Bio.Align.substitution_matrices package
Module contents
Substitution matrices.
- class Bio.Align.substitution_matrices.Array(alphabet=None, dims=None, data=None, dtype=float)
Bases:
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__(out_arr, context=None)
- __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.
- 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()