n"; $outstring .= "Genetic code " . $cut->genetic_code() ."\n\n\n"; $self->_print ($outstring); $self->flush();
}
_parsedescriptionprevnextTop
sub _parse {
	my $self = shift;
	my $cdtableobj = Bio::CodonUsage::Table->new();
	while (my $line = $self->_readline() ) {
		next if $line =~ /^$/ ;
		$line =~ s/End/Ter/;
		## now parse in species name, cds number
if ($line =~ /^(.+?)\s*\[(\w+)\].+?(\d+)/) { $cdtableobj->species($1); $cdtableobj->{'_gb_db'} = $2; $cdtableobj->cds_count($3); } ## now parse in bulk of codon usage table
elsif ( $line =~ /^(\w\w\w)\s+(\w+)\s+(\d+\.\d+)
\s+(\d+\.\d+)\s+(\d+\.\d+)/x
){ if (defined ($1)) { $cdtableobj->{'_table'}{$1}{$2} = { 'abs_count'=>$3, 'per1000'=> $4, 'rel_freq'=> $5, }; } } ## now parse in gc data ####
if($line =~ /^Cod.+?(\d\d\.\d\d)/ ){ $cdtableobj->{'_coding_gc'}{'all'} = $1; } elsif ($line =~ /^1st.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'1'} = $1; } elsif($line =~ /^2nd.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'2'} = $1; } elsif ($line =~ /^3rd.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'3'} = $1; } elsif ($line =~ /^Gen.+?(\d+)/){ $cdtableobj->{'_genetic_code'} = $1; } } ## check has been parsed ok ##
if (scalar keys %{$cdtableobj->{'_table'}} != 21) { $cdtableobj->warn("probable parsing error - should be 21 entries for 20aa + stop codon"); } return $cdtableobj; } 1; __END__
}
General documentation
SEE ALSOTop
Bio::Tools::CodonTable,
Bio::WebAgent,
Bio::CodonUsage::Table,
Bio::CodonUsage::IO
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 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
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/
AUTHORSTop
Richard Adams, Richard.Adams@ed.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _