Bio.Align.substitution_matrices package¶
Module contents¶
Substitution matrices.
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class
Bio.Align.substitution_matrices.
Array
(alphabet=None, dims=None, data=None, dtype=<class 'float'>)¶ Bases:
numpy.ndarray
numpy array subclass indexed by integers and by letters.
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static
__new__
(cls, alphabet=None, dims=None, data=None, dtype=<class 'float'>)¶ Create a new Array instance.
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__array_finalize__
(self, obj)¶ None.
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__getitem__
(self, key)¶ Return self[key].
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__setitem__
(self, key, value)¶ Set self[key] to value.
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__contains__
(self, key)¶ Return key in self.
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__array_prepare__
(self, out_arr, context=None)¶
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__array_wrap__
(self, out_arr, context=None)¶
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__array_ufunc__
(self, ufunc, method, *inputs, **kwargs)¶
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transpose
(self, axes=None)¶ Transpose the array.
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property
alphabet
¶ Return the alphabet property.
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copy
(self)¶ Create and return a copy of the array.
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get
(self, key, value=None)¶ Return the value of the key if found; return value otherwise.
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items
(self)¶ Return an iterator of (key, value) pairs in the array.
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keys
(self)¶ Return a tuple with the keys associated with the array.
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values
(self)¶ Return a tuple with the values stored in the array.
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update
(self, E=None, **F)¶ Update the array from dict/iterable E and F.
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__format__
(self, fmt)¶ Default object formatter.
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__str__
(self)¶ Return str(self).
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__repr__
(self)¶ Return repr(self).
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static
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Bio.Align.substitution_matrices.
read
(handle, dtype=<class 'float'>)¶ Parse the file and return an Array object.
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Bio.Align.substitution_matrices.
load
(name=None)¶ Load and return a precalculated substitution matrix.
>>> from Bio.Align import substitution_matrices >>> names = substitution_matrices.load()