def alignment_similarity(self, seq1, seq2, homopolymer_correction) :
# write out
f = open(System.tempfilename(ext='cluster'), 'w')
print >> f, seq1.fasta()
print >> f, seq2.fasta()
f.close()
# align
aligned = []
if homopolymer_correction :
fq = Pagan().get_454_alignment(f.name)
else :
fq = Pagan().get_alignment(f.name)
fq.open()
for seq in fq :
if seq.id == ">consensus" :
continue
aligned.append(seq.sequence)
fq.close()
# delete tmp files
os.remove(f.name)
os.remove(fq.get_filename())
# if things are really dissimilar they do not align
# so just give up here for this cluster
if len(aligned) != 2 :
return 0.0
return self.distance2(aligned, homopolymer_correction)
