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__(obj, /)

Present so subclasses can call super. Does nothing.

__getitem__(key)

Return self[key].

__setitem__(key, value)

Set self[key] to value.

__contains__(key)

Return key in self.

__array_prepare__(array, [context, ]/)

Returns a view of array with the same type as self.

__array_wrap__(array, [context, ]/)

Returns a view of array with the same type as self.

__array_ufunc__(ufunc, method, *inputs, **kwargs)

__reduce__()

For pickling.

__setstate__(state, /)

For unpickling.

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

Parameters

versionint

optional pickle version. If omitted defaults to 0.

shapetuple

dtypedata-type

isFortranbool

rawdatastring or list

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

transpose(axes=None)

Transpose the array.

property alphabet

Return the alphabet property.

copy()

Create and return a copy of the array.

get(key, value=None)

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

items()

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

keys()

Return a tuple with the keys associated with the array.

values()

Return a tuple with the values stored in the array.

update(E=None, **F)

Update the array from dict/iterable E and F.

select(alphabet)

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

__format__(fmt)

Default object formatter.

format(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.

__str__()

Return str(self).

__repr__()

Return repr(self).

Bio.Align.substitution_matrices.read(handle, dtype=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()