ASPL Manual v 1.00
© 2024 by SetSphere.COM

The following script shows how to align the DNA of a mutant. The script call ASPL GGs grouping function ggAlignDnaSeq() on two set variables to be aligned in the context of the element grouping class DNASEQUENCE. A mutant is creature whose DNA is altered (and archived within ASPL symbol table). The script can also align the DNA of two creatures, say for example man1 and man2 whose DNA are saved in set variable man1 and man2 respectively.


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 -L- Listing. 12.6.1   [LISTING mutant.aspl][ASPL Script mutant.aspl]

(raw text)

1.     #!/usr/bin/env aspl
2.     #ENVARG= -wsname DNASEQ1 -groupingclass DNASEQUENCE -nostrictld
3.     
4.     ;;***********************************************************************
5.     ;;   mutant.aspl
6.     ;;   Using workspace DNASEQ1 for DNA example 
7.     ;;   Copyright © 2024 Bassem W. Jamaleddine
8.     ;;   All rights reserved.
9.     ;;   
10.    ;;***********************************************************************
11.    
12.    endScriptIfShellArgsLessThan 3
13.    
14.    dm 3
15.    v sorted
16.    ggAlignDnaSeq(v1,$1,v2,$2,fragsize,$3)
17.    
18.    endscript
19.    
20.    __END__
21.    
22.     $00 must be followed by three arguments
23.    
24.        $00 var1 var2 fragmentsize
25.    
26.      where var1 and var2 are set variables that are saved in sample workspace 
      DNASEQ1, 
27.      and fragmentsize is the size to fragment the DNA to be aligned. 
28.    
29.      For example, to show alignment of DNA for man3 variable that is a mutant:
30.        $00  man3 man3@1 3
31.    
32.      to show alignment of DNA for man1 and man3, but neither one is a mutant of 
      the other: 
33.        $00  man1 man3 3
34.        $00  man1 man2 5
35.    

ASPL(C) 2024 Bassem Jamaleddine

This example is shown in the following terminal.

       display or terminal for Example: Script mutant.aspl

viewme

 -E- Display. 12.6.1   [Script mutant.aspl][Script mutant.aspl]

run for mutant-aspl-links