[Biopython] Primer3Commandline rookie question

[Brad Chapman]

JP;

> Thanks Peter for the response.
> 
> Though doing
> 
> test = Primer3Commandline(sequence="sequence", auto=True, hybridprobe=True)
> 
> doesn't fix the problem (no output is created). Other suggestions?

In addition to what Peter mentioned, your code here creates a
commandline object, but never actually runs it:

> test = Primer3Commandline(sequence = sequence_handle, auto=True, hybridprobe=True)
> test.explainflag = True
> test.oligosize=20
> test.psizeopt=200
> test.outfile = "output.pr3"
> print test

This is probably why you weren't seeing any error messages from passing in
a file handle, and explains why there is no output file. You can
either call your command line directly:

test()

or use the Python subprocess module:

subprocess.check_call(str(test))

[As an aside, it's good practice to use meaningful variable names.
 At least a 'cl' for commandline would be nice here and may help
 you spot these types of issues.]

Hope this helps,
Brad