[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