iid_exponential_mle_test.py

High-level description

This file contains unit tests for the IIDExponentialMLE class, which is a branch length estimator in the Cassiopeia package. The tests cover various scenarios, including degenerate cases (no mutations or saturation), hand-solvable problems, regression tests, and simulations.

Code Structure

The code consists of a single class TestIIDExponentialMLE which inherits from unittest.TestCase. This class contains multiple test methods, each testing a specific aspect of the IIDExponentialMLE class. The test methods are decorated with parameterized.expand to run the same test with different solvers (“ECOS” and “SCS”).

References

The tests reference the following classes:

• cassiopeia.data.CassiopeiaTree: Represents a phylogenetic tree with character states.
• cassiopeia.simulator.Cas9LineageTracingDataSimulator: Simulates Cas9-based lineage tracing data.
• cassiopeia.tools.IIDExponentialMLE: The branch length estimator being tested.

Symbols

TestIIDExponentialMLE

Description

This class contains unit tests for the IIDExponentialMLE class.

Inputs

None

Outputs

None

Internal Logic

The class defines several test methods, each testing a specific aspect of the IIDExponentialMLE class. The test methods use assertions to verify the expected behavior of the estimator.

Side Effects

The tests modify the CassiopeiaTree objects passed to the IIDExponentialMLE estimator.

Performance Considerations

None

---

test_no_mutations

Description

Tests the behavior of the estimator when there are no mutations in the character matrix.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a simple tree with two nodes and no mutations.
• Initializes an IIDExponentialMLE object.
• Asserts that a ValueError is raised when calling estimate_branch_lengths.

---

test_saturation

Description

Tests the behavior of the estimator when the character matrix is saturated (all characters are mutated).

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a simple tree with two nodes and a single mutated character.
• Initializes an IIDExponentialMLE object.
• Asserts that a ValueError is raised when calling estimate_branch_lengths.

---

test_hand_solvable_problem_1, test_hand_solvable_problem_2, test_hand_solvable_problem_3

Description

These tests verify the estimator’s results against hand-solvable problems with simple tree topologies and a small number of characters.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a simple tree with two nodes and a specified character matrix.
• Initializes an IIDExponentialMLE object.
• Calls estimate_branch_lengths and asserts that the estimated branch lengths, mutation rate, and log-likelihood match the expected values calculated by hand.

---

test_small_tree_with_one_mutation

Description

Tests the estimator on a small perfect binary tree with a single mutation.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a perfect binary tree with one mutation at a specific node.
• Initializes an IIDExponentialMLE object.
• Calls estimate_branch_lengths and asserts that the estimated branch lengths, mutation rate, and log-likelihood match the expected values calculated by hand.

---

test_small_tree_regression

Description

This is a regression test on a small perfect binary tree with a “normal” amount of mutations.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a perfect binary tree with a predefined character matrix.
• Initializes an IIDExponentialMLE object.
• Calls estimate_branch_lengths and asserts that the estimated branch lengths, mutation rate, and log-likelihood match the expected values from a previous run.

---

test_on_simulated_data

Description

Tests the estimator on data simulated using the Cas9LineageTracingDataSimulator.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a perfect binary tree and sets predefined node times.
• Simulates Cas9-based lineage tracing data using the Cas9LineageTracingDataSimulator.
• Initializes an IIDExponentialMLE object.
• Calls estimate_branch_lengths and asserts that the estimated node times and mutation rate are close to the ground truth values used for simulation.

---

test_subtree_collapses_when_no_mutations

Description

Tests the behavior of the estimator when a subtree has no mutations, ensuring it collapses to 0 length.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a tree with a subtree containing no mutations.
• Initializes an IIDExponentialMLE object.
• Calls estimate_branch_lengths and asserts that the branch lengths of the mutationless subtree are 0 and the remaining branch lengths, mutation rate, and log-likelihood match the expected values.

---

test_minimum_branch_length

Description

Tests the functionality of the minimum_branch_length parameter.

Inputs

Name	Type	Description
name	str	Name of the test case
solver	str	Solver to use (“ECOS” or “SCS”)

Outputs

None

Internal Logic

• Creates a perfect binary tree with a single mutation.
• Initializes an IIDExponentialMLE object with a specified minimum_branch_length.
• Calls estimate_branch_lengths and asserts that the estimated branch lengths, mutation rate, and log-likelihood match the expected values, taking into account the minimum branch length constraint.

---

test_hand_solvable_problem_with_site_rates, test_larger_hand_solvable_problem_with_site_rates

Description

These tests verify the estimator’s results against hand-solvable problems with specified site-specific mutation rates.

Inputs

Name	Type	Description
name	str	Name of the test case
solver_rates	List[float]	Site-specific mutation rates used by the solver
math_rates	List[float]	Site-specific mutation rates used for hand calculations

Outputs

None

Internal Logic

• Creates a tree with a specified character matrix.
• Initializes an IIDExponentialMLE object with the relative_mutation_rates parameter set to solver_rates.
• Calls estimate_branch_lengths and asserts that the estimated branch lengths, node times, and mutation rates match the expected values calculated by hand using math_rates.

---

test_invalid_site_rates

Description

Tests the behavior of the estimator when invalid site-specific mutation rates are provided.

Inputs

Name	Type	Description
name	str	Name of the test case
rates	List[float]	Invalid site-specific mutation rates

Outputs

None

Internal Logic

• Creates a tree with a specified character matrix.
• Initializes an IIDExponentialMLE object with the relative_mutation_rates parameter set to rates.
• Asserts that a ValueError is raised when calling estimate_branch_lengths.

Dependencies

• networkx: For working with graph structures.
• numpy: For numerical operations.
• parameterized: For parameterized testing.
• cvxpy: For convex optimization.

Error Handling

The tests check for ValueError and IIDExponentialMLEError exceptions in various scenarios.

API/Interface Reference

None