Testing Guide

This guide covers running tests, adding new tests, and accuracy validation for py-gbcms.

Running Tests

Quick Test

# Run all tests
pytest -v

# Run with coverage
pytest --cov=gbcms --cov-report=html

# Run specific test file
pytest tests/test_accuracy.py -v

Test Categories

Category	Files	Purpose
Accuracy	test_accuracy.py	SNP, indel, complex variant counting
CLI	test_cli_sample_id.py	Command-line parsing
Filters	test_filters.py	Read filtering logic
MAF	test_maf_*.py	MAF column preservation
Pipeline	test_pipeline_v2.py	End-to-end workflow
Strand	test_strand_counts.py	Strand-specific counts

---

Test Structure

tests/
├── test_accuracy.py        # Variant type accuracy
├── test_cli_sample_id.py   # CLI argument parsing
├── test_filters.py         # Read filtering
├── test_maf_preservation.py
├── test_maf_reader.py
├── test_pipeline_v2.py
└── test_strand_counts.py

---

Writing Tests

Basic Test Template

import pytest
from pathlib import Path

def test_my_feature(tmp_path):
    """Test description."""
    # Arrange
    input_file = tmp_path / "input.txt"
    input_file.write_text("test data")
    
    # Act
    result = my_function(input_file)
    
    # Assert
    assert result.success
    assert result.count == 42

Accuracy Test Template

def test_snp_accuracy():
    """Verify SNP counting against known BAM."""
    # Create variant
    variant = Variant("chr1", 100, "A", "T", "SNP")
    
    # Run counting
    results = count_bam(bam_path, [variant], fasta_path)
    
    # Validate
    assert results[0].ref_count == 50
    assert results[0].alt_count == 10

---

Manual Validation

Using samtools for Spot-Check

# Check counts at specific position
samtools mpileup -r chr1:100-100 -q 20 \
    -f ref.fa sample.bam 2>/dev/null | \
    awk '{print "DP="$4}'

Comparing with gbcms Output

# Run gbcms
gbcms run -v variants.maf -b sample.bam -f ref.fa -o output/

# Check output
awk -F'\t' 'NR==2 {print "REF="$41, "ALT="$42}' output/*.maf

---

Accuracy Validation

Variant Types Tested

Type	Test	Status
SNP	test_snp_accuracy	✅
Insertion	test_insertion_accuracy	✅
Deletion	test_deletion_accuracy	✅
Complex	test_complex_accuracy	✅
MNP	test_mnp_accuracy	✅

Real-World Validation

# Compare gbcms vs samtools for a SNP
# Position: chr1:11168293 G>A

# gbcms output
awk -F'\t' '$5=="1" && $6=="11168293" {print "REF="$41, "ALT="$42}' output.maf

# samtools output
samtools mpileup -r 1:11168293-11168293 -q 20 -f ref.fa sample.bam | \
    awk '{gsub(/\^.|\$/,"",$5); print "DP="$4, "Pileup="$5}'

---

Coverage Targets

Module	Target	Current
cli.py	80%	79%
pipeline.py	70%	29%
io/input.py	85%	82%
io/output.py	90%	96%
models/core.py	90%	90%

Run coverage report:

pytest --cov=gbcms --cov-report=html
open htmlcov/index.html