Add a basic test for merge_fastqs.py script

micall/tests/test_merge_fastqs.py

@@ -0,0 +1,49 @@
+import pytest
+import os
+import sys
+
+from micall.core.merge_fastqs import main
+
+FASTQ_DATA_A = """@SEQ_ID_A1
+AAGTCGACGAATG
++
+ABCDEFGHIJKLM"""
+FASTQ_DATA_A2 = """@SEQ_ID_A2
+AACCTGAAGGGTT
++
+ABCDEFGHIJKLM"""
+FASTQ_DATA_B = """@SEQ_ID_B1
+CCCTAAAGGTTTG
++
+ABCDEFGHIJKLM"""
+FASTQ_DATA_B2 = """@SEQ_ID_B2
+ACGTACGTACGTA
++
+ABCDEFGHIJKLM"""
+
+@pytest.fixture
+def fastq_files(tmp_path):
+    # Create forward and reverse fastq files for two samples: A and B.
+    fastq1_a = tmp_path / "fastq1_a.fastq"
+    fastq2_a = tmp_path / "fastq2_a.fastq"
+    fastq1_b = tmp_path / "fastq1_b.fastq"
+    fastq2_b = tmp_path / "fastq2_b.fastq"
+    fastq1_a.write_text(FASTQ_DATA_A)
+    fastq2_a.write_text(FASTQ_DATA_A2)
+    fastq1_b.write_text(FASTQ_DATA_B)
+    fastq2_b.write_text(FASTQ_DATA_B2)
+
+    # Paths for output files
+    fastq1_result = tmp_path / "fastq1_result.fastq"
+    fastq2_result = tmp_path / "fastq2_result.fastq"
+
+    args = [str(fastq1_a), str(fastq2_a), str(fastq1_b), str(fastq2_b), '--unzipped', str(fastq1_result), str(fastq2_result)]
+    return args
+
+def test_basic_main(fastq_files):
+    main(fastq_files)
+
+    # Add some assertions
+    assert os.path.exists(fastq_files[-2])  # assert fastq1_result exists
+    assert os.path.exists(fastq_files[-1])  # assert fastq2_result exists
+    # ...plus more assertions to check content of results...