__init__.py

Here’s a documentation for the target file cassiopeia/data/__init__.py:

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High-level description

This file serves as the top-level initialization for the cassiopeia.data module. It imports and exposes key classes and utility functions from the module, making them easily accessible to users of the Cassiopeia package.

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Symbols

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CassiopeiaTree

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Description

Imports the CassiopeiaTree class from the CassiopeiaTree module. This class is the core data structure in Cassiopeia, representing a phylogenetic tree with associated character matrices and metadata.

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Utility Functions

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Description

Imports several utility functions from the utilities module. These functions provide various operations and computations related to phylogenetic trees and character matrices.

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Imported Functions:

1. compute_dissimilarity_map: Computes pairwise dissimilarities between samples in a character matrix.
2. compute_inter_cluster_distances: Calculates mean distances between categories in a categorical variable.
3. compute_phylogenetic_weight_matrix: Computes distances or proximities between all leaves in a tree.
4. get_lca_characters: Builds the character vector of the lowest common ancestor (LCA) of a list of character vectors.
5. net_relatedness_index: Computes the net relatedness index between two groups of indices.
6. sample_bootstrap_allele_tables: Generates bootstrap character matrices from an allele table.
7. sample_bootstrap_character_matrices: Creates bootstrapped character matrices from a given character matrix.
8. to_newick: Converts a networkx graph to a Newick string representation.

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Dependencies

Note: This file acts as a convenient entry point for users of the Cassiopeia package, allowing them to import commonly used classes and functions directly from cassiopeia.data without needing to know the exact submodule structure.