[BioPython] os.system problem with clustalw

[Peter]

Emanuel Hey wrote:
> If I have clustalw.exe in the current directory then I
> should be able to execute just using
> 
>>>> os.sytem('clustalw ' + 'data.faa')
> 
> Indeed this works fine

Yes, and if you try this at the windows command prompt it also works:

clustalw data.faa

or:

clustalw.exe data.faa

> However if I give it the full path
>>>> os.system('clustalw ' +
> 'C:\temp\pythonplay\hcgplay\data.faa')

That should fail due to the way python uses slashes as escape 
characters, so \t means a tab for example.

> or
>>>> os.system('clustalw ' +
> 'C:\\temp\\pythonplay\\hcgplay\\data.faa')
> 
> then the clustalw run crashes and returns 
 > Error: unknown option
 > /-INFILE=C:\temp\pythonplay\hcgplay\data.faa

Its not crashing, its just returning with an error message.

You are not dealing with a Biopython or even a python problem here - you 
are simply (but understandably) having trouble with the clustalw command 
line options.

Notice that clustalw.exe will tolerate this:

clustalw.exe data.faa

as shorthand for:

clustalw.exe /infile=data.faa

However, for some reason it does not seem to work with full paths like this:

clustalw.exe C:\temp\pythonplay\hcgplay\data.faa

You have to be very explicit:

clustalw.exe /infile=C:\temp\pythonplay\hcgplay\data.faa

This may be a (windows only?) bug in clustalw. Its certainly not 
intuitive as is.

Peter

P.S. Did you not like using Bio.Clustalw to build the command line 
string for you?