Bio.Align.substitution_matrices package

Module contents

Substitution matrices.

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.

static __new__(cls, alphabet=None, dims=None, data=None, dtype=<class 'float'>)

Create a new Array instance.

__array_finalize__(self, obj)

None.

__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)

transpose(self, axes=None)

Transpose the array.

property alphabet

Return the alphabet property.

copy(self)

Create and return a copy of the array.

get(self, key, value=None)

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

items(self)

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

keys(self)

Return a tuple with the keys associated with the array.

values(self)

Return a tuple with the values stored in the array.

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

Update the array from dict/iterable E and F.

__format__(self, fmt)

Default object formatter.

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

Bio.Align.substitution_matrices.read(handle, dtype=<class 'float'>)

Parse the file and return an Array object.

Bio.Align.substitution_matrices.load(name=None)

Load and return a precalculated substitution matrix.

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