base_entropy 
 
Classpackage  
G::Seq::Consensus; 
 
 
Function 
Calculates the entropy of base_counter 
 
 
Description 
By recieving the returned result of base_counter,  this method calculates 
the entropy near the start/end codon. 
 
Entropy is calculated per position from the start/end codon. 
Entropy is calculated by the following equation. 
entropy[H]=-¦²Pi*log2*Pi (Pi=expectation) 
 
 
Requirements 
modules   
SubOpt.pm 
 
applications 
none 
 
data 
none 
 
Parameters 
essential 
 
first     instance  G                  G_instance  
 
base_counter 
 
option 
output    string  [stdout/f/g/show]    default=show 
filename  string  file_name            default=consensus.csv  
PatLength int     pattern_length       default=3 
upstream  int     upstream             default=30 
downstream int    downstream           default=30 
position   string  position            default=end 
 
Returns 
first     variable     result     pointer of the array 
 
Usage 
(array result)=&base_entropy(hash base_counter_result, (output=>"show",filename=>"consensus.csv",PatLength=>3,upstream=>30,downstream=>30,position=>"end"); 
 
Input file  
csv file in text format.   
 
 
Output file  
none 
 
References 
none  
 
Comments 
none 
 
Authors 
This method was written by Koya Mori(mory@g-language.org) at Institute for  
 
Advanced Biosciences Keio Univ.  
 
 
History