Method 
view_cds 
 
Class 
G::Seq::GCskew; 
 
 
Function 
Creates a graph showing the average A, T, G, C contents around the  
 
start/stop codons.   
 
Description 
THis modthod creates a graph showing the average A, T, G, C contents  
 
around the start/stop codons. This is useful to view consensus around  
 
start/stop codons and to find characteristic patterns in CDS. 
Option -length sets the length in bases to show around start/stop  
 
codons.  -gap sets the gap shown inbetween start/stop codon neighbors in  
 
the output graphs.   Output filename can be set by option -filename,  
 
where the default is "view-cds.gif#" for graph, and "vied_cds.csv" for  
 
file.   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.  
 
Requirements 
modules   
SupOpt.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 
length       int       base_length             default=100 
gap          int       gap                     default= 3  
filename     string    filename                default="view_cds.gif" 
 
Returns 
first     array    gcskew   array of gcskew 
 
 
Usage 
array view_cds = &view_cds(pointer sequence, -length=>100,  
 
-filename=>'view_cds.gif', -gap=>3, -output=>'show'); 
 
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 06 Sept    2001 - Kazuharu Arakawa