sequential_lineage_tracing_simulator_test.py
High-level description
This file contains unit tests for the SequentialLineageTracingDataSimulator class in the Cassiopeia library. It tests various aspects of the simulator, including basic setup, error handling, data overlay functionality, and specific scenarios like handling missing data and multiple edits on a branch.
Code Structure
The code defines a test class TestSequentialLineageTracingDataSimulator that inherits from unittest.TestCase. It contains several test methods, each focusing on a specific aspect of the simulator’s functionality. The setUp method initializes common objects used across multiple tests.
Symbols
TestSequentialLineageTracingDataSimulator
Description
This class contains unit tests for the SequentialLineageTracingDataSimulator class.
Internal Logic
- Sets up a basic tree structure and simulator instances in the
setUpmethod. - Tests basic setup, error handling, and data overlay functionality.
- Verifies the simulator’s behavior with and without missing data.
- Checks for correct handling of multiple edits on a branch.
setUp
Description
Initializes the test environment by creating a basic tree structure and two simulator instances.
Internal Logic
- Creates a directed graph representing a tree topology.
- Sets up a
CassiopeiaTreewith the topology and node times. - Initializes two
SequentialLineageTracingDataSimulatorinstances, one without missing data and one with missing data.
test_basic_setup
Description
Tests the basic setup of the simulator, verifying that the initialization parameters are correctly set.
Internal Logic
Checks various attributes of the simulator, such as the number of characters, silencing rates, state priors, and initiation/continuation rates.
test_setup_errors
Description
Tests error handling for invalid initialization parameters of the simulator.
Internal Logic
Attempts to create simulator instances with invalid parameters and checks that the appropriate DataSimulatorError is raised.
test_simulator_basic
Description
Tests the basic functionality of the simulator by overlaying data on the tree and verifying the results.
Internal Logic
- Overlays data on the basic tree.
- Compares the resulting character matrix with an expected matrix.
- Checks inheritance patterns in the tree after reconstructing ancestral characters.
test_simulator_with_missing
Description
Tests the simulator’s behavior when dealing with missing data (i.e., when heritable and stochastic silencing rates are non-zero).
Internal Logic
Overlays data on the basic tree using the simulator with missing data and compares the resulting character matrix with an expected matrix containing missing values (-1).
test_branch_multiple_edits
Description
Tests the simulator’s ability to handle multiple edits on a single branch.
Internal Logic
- Creates a simple tree with a long branch.
- Overlays data using a simulator with specific parameters.
- Verifies that the resulting character matrix contains multiple edits along the branch.
Dependencies
The code relies on the following external libraries and modules:
| Dependency | Purpose |
|---|---|
| unittest | Provides the testing framework |
| networkx | Used for creating and manipulating graph structures |
| numpy | Not directly used in the test file, but likely used in the simulator |
| pandas | Used for creating and comparing DataFrames |
| cassiopeia | The library being tested, including its simulator and data structures |
Error Handling
The code tests for various error conditions in the test_setup_errors method, ensuring that the simulator raises appropriate DataSimulatorError exceptions when given invalid input parameters.