filter_bam_test.py

High-level description

This file contains unit tests for the filter_bam function from the cassiopeia.preprocess.pipeline module. The tests verify that the function correctly filters BAM files based on a specified read quality threshold.

Symbols

TestFilterBam

Description

This is a test class that inherits from unittest.TestCase. It contains test methods to verify the functionality of the filter_bam function.

Internal Logic

1. Sets up the test environment by defining the path to a test BAM file.
2. Implements a test method test_filter to check the filtering functionality with different quality thresholds.

setUp

Description

This method is called before each test method to set up the test environment.

Internal Logic

1. Determines the directory path of the current file.
2. Constructs the path to the test files directory.
3. Sets the path to a 10x Genomics v3 unmapped BAM file for testing.

test_filter

Description

This method tests the filter_bam function with different quality thresholds.

Internal Logic

1. Calls filter_bam with a quality threshold of 10 and verifies that 2 alignments pass the filter.
2. Calls filter_bam with a quality threshold of 20 and verifies that 0 alignments pass the filter.
3. Uses pysam.AlignmentFile to read the filtered BAM files and count the number of alignments.
4. Uses assertEqual to check if the number of filtered alignments matches the expected count.

Dependencies

Dependency	Purpose
os	File path operations
unittest	Unit testing framework
tempfile	Creating temporary directories
pysam	Reading BAM files
ngs_tools	Not directly used in the test file, but imported as ngs
cassiopeia.preprocess.pipeline	Module containing the filter_bam function being tested

Error Handling

The test class uses the unittest framework’s assertion methods to check for expected outcomes. If any assertion fails, the test will raise an exception, indicating a test failure.

Notes

1. The test file uses a specific 10x Genomics v3 unmapped BAM file for testing, located in the “test_files” directory.
2. The filter_bam function is called with temporary directories created using tempfile.mkdtemp() to store the output filtered BAM files.
3. The tests check two scenarios: one where some reads pass the quality filter (threshold 10) and another where no reads pass the filter (threshold 20).
4. The pysam library is used to read the filtered BAM files and count the number of alignments.
5. The ngs_tools module is imported but not used directly in this test file.