[Biopython] slow pairwise2 alignment

[Ogan ABAAN]

Hello everyone

I am relatively new to Python/Biopython, but I am learning quickly. So 
you may see me sending questions your way every once in a while. Please 
be patient with me :)

I have a naive question regarding the use of pairwise2. I am trying to 
get alignment scores for two 22mer primer sequences over a few million 
short DNA sequences using pairwise2. To speed thing up I am using 
'score_only=1' argument. So I am averaginh about 5-6min per 500,000 
sequences. I also found online that the c module could speed things up 
further. so when I load cpairwise2 no error message is displayed 
suggesting that it has been loaded. However when I do 
cpairwise2.align.globalxx(seq1,seq2) I get the error message 
"AttributeError: 'module' object has no attribute 'align'". So does that 
mean cpairwise2 is not loaded. I would appreciate if someone can help me 
with this. If it matters I am using python 2.6.2, Bio module 1.50 on 
OSX.5.7.

Thank you

Ogan