def __add__(self, other):
"""Combine two codonalignments with the same number of rows by adding them.
The method also allows to combine a CodonAlignment object with a
MultipleSeqAlignment object. The following rules apply:
* CodonAlignment + CodonAlignment -> CodonAlignment
* CodonAlignment + MultipleSeqAlignment -> MultipleSeqAlignment
"""
if isinstance(other, CodonAlignment):
if len(self) != len(other):
raise ValueError("When adding two alignments they must have the same length"
" (i.e. same number or rows)")
if compare_codon_alphabet(self._alphabet, other._alphabet):
alpha = self._alphabet
# merged = (left + right for left, right in zip(self, other))
merged = (SeqRecord(seq=CodonSeq(str(left.seq) + str(right.seq), alphabet=left.seq.alphabet)) for left, right in zip(self, other))
return CodonAlignment(merged, alphabet=alpha)
else:
raise TypeError("Only CodonAlignment with the same CodonAlphabet can be "
"combined.")
elif isinstance(other, MultipleSeqAlignment):
if len(self) != len(other):
raise ValueError("When adding two alignments they must have the same length"
" (i.e. same number or rows)")
return self.toMultipleSeqAlignment() + other
else:
raise TypeError("Only CodonAlignment or MultipleSeqAlignment object can be "
"added with a CodonAlignment object. "
"{} detected.".format(object(other)))
def __add__(self, other):
"""Combine two codonalignments with the same number of rows by adding them.
The method also allows to combine a CodonAlignment object with a
MultipleSeqAlignment object. The following rules apply:
* CodonAlignment + CodonAlignment -> CodonAlignment
* CodonAlignment + MultipleSeqAlignment -> MultipleSeqAlignment
"""
if isinstance(other, CodonAlignment):
if len(self) != len(other):
raise ValueError(
"When adding two alignments they must have the same length"
" (i.e. same number or rows)")
if compare_codon_alphabet(self._alphabet, other._alphabet):
alpha = self._alphabet
# merged = (left + right for left, right in zip(self, other))
merged = (SeqRecord(seq=CodonSeq(str(left.seq) +
str(right.seq),
alphabet=left.seq.alphabet))
for left, right in zip(self, other))
return CodonAlignment(merged, alphabet=alpha)
else:
raise TypeError(
"Only CodonAlignment with the same CodonAlphabet can be combined."
)
elif isinstance(other, MultipleSeqAlignment):
if len(self) != len(other):
raise ValueError(
"When adding two alignments they must have the same length"
" (i.e. same number or rows)")
return self.toMultipleSeqAlignment() + other
else:
raise TypeError(
"Only CodonAlignment or MultipleSeqAlignment object can be"
f" added with a CodonAlignment object. {object(other)} detected."
)