[Biopython] pairwise2 and cpairwise2

[Ivan Gregoretti]

Thank you Peter, my system is indeed using the C version.

Ivan

Ivan Gregoretti, PhD
Bioinformatics



On Thu, May 23, 2013 at 10:42 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, May 23, 2013 at 3:33 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> 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
>
> If the C version not available,
>
> Jython 2.5.2 (Release_2_5_2:7206, Mar 2 2011, 23:12:06)
> [Java HotSpot(TM) 64-Bit Server VM (Apple Inc.)] on java1.6.0_45
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from Bio import pairwise2
>>>> from Bio import cpairwise2
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ImportError: cannot import name cpairwise2
>
> If the C version is installed, this should work:
>
> Python 2.7.2 (default, Oct 11 2012, 20:14:37)
> [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from Bio import pairwise2
>>>> from Bio import cpairwise2
>>>> pairwise2.rint is cpairwise2.rint
> True
>>>> pairwise2._make_score_matrix_fast is cpairwise2._make_score_matrix_fast
> True
>
> Peter