Method 
codon_usage 
 
Class 
G::Seq::Codon; 
 
 
Function 
Calculates the codon usage in one CDS 
 
Description 
This method refers to the number of codons and amino acids per CDS, and 
caluculates the codon usage.   
When the CDS is not specified, the codon usage of the entire genome is  
calculated.   
By using the option, a codon table can be ouputted in gif format. 
 
Requirements 
modules   
SubOpt.pm 
GD.pm 
G::Messenger 
 
applications 
none 
 
data 
none 
 
Parameters 
essential 
 
first     pointer   Genome       G's instance 
 
option 
CDSid     string  key               default=" " 
filename  string  file_name         default=codon_usage.csv 
output    string  [stdout or f]     default=show 
  
 
Returns 
first     variable   usage   The pointer of the hash 
 
Usage 
(pointer result)=&codon_counter(pointer Genome,  -CDSid=>" ", filename=>'codon.csv',output=>'show'); 
 
Input file  
none 
 
 
Output file  
csv file in text format 
 
References 
none  
 
Comments 
none 
 
Authors 
This method was written by Koya Mori(mory@g-language.org) at Institute for Advanced Biosciences Keio Univ.  
 
 
History 
Written 21 July   2001 - Koya Mori