Source code for tskit.stats

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"""
Module responsible for computing various statistics on tree sequences.
"""
import sys
import threading

import numpy as np

import _tskit


[docs]class LdCalculator: """ Class for calculating `linkage disequilibrium <https://en.wikipedia.org/wiki/Linkage_disequilibrium>`_ coefficients between pairs of sites in a :class:`TreeSequence`. .. note:: This interface is deprecated and a replacement is planned. Please see https://github.com/tskit-dev/tskit/issues/1900 for more information. Note also that the current implementation is quite limited (see warning below). .. warning:: This class does not currently support sites that have more than one mutation. Using it on such a tree sequence will raise a LibraryError with an "Only infinite sites mutations supported" message. Silent mutations are also not supported and will result in a LibraryError. :param TreeSequence tree_sequence: The tree sequence of interest. """ def __init__(self, tree_sequence): self._tree_sequence = tree_sequence self._ll_ld_calculator = _tskit.LdCalculator( tree_sequence.get_ll_tree_sequence() ) # To protect low-level C code, only one method may execute on the # low-level objects at one time. self._instance_lock = threading.Lock() def get_r2(self, a, b): # Deprecated alias for r2(a, b) return self.r2(a, b)
[docs] def r2(self, a, b): """ Returns the value of the :math:`r^2` statistic between the pair of sites at the specified indexes. This method is *not* an efficient method for computing large numbers of pairwise LD values; please use either :meth:`.r2_array` or :meth:`.r2_matrix` for this purpose. :param int a: The index of the first site. :param int b: The index of the second site. :return: The value of :math:`r^2` between the sites at indexes ``a`` and ``b``. :rtype: float """ with self._instance_lock: return self._ll_ld_calculator.get_r2(a, b)
def get_r2_array(self, a, direction=1, max_mutations=None, max_distance=None): # Deprecated alias for r2_array return self.r2_array( a, direction=direction, max_mutations=max_mutations, max_distance=max_distance, )
[docs] def r2_array( self, a, direction=1, max_mutations=None, max_distance=None, max_sites=None ): """ Returns the value of the :math:`r^2` statistic between the focal site at index :math:`a` and a set of other sites. The method operates by starting at the focal site and iterating over adjacent sites (in either the forward or backwards direction) until either a maximum number of other sites have been considered (using the ``max_sites`` parameter), a maximum distance in sequence coordinates has been reached (using the ``max_distance`` parameter) or the start/end of the sequence has been reached. For every site :math:`b` considered, we then insert the value of :math:`r^2` between :math:`a` and :math:`b` at the corresponding index in an array, and return the entire array. If the returned array is :math:`x` and ``direction`` is :data:`tskit.FORWARD` then :math:`x[0]` is the value of the statistic for :math:`a` and :math:`a + 1`, :math:`x[1]` the value for :math:`a` and :math:`a + 2`, etc. Similarly, if ``direction`` is :data:`tskit.REVERSE` then :math:`x[0]` is the value of the statistic for :math:`a` and :math:`a - 1`, :math:`x[1]` the value for :math:`a` and :math:`a - 2`, etc. :param int a: The index of the focal sites. :param int direction: The direction in which to travel when examining other sites. Must be either :data:`tskit.FORWARD` or :data:`tskit.REVERSE`. Defaults to :data:`tskit.FORWARD`. :param int max_sites: The maximum number of sites to return :math:`r^2` values for. Defaults to as many sites as possible. :param int max_mutations: Deprecated synonym for max_sites. :param float max_distance: The maximum absolute distance between the focal sites and those for which :math:`r^2` values are returned. :return: An array of double precision floating point values representing the :math:`r^2` values for sites in the specified direction. :rtype: numpy.ndarray """ if max_mutations is not None and max_sites is not None: raise ValueError("max_mutations is a deprecated synonym for max_sites") if max_mutations is not None: max_sites = max_mutations max_sites = -1 if max_sites is None else max_sites if max_distance is None: max_distance = sys.float_info.max with self._instance_lock: return self._ll_ld_calculator.get_r2_array( a, direction=direction, max_sites=max_sites, max_distance=max_distance, )
def get_r2_matrix(self): # Deprecated alias for r2_matrix return self.r2_matrix()
[docs] def r2_matrix(self): """ Returns the complete :math:`m \\times m` matrix of pairwise :math:`r^2` values in a tree sequence with :math:`m` sites. :return: An 2 dimensional square array of double precision floating point values representing the :math:`r^2` values for all pairs of sites. :rtype: numpy.ndarray """ m = self._tree_sequence.num_sites A = np.ones((m, m), dtype=float) for j in range(m - 1): a = self.get_r2_array(j) A[j, j + 1 :] = a A[j + 1 :, j] = a return A