def aln_identity(aln1: AASeq, aln2: AASeq) -> float:
"""
:param aln1: alignment sequence (with gaps)
:param aln2: alignment sequence (with gaps)
:return: the identity calculated by: (# identities)/(aln1 length, no gaps)
>>> a = AASeq(aligned='-ABC-D')
>>> b = AASeq(aligned='-ABCED')
>>> aln_identity(a, b)
1.0
>>> b = AASeq(string='-BBCED')
>>> aln_identity(a, b)
0.75
"""
res = 0.
for i, aa in enumerate(aln1):
res += 1. if aln1.get_aligned()[i] == aln2.get_aligned()[i] != '-' else 0.
length = float(len(len(aln1)))
return res/length
def aln_identity(aln1: AASeq, aln2: AASeq) -> float:
"""
:param aln1: alignment sequence (with gaps)
:param aln2: alignment sequence (with gaps)
:return: the identity calculated by: (# identities)/(aln1 length, no gaps)
>>> a = AASeq(aligned='-ABC-D')
>>> b = AASeq(aligned='-ABCED')
>>> aln_identity(a, b)
1.0
>>> b = AASeq(string='-BBCED')
>>> aln_identity(a, b)
0.75
"""
res = 0.
for i, aa in enumerate(aln1):
res += 1. if aln1.get_aligned()[i] == aln2.get_aligned(
)[i] != '-' else 0.
length = float(len(len(aln1)))
return res / length
