[Biopython] Primer3Commandline rookie question

[Jukka-Pekka Verta]

You're right, thats the case. Still, with -oligosize changed to -osizeopt Python returns me an error and running the eprimer3 on the command line gives me 

   EMBOSS An error in eprimer3.c at line 317:
eprimer3: Could not exec primer3_core
Segmentation fault

JP


On 2010-11-04, at 1:10 PM, Peter wrote:

> 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