[Biopython] Primer3Commandline rookie question

[Peter]

On Thu, Nov 4, 2010 at 4:55 PM, Jukka-Pekka Verta <jp.verta at gmail.com> wrote:
>
> Thanks Peter,
>
> indeed I hadn't. I'm a rookie as I mentioned....
>
> I installed EMBOSS tools (works from command line) and the primer3 program,
> set the path for primer3_core and I am able to run eprimer3 from the command
> line. When I tried to call my function test() from Python though, I got an error message
>
> RuntimeError: Command eprimer3 -auto -outfile=output.pr3 -sequence=sequence
> -hybridprobe=True -psizeopt=200 -oligosize=20 -explainflag=True returned non-zero
> exit status 1
>
> Thanks for your patient help!
>
> JP

Excellent - you are making progress.

That RuntimeError is Biopython saying that eprimer3 returned with an error.
Command line tools give an integer return code or error level -- zero means
success by convention.

What happens if you try this command at the command line prompt (outside
python), in the directory where your sequence file is:

eprimer3 -auto -outfile=output.pr3 -sequence=sequence
-hybridprobe=True -psizeopt=200 -oligosize=20 -explainflag=True

My guess is you are using a recent version of EMBOSS, in which case
you'll see this: Died: Unknown qualifier -oligosize=20

If so you should be using -osizeopt rather than -oligosize, which the
Biopython documentation does try to explain - I've made a small
clarification here:

https://github.com/biopython/biopython/commit/065e235ca76c6656a7f7d73de57c8bf8743ce25f

Peter