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#cython: language_level=3
'''
Created on 17 mai 2010
@author: coissac
'''
from obitools3.libalign import columnIterator
def iterOnAligment(ali):
pos0=0
pos1=0
begin0=False
end0=False
begin1=False
end1=False
for nuc0,nuc1 in columnIterator(ali):
if nuc0==b"-":
if begin0:
if not end0:
score0 = ( ali[0].wrapped.quality_array[pos0-1]
+ali[0].wrapped.quality_array[pos0]
)/2
else:
score0 = 1.
else:
score0 = 0.
else:
begin0=True
score0 = ali[0].wrapped.quality_array[pos0]
pos0+=1
end0= pos0==len(ali[0].wrapped)
if nuc1==b"-":
if begin1:
if not end1:
score1 = ( ali[1].wrapped.quality_array[pos1-1]
+ali[1].wrapped.quality_array[pos1]
)/2
else:
score1 = 0.
else:
score1 = 1.
else:
begin1=True
score1 = ali[1].wrapped.quality_array[pos1]
pos1+=1
end1= pos1==len(ali[1].wrapped)
result = (nuc0,score0,nuc1,score1)
yield result
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