call_lineage_groups_test.py

​

High-level description

This file contains unit tests for the call_lineage_groups function in the Cassiopeia preprocessing pipeline. The tests verify the functionality of lineage group assignment, including basic grouping, doublet handling, reassignment, and filtering.

​

Code Structure

The main class TestCallLineageGroup contains several test methods, each testing different aspects of the call_lineage_groups function. The setUp method initializes test data for various scenarios.

​

Symbols

​

TestCallLineageGroup

​

Description

A unittest.TestCase subclass containing tests for the call_lineage_groups function.

​

Internal Logic

1. Sets up test data in setUp method
2. Defines multiple test methods to check different aspects of lineage group assignment

​

setUp

​

Description

Initializes test data for various scenarios, including basic grouping, reassignment, filtering, and doublet handling.

​

Internal Logic

1. Creates multiple pandas DataFrames with test data
2. Sets up different scenarios for lineage group assignment testing

​

test_format

​

Description

Tests if the output of call_lineage_groups has the expected columns.

​

Internal Logic

1. Calls call_lineage_groups with test data
2. Checks if the output DataFrame contains all expected columns

​

test_basic_grouping

​

Description

Tests basic lineage group assignment functionality.

​

Internal Logic

1. Calls call_lineage_groups with basic test data
2. Verifies if the assigned lineage groups and UMI counts match expected values

​

test_doublet

​

Description

Tests lineage group assignment with potential doublets.

​

Internal Logic

1. Calls call_lineage_groups with doublet test data
2. Checks if doublets are correctly identified and assigned

​

test_reassign

​

Description

Tests reassignment of cells to lineage groups.

​

Internal Logic

1. Calls call_lineage_groups with reassignment test data
2. Verifies if cells are correctly reassigned to appropriate lineage groups

​

test_filter_reassign

​

Description

Tests filtering and reassignment of lineage groups.

​

Internal Logic

1. Calls call_lineage_groups with filter and reassign test data
2. Checks if filtering and reassignment are performed correctly

​

test_filter_lineage_group_to_allele_table_single_lineage

​

Description

Tests the conversion of filtered lineage groups to an allele table for a single lineage.

​

Internal Logic

1. Calls filtered_lineage_group_to_allele_table with test data
2. Verifies if the resulting allele table is correct for a single lineage

​

Dependencies

• unittest
• numpy
• pandas
• cassiopeia (specifically the pipeline and lineage_utils modules)

The test file relies on the cassiopeia package, particularly the pipeline and lineage_utils modules, to perform lineage group assignments and related operations.