Hello Erez,
On Apr 17, 2007, at 3:56PM , Erez Lieberman wrote:
> Hey All -
>
> I'd really love to get some insight into this, I'm just totally
> puzzled!
>
> I'm trying to make system calls to clustalw, a sequence aligner
> which takes arguments like filenames. The main point is just that I
> need to make a system call, and I need to have a blank space before
> the arguments begin.
>
> So what I do is:
>
> import os
> os.system('Z:\Data\ClustalW\clustalw Z:\Data\Output\junk.fasta')'
>
> and this works just fine and clustalw runs and everything is fine.
>
> Now the trouble is that when I do
>
> import rpy
> import os
> os.system('Z:\Data\ClustalW\clustalw Z:\Data\Output\junk.fasta')'
>
> Then clustalw executes and immediate fails, saying "Error: unknown
> option /Z:\Data\Output\junk.fasta" First, that's not the error
> clustalw gives for a missing file, but the one for an incorrect
> keyword. Second, it actually shows you the slash in the error
> message. Basically, I've concluded that it's somehow adding a slash
> after the blank space.
>
Hmm. This certainly seems to be odd behavior.
> I tried many workarounds,
>
> a) importing less or more of rpy
> b) writing a script which writes a batch file with my system call
> and then runs the batch file (so the Python system call has no spaces)
> c) calling r.system() from python and seeing if I can run the
> system call through r.
>
> Nothing works at all, every method seems to fail identically. When
> I put the system() command in R directly (though I have to add
> slashes to ensure the path is formatted correctly) it works but
> then same string doesn't work with r.system, e.g..
>
> system('Z:\\Data\\ClustalW\\clustalw /Z:\\Data\\Output\\junk.fasta')
>
> works when put directly into R, but
>
Um, you did notice the slash in there?
> r.system('Z:\\Data\\ClustalW\\clustalw /Z:\\Data\\Output\\junk.fasta')
>
Hmm, you have a slash before the string here, too...
Can you send an actual RPy transcript?
-G
> fails, with the same unknown option error, when put into Python.
>
> I have no idea what to do. I'm totally mystified.
>
> Anyone has any ideas as to what is going on here? I would be
> greatly appreciative.
>
> Thanks so much!
>
> -Erez
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