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Here’s a detailed documentation of the target file test/preprocess_tests/convert_fastqs_to_unmapped_bam_test.py:

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High-level description

This file contains unit tests for the convert_fastqs_to_unmapped_bam function in the cassiopeia.preprocess.pipeline module. The tests verify the correct conversion of FASTQ files to unmapped BAM files for different sequencing chemistries.

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Code Structure

The main class TestConvertFastqsToUnmappedBam contains several test methods, each testing a different sequencing chemistry. The tests use sample FASTQ files and verify the correct conversion to BAM format, including proper tag assignments.

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Symbols

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TestConvertFastqsToUnmappedBam

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Description

A unittest.TestCase subclass that contains test methods for the convert_fastqs_to_unmapped_bam function.

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Internal Logic

  • Sets up test FASTQ file paths in the setUp method
  • Implements test methods for different sequencing chemistries (dropseq, 10xv2, 10xv3, indropsv3, slideseq2)
  • Each test method:
    1. Calls convert_fastqs_to_unmapped_bam with appropriate parameters
    2. Reads the resulting BAM file
    3. Verifies the correct number of alignments, query names, sequences, and qualities
    4. Checks the correct assignment of BAM tags (UR, UY, CR, CY, RG)

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setUp

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Description

Initializes the test environment by setting up file paths for test FASTQ files.

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test_dropseq

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Description

Tests the conversion of FASTQ files to BAM for the Drop-seq chemistry.

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test_10xv2

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Description

Tests the conversion of FASTQ files to BAM for the 10x Genomics v2 chemistry.

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test_10xv3

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Description

Tests the conversion of FASTQ files to BAM for the 10x Genomics v3 chemistry.

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test_indropsv3

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Description

Tests the conversion of FASTQ files to BAM for the inDrops v3 chemistry.

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test_slideseq2

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Description

Tests the conversion of FASTQ files to BAM for the Slide-seq v2 chemistry.

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Dependencies

DependencyPurpose
osFile path operations
unittestUnit testing framework
tempfileCreating temporary directories
pysamReading and manipulating BAM files
ngs_toolsFASTQ file handling
cassiopeia.preprocess.pipelineModule containing the function being tested

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Error Handling

The tests use assertions to verify the correctness of the BAM conversion. If any assertion fails, the test will raise an AssertionError, indicating a problem with the conversion process. This test file is crucial for ensuring the correct functionality of the FASTQ to BAM conversion process in the Cassiopeia preprocessing pipeline, covering various sequencing chemistries and verifying the proper assignment of BAM tags.