test_count_coverage.py

#!/usr/bin/env pypy3

# test_count_coverage.py
# ----------------------
# Unit tests for count_coverage.py

import io
import pytest
from count_coverage import count_coverage

def test_count_coverage_basic(capsys):
    """
    Test that count_coverage correctly counts samples with nonzero coverage.
    """
    # Simulated input (tab-separated)
    input_data = io.StringIO(
        "chrM\t1\t0\t88\t65\n"
        "chrM\t2\t55\t77\t8\n"
        "chrM\t3\t58\t64\t0\n"
    )

    # Run the function
    count_coverage(input_data)

    # Capture printed output
    captured = capsys.readouterr()

    # Expected output: zero-based, half-open intervals
    expected_output = (
        "chrM\t0\t1\t2\n"
        "chrM\t1\t2\t3\n"
        "chrM\t2\t3\t2\n"
    )

    assert captured.out == expected_output

def test_count_coverage_noninteger(capsys):
    """
    Test that non-integer coverage values cause the script to exit with an error.
    """
    input_data = io.StringIO("chr1\t1\t10\tnan\t5\n")
    with pytest.raises(SystemExit):
        count_coverage(input_data)
    captured = capsys.readouterr()
    assert "non-integer value" in captured.err.lower()

def test_count_coverage_too_few_fields(capsys):
    """
    Test that lines with fewer than 2 fields cause the script to exit with an error.
    """
    input_data = io.StringIO("chr1\n")
    with pytest.raises(SystemExit):
        count_coverage(input_data)
    captured = capsys.readouterr()
    assert "fewer than 2 fields" in captured.err.lower()

def test_count_coverage_zero_only(capsys):
    """
    Test that positions with zero coverage across all samples are skipped.
    """
    input_data = io.StringIO("chr2\t1\t0\t0\t0\n")
    count_coverage(input_data)
    captured = capsys.readouterr()
    assert captured.out == ""