Method 
genomicskew 
 
Class 
G::Seq::GCskew; 
 
 
Function 
Graphs the GC skew for the whole genome, coding regions, intergenic regions,  
 
and the third codon. 
 
Description 
 
This program graphs the GC skew for the whole genome, coding regions,   
 
intergenic regions, and the third codon.  
 
 Option -divide sets the window number to divide into.  By setting -at to 1,  
 
AT skew can be ovserved instead of the default GCskew cskew.csv>"(0).  There  
 
are three output forms; f for file output in directory "data", g for graph  
 
output in directory "graph", and "show for graph output and display.  The  
 
option -filename is set to "g" for "cum_gcskew.gif" and "f" for  
 
"cum_gcskew.csv".   Option -application sets the application to open the gif  
 
image.   
 
 
 
Requirements 
  applications   
SubOpt.pm 
Chart::Graph qw(gnuplot); 
 
applications 
GNUplot(http://www.cs.dartmouth.edu/gnuplot_info.html) 
 
data 
none 
 
Parameters 
essential 
 
first     pointer   G instance     G's instance 
 
 
option 
divide       int       divide                  default=25  
at           boolean   [1 or 0]                default=0 
output       string    ["f", "g", or "show"]   default="show" 
application  string    application             default="gimp" 
filename     string    filename                default="genomicskew.gif" 
 
Returns 
first        1         ??? 
 
 
Usage 
1 = &genomicskew(pointer G instance, divide=>25, at=>0, output=>'show',  
 
application=>'gimp',  filename=>'genomicskew.gif'); 
 
Input file  
none 
 
Output file  
graph in gif format. 
csv file in text format. 
 
References 
none  
 
Comments 
none 
 
Authors 
This method was written by Kazuharu Arakawa(gaou@g-language.org) at Institute  
 
for Advanced Biosciences Keio Univ.  
 
 
History 
Written 27 July   2001 - Kazuharu Arakawa 
Written 05 Sept    2001 - Kazuharu Arakawa