simple_fit_subclone_simulator_test.py

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High-level description

This file contains unit tests for the SimpleFitSubcloneSimulator class, which simulates a clonal population that develops one fit subclone. The tests verify the correctness of the simulated phylogenetic tree structure and branch lengths in both deterministic and stochastic scenarios.

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Symbols

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TestSimpleFitSubcloneSimulator

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Description

A unittest.TestCase subclass that contains test methods for the SimpleFitSubcloneSimulator class.

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test_deterministic

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Description

Tests the SimpleFitSubcloneSimulator with deterministic branch lengths to ensure the generated phylogeny is correct.

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Internal Logic

1. Creates a SimpleFitSubcloneSimulator instance with specific parameters.
2. Simulates a tree using the simulator.
3. Asserts that the generated tree has the expected structure:
   • Correct node names
   • Correct edge connections
   • Correct node times

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test_stochastic

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Description

Tests the SimpleFitSubcloneSimulator with stochastic branch lengths to ensure non-deterministic behavior.

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Internal Logic

1. Sets a random seed for reproducibility.
2. Defines two functions for generating random branch lengths:
   • branch_length_neutral: Returns an exponentially distributed value with mean 1.0
   • branch_length_fit: Returns an exponentially distributed value with mean 0.5
3. Creates a SimpleFitSubcloneSimulator instance with the random branch length functions.
4. Simulates a tree using the simulator.
5. Extracts branch lengths for non-leaf nodes.
6. Asserts that all branch lengths are distinct, confirming non-determinism.

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Dependencies

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Notes

• The tests cover both deterministic and stochastic scenarios, ensuring the simulator works correctly in different conditions.
• The stochastic test uses a fixed random seed to ensure reproducibility while still testing random behavior.
• The tests focus on verifying the tree structure, node naming, and branch length generation, which are key aspects of the SimpleFitSubcloneSimulator’s functionality.