Method 
cum_gcskew 
 
Class 
G::Seq::GCskew; 
 
 
Function 
calculates the GC skew. 
 
Description 
 
This program calculates the cumulative GC skew.  
 
Option -window specifies window size to observe.  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 
modules   
SubOpt.pm 
Chart::Graph qw(gnuplot); 
 
applications 
GNUplot(http://www.cs.dartmouth.edu/gnuplot_info.html) 
 
data 
none 
 
Parameters 
essential 
 
first     pointer   sequence       ????? 
 
 
option 
window       int       window_size             default=10000 
at           boolean   [1 or 0]                default= 0  
output       string    ["f", "g", or "show"]   default="show" 
application  string    application             default="gimp" 
filename     string    filename                default="cum_gcskew.gif" 
 
Returns 
first     array    gcskew   array of gcskew 
 
 
Usage 
array cum_gcskew = &cum_gcskew(pointer sequence, -window=>10000, -at=>0,  
 
-output=>'show', -application=>'gimp', -filename=>'cum_gcskew.gif'); 
 
Input file  
none 
 
Output file  
csv file in text format 
graph in gif 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