Function to write GOC scores to a file

scripts/pipeline/orthology_benchmark.py

@@ -694,6 +694,37 @@ def calculate_goc_genomes(core_name1: str, core_name2: str, gtf_dir: str, res_di
     return goc
 
 
+def write_goc_scores(goc_scores: List[Tuple[str, str, float]], output_file: str) -> None:
+    """Writes (appends) calculated GOC scores for putative orthologs to a specified file.
+
+    Format: gene1_id \t gene2_id \t goc_score \n. If the file does not exist, the function creates it.
+
+    Args:
+        goc_scores: A list with putative orthologs and corresponding GOC scores.
+        output_file: Path to the output file.
+
+    Raises:
+        OSError: If `output_file` does not exist and cannot be created. If `output_file` exists but cannot be
+            opened for writing.
+
+    """
+    if not os.path.exists(output_file):
+        try:
+            with open(output_file, "a") as file_handler:
+                file_handler.write("gene_1_id\tgene_2_id\tgoc_score\n")
+        except OSError as e:
+            msg = f"Could not create a file '{output_file}' for writing."
+            raise OSError(msg) from e
+
+    try:
+        with open(output_file, "a") as file_handler:
+            for i in goc_scores:
+                file_handler.write(f"{i[0]}\t{i[1]}\t{i[2]}\n")
+    except OSError as e:
+        msg = f"Could not open a file '{output_file}' for writing."
+        raise OSError(msg) from e
+
+
 def calculate_goc_scores():
     """Docstring"""
 

src/python/tests/test_orthology_benchmark.py

@@ -681,3 +681,34 @@ def test_calculate_goc_genomes() -> None:
             "species_species1_core_51_104_3", "species_species2_core_51_104_5", test_files_dir,
             orthofinder_res, 2, 3
         ) == exp_out
+
+
+def test_write_goc_scores(tmp_dir: Path) -> None:
+    """Tests :func:`orthology_benchmark.write_goc_scores()`.
+
+    Args:
+        tmp_dir:Unit test temp directory (fixture).
+
+    """
+    out_file = tmp_dir / "test_goc_out.txt"
+    orthology_benchmark.write_goc_scores([("11", "35", 0), ("21", "35", 50), ("22", "36", 50)], out_file)
+    orthology_benchmark.write_goc_scores([("23", "31", 50), ("23", "38", 50)], out_file)
+
+    # pylint: disable-next=no-member
+    test_files_dir = pytest.files_dir / "orth_benchmark"  # type: ignore[attr-defined, operator]
+    assert file_cmp(out_file, test_files_dir / "goc_scores.txt")
+
+
+def test_write_goc_scores_errors() -> None:
+    """Tests :func:`orthology_benchmark.write_goc_scores()` when it fails to write to an output file.
+    """
+    scores = [("23", "31", 50), ("23", "38", 50)]
+
+    with raises(OSError, match=r"Could not create a file '/compara/goc.txt' for writing."):
+        orthology_benchmark.write_goc_scores(scores, "/compara/goc.txt")
+
+    # pylint: disable-next=no-member
+    test_dir = pytest.files_dir / "orth_benchmark"  # type: ignore[attr-defined, operator]
+    test_file = test_dir / "goc_no_permission.txt"
+    with raises(OSError, match=fr"Could not open a file '{test_file}' for writing."):
+        orthology_benchmark.write_goc_scores(scores, test_file)

src/test_data/flatfiles/orth_benchmark/goc_no_permission.txt

@@ -0,0 +1,3 @@
+gene_1_id	gene_2_id	goc_score
+11	35	0
+

src/test_data/flatfiles/orth_benchmark/goc_scores.txt

@@ -0,0 +1,6 @@
+gene_1_id	gene_2_id	goc_score
+11	35	0
+21	35	50
+22	36	50
+23	31	50
+23	38	50