Struct lightmotif_py::CountMatrix

pub struct CountMatrix { /* private fields */ }

A matrix storing the count of a motif letters at each position.

Implementations

impl CountMatrix

pub fn __init__<'py>( alphabet: Bound<'py, PyString>, values: Bound<'py, PyDict>, ) -> PyResult<PyClassInitializer<Self>>

Create a new count matrix.

pub fn __eq__<'py>(&self, object: Bound<'py, PyAny>) -> PyResult<bool>

pub fn __len__(&self) -> usize

pub fn __getitem__<'py>( slf: PyRef<'py, Self>, index: isize, ) -> PyResult<PyObject>

pub fn normalize(&self, pseudocount: Option<PyObject>) -> PyResult<WeightMatrix>

Normalize this count matrix to obtain a position weight matrix.

This method converts the count matrix to a weight matrix. Each row from the matrix is normalized so that they sum to 1.0. Each element is then divided by a uniform background probability to obtain odds-ratio at every position of the motif. Pseudocounts can be given to prevent zero elements, which may translate into -∞ scores in the final position-specific scoring matrix.

Arguments: pseudocount (float, dict or None): The pseudocounts to apply before normalizing the count matrix. If a float is given, then a similar pseudocount is applied to every column of the matrix (excluding the default symbol). Otherwise, a dict may be given to map each symbol of the alphabet to a distinct pseudocount. If None given, no pseudocount is used.

Trait Implementations

impl Clone for CountMatrix

fn clone(&self) -> CountMatrix

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for CountMatrix

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl From<CountMatrix<Dna>> for CountMatrix

fn from(data: CountMatrix<Dna>) -> Self

Converts to this type from the input type.

impl IntoPy<Py<PyAny>> for CountMatrix

fn into_py(self, py: Python<'_>) -> PyObject

Performs the conversion.

impl PyClass for CountMatrix

type Frozen = False

Whether the pyclass is frozen.

impl PyClassImpl for CountMatrix

const IS_BASETYPE: bool = false

#[pyclass(subclass)]

const IS_SUBCLASS: bool = false

#[pyclass(extends=…)]

const IS_MAPPING: bool = false

#[pyclass(mapping)]

const IS_SEQUENCE: bool = true

#[pyclass(sequence)]

type BaseType = PyAny

Base class

type ThreadChecker = SendablePyClass<CountMatrix>

This handles following two situations:

type PyClassMutability = <<PyAny as PyClassBaseType>::PyClassMutability as PyClassMutability>::MutableChild

Immutable or mutable

type Dict = PyClassDummySlot

Specify this class has #[pyclass(dict)] or not.

type WeakRef = PyClassDummySlot

Specify this class has #[pyclass(weakref)] or not.

type BaseNativeType = PyAny

The closest native ancestor. This is PyAny by default, and when you declare #[pyclass(extends=PyDict)], it’s PyDict.

fn items_iter() -> PyClassItemsIter

fn doc(py: Python<'_>) -> PyResult<&'static CStr>

Rendered class doc

fn lazy_type_object() -> &'static LazyTypeObject<Self>

fn dict_offset() -> Option<isize>

fn weaklist_offset() -> Option<isize>

impl PyClassNewTextSignature<CountMatrix> for PyClassImplCollector<CountMatrix>

fn new_text_signature(self) -> Option<&'static str>

impl PyClass__eq__SlotFragment<CountMatrix> for PyClassImplCollector<CountMatrix>

unsafe fn __eq__( self, py: Python<'_>, _raw_slf: *mut PyObject, arg0: *mut PyObject, ) -> PyResult<*mut PyObject>

Safety: _slf and _other must be valid non-null Python objects

impl<'a, 'py> PyFunctionArgument<'a, 'py> for &'a CountMatrix

type Holder = Option<PyRef<'py, CountMatrix>>

fn extract( obj: &'a Bound<'py, PyAny>, holder: &'a mut Self::Holder, ) -> PyResult<Self>

impl<'a, 'py> PyFunctionArgument<'a, 'py> for &'a mut CountMatrix

type Holder = Option<PyRefMut<'py, CountMatrix>>

fn extract( obj: &'a Bound<'py, PyAny>, holder: &'a mut Self::Holder, ) -> PyResult<Self>

impl PyMethods<CountMatrix> for PyClassImplCollector<CountMatrix>

fn py_methods(self) -> &'static PyClassItems

impl PyTypeInfo for CountMatrix

const NAME: &'static str = "CountMatrix"

Class name.

const MODULE: Option<&'static str> = _

Module name, if any.

fn type_object_raw(py: Python<'_>) -> *mut PyTypeObject

Returns the PyTypeObject instance for this type.

fn type_object_bound(py: Python<'_>) -> Bound<'_, PyType>

Returns the safe abstraction over the type object.

fn is_type_of_bound(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type or a subclass of this type.

fn is_exact_type_of_bound(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type.

impl DerefToPyAny for CountMatrix