Method 
base_counter 
 
Classpackage  
G::Seq::Consensus; 
 
 
Function 
Analyzes bases around the start codon. 
 
Description 
To find consensus sequences around the start/end codon, this method 
counts bases.   
Beginning from the start/end codon position which is set to 0, its down/upstream is  
calculated. 
The results are stored and returned. 
 
Requirements 
modules   
SubOpt.pm 
 
applications 
none 
 
data 
none 
 
Parameters 
essential 
 
first     pointer   Genome      G's instance 
 
option 
string    position                  default=end 
int       pattern_length            default=3 
int       upstream_limit            default=30 
int       downstream_limit               default=30 
filename  string  file_name              default=consensus.csv  
output    string  [stdout or f]          default=stdout  
 
 
Returns 
first     variable    result     pointer of the hash 
Usage 
(hash result)=&base_counter(pointer Genome,  -position=>'end',  -PatLength=>3, -upstream=>30,  -downstream=>30,- output=>'stdout', filename=>'consensus.csv'); 
 
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 23 June   2001 - Koya Mori