[Biopython] Primer3Commandline rookie question

[Jukka-Pekka Verta]

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?

JP



On 2010-11-03, at 3:13 PM, Peter wrote:

> On Wed, Nov 3, 2010 at 6:58 PM, Jukka-Pekka Verta <jp.verta at gmail.com> wrote:
>> Hi all,
>> 
>> I'm just starting with Python so mine's a rookie question.
>> 
>> I'm trying to write a little program that would do primer design with
>> Primer3Commandline, yet I can't figure out how to access the output.
>> For example, when I try the same example as in the Application.py
>> file under Primer3Commandline function
>> 
>> ######
>> 
>> from Bio.Emboss.Applications import Primer3Commandline
>> from Bio.Emboss import Primer3
>> 
>> sequence_handle = open("sequence", "w").write("...\n")
> 
> Here you've created a file called "sequence" (with no extension). I'd
> have gone for something like "sequence.fasta" but it doesn't mater.
> 
>> test = Primer3Commandline(sequence = sequence_handle, auto=True, hybridprobe=True)
> 
> Here you should be passing the filename, in your case "sequence".
> Maybe we should add a check here for people passing non-strings
> to arguments expecting filenames.
> 
> Does that help?
> 
> Peter
> 
> [Note It is possible to avoid the temporary file by writing to the tool's
> stdin but this is fiddly and requires you to work with the subprocess
> module directly.]