Bio.Align.substitution_matrices package

Module contents

Substitution matrices.

class Bio.Align.substitution_matrices.Array(alphabet=None, dims=None, data=None, dtype=float)

Bases: numpy.ndarray

numpy array subclass indexed by integers and by letters.

static __new__(cls, alphabet=None, dims=None, data=None, dtype=float)

Create a new Array instance.

__array_finalize__(self, obj)


__getitem__(self, key)

Return self[key].

__setitem__(self, key, value)

Set self[key] to value.

__contains__(self, key)

Return key in self.

__array_prepare__(self, out_arr, context=None)
__array_wrap__(self, out_arr, context=None)
__array_ufunc__(self, ufunc, method, *inputs, **kwargs)

For pickling.

__setstate__(state, /)

For unpickling.

The state argument must be a sequence that contains the following elements:


optional pickle version. If omitted defaults to 0.

rawdatastring or list

a binary string with the data (or a list if ‘a’ is an object array)

transpose(self, axes=None)

Transpose the array.

property alphabet

Return the alphabet property.


Create and return a copy of the array.

get(self, key, value=None)

Return the value of the key if found; return value otherwise.


Return an iterator of (key, value) pairs in the array.


Return a tuple with the keys associated with the array.


Return a tuple with the values stored in the array.

update(self, E=None, **F)

Update the array from dict/iterable E and F.

select(self, alphabet)

Subset the array by selecting the letters from the specified alphabet.

__format__(self, fmt)

Default object formatter.

format(self, fmt='')

Return a string representation of the array.

The argument fmt specifies the number format to be used. By default, the number format is “%i” if the array contains integer numbers, and “%.1f” otherwise.


Return str(self).


Return repr(self)., dtype=float)

Parse the file and return an Array object.


Load and return a precalculated substitution matrix.

>>> from Bio.Align import substitution_matrices
>>> names = substitution_matrices.load()