added test_count_coverage.py

Author: PuertoRicanGenome

test_count_coverage.py

@@ -0,0 +1,63 @@
+# 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 == ""
+