[Biopython-dev] AlignAce help

[bartek wilczynski]

Cytowanie xuncheng wang <wxuncheng at yahoo.com.cn>:

> Hello everyone,
>   T'm newer for Biopython.I run it in windows.I have no programming 
> experience.Now I use AlignAce module in Bio. My programming process is:
> >>> from Bio.AlignAce.AlignAceStandalone import AlignAce
> >>> from Bio.AlignAce.Parser import AlignAceParser
> >>> AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
>  
> the error is:
> 
> Traceback (most recent call last):
>   File "<pyshell#27>", line 1, in -toplevel-
>     AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
>   File 
> "D:\Python24\Lib\site-packages\Bio\AlignAce\AlignAceStandalone.py", line 63,
> in AlignAce
>     raise IOError, "Executable does not exist at %s" % cmd
> IOError: Executable does not exist at AlignACE
> 
>  
> 
> What can i do with this error. How can I programme this modules 
> exactly. thanks!
> 

In order to use AlignAce, you have to have AlignACE executable present in your
system. It seems that your script cannot find AlignACE executable. you can
download it from here: http://atlas.med.harvard.edu/download/index.html. 

If you have AlignACE in your system, then make sure that it is either in your
path or that you supply its location by using cmd parameter (like
cmd="/opt/AlignAce/AlignACE").


-- 
regards
   Bartek Wilczynski