[Biopython] pairwise2 and cpairwise2

[Ivan Gregoretti]

Hello Peter,

I installed Biopython form biopython-1.61.tar.gz. No customisation, just

python setup.py build
python setup.py test
sudo python setup.py install

Is there a way to show that pairwise2 is not falling back to pure python?
Alignment feels a bit slow in my machine.

Thank you,

Ivan


Ivan Gregoretti, PhD
Bioinformatics





On Thu, May 23, 2013 at 9:44 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, May 23, 2013 at 2:36 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> One more about pairwise2:
>>
>> At the bottom of this page
>> http://biopython.org/DIST/docs/api/Bio.pairwise2-pysrc.html
>>
>> and in the Biopython tutorial, there are references to a C
>> implementation of pairwise2, called cpairwise2.
>>
>> How do you run that C implementation without falling back to pure python?
>>
>> Thank you,
>>
>> Ivan
>
> It should happen automatically, assuming you're not running
> under Jython or PyPy where the C code isn't used. How did
> you install Biopython?
>
> Peter