ecdna_birth_death_simulator_test.py
Here’s a documentation for the target file test/simulator_tests/ecdna_birth_death_simulator_test.py:
High-level description
This file contains unit tests for the ecDNABirthDeathSimulator class in the Cassiopeia package. It tests various aspects of the simulator, including ecDNA splitting, lineage sampling, tree population, and cosegregation of ecDNA species.
Code Structure
The main class ecDNABirthDeathSimulatorTest inherits from unittest.TestCase and contains several test methods. These methods test different functionalities of the ecDNABirthDeathSimulator class, such as ecDNA splitting, initial sample events, lineage sampling, tree population, and cosegregation.
References
cassiopeia.simulator.ecDNABirthDeathSimulator.ecDNABirthDeathSimulatorcassiopeia.data.CassiopeiaTreecassiopeia.data.utilities
Symbols
node_name_generator()
Description
A generator function that yields unique node names for the tree.
Outputs
| Name | Type | Description |
|---|---|---|
| node_name | str | A unique node name |
extract_tree_statistics(tree)
Description
A helper function for testing simulated trees. It extracts various statistics from the given tree.
Inputs
| Name | Type | Description |
|---|---|---|
| tree | CassiopeiaTree | The tree to analyze |
Outputs
| Name | Type | Description |
|---|---|---|
| times | List[float] | Total lived time for each extant lineage |
| num_leaves | int | Number of extant lineages |
| correct_degrees | bool | Whether the tree has the expected node degrees |
ecDNABirthDeathSimulatorTest
Description
The main test class containing various test methods for the ecDNABirthDeathSimulator.
Test Methods
test_ecdna_splitting: Tests the ecDNA splitting functionality.test_initial_sample_event: Tests the initial sample event in the simulation.test_basic_sample_lineage_events: Checks that sample_lineage_event behaves as expected under edge cases.test_populate_tree_from_simulation: Tests the population of a tree from simulation results.test_basic_cosegregation: Tests basic cosegregation of ecDNA species.test_perfect_cosegregation: Tests perfect cosegregation of ecDNA species.test_low_capture_efficiency: Tests the simulator with low capture efficiency.
Dependencies
- unittest
- heapq
- typing
- queue
- networkx
- numpy
- pandas
- cassiopeia.data.CassiopeiaTree
- cassiopeia.simulator.ecDNABirthDeathSimulator
- cassiopeia.data.utilities
Error Handling
The tests use assertions to check for expected behavior and raise unittest.TestCase assertion errors if the behavior doesn’t match the expected outcome.
TODOs
None explicitly mentioned in the code.