[Biopython] Primer3Commandline rookie question

[Jukka-Pekka Verta]

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


On 2010-11-03, at 5:04 PM, Peter wrote:

> On Wed, Nov 3, 2010 at 8:30 PM, Jukka-Pekka Verta <jp.verta at gmail.com> wrote:
>> 
>> 
>> Thanks Brad,
>> calling
>> test()
>> results in error
>> 
>> Traceback (most recent call last):
>> ...
>> RuntimeError: Command eprimer3 -auto -outfile=output.pr3 -sequence=sequence
>> -hybridprobe=True -psizeopt=200 -oligosize=20 -explainflag=True returned
>> non-zero exit status 127
> 
> On Linux error 127 means the command was not found.
> 
>> as does calling
>> import subprocess
>> subprocess.check_call(str(test))
>> 
>> Traceback (most recent call last):
>> ...
>> OSError: [Errno 2] No such file or directory
>> Ummm.... ?
>> JP
> 
> Have you installed the EMBOSS command line tools? Are they on
> the system path? What happens at the command line if you type
> eprimer3 (or the longer version Biopython is trying to use)?
> 
> Peter