[Biopython-dev] AlignAce help

[Peter]

xuncheng wang wrote:
> 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!

I've not used the module myself, but there are a few things I suggest
you check.

(1) Have you installed the standalone AlignAce program?

http://atlas.med.harvard.edu/

Note that they do warn that the Windows version is "out of date".

(2) Is the AlignACE program on the path?

i.e. If you type AlignACE at the command prompt, what happens?

The program might be called AlignACE.exe or AlignACE.com, but in any
case, just AlignACE should work.

(Note that linux is case sensitive, I'm not sure what the proper
capitalisation should be.  It doesn't matter on Windows)

If this fails (something like "command not found" or "'alignace' is not
recognized as an internal or external command, operable program or batch
file." etc depending on the version of windows) then...

(3) Try adding the program's directory to the path.

(4) In python, try modifying the cmd='AlignACE' to include a full path
to the program executable file.

Good luck

Peter