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.
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
r.system('Z:\\Data\\ClustalW\\clustalw /Z:\\Data\\Output\\junk.fasta')
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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