Merge pull request #38 from MolecularBioinformatics/feature/mat-cli

adding .mat file support to CLI

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gemcat"
-version = "1.1.0"
+version = "1.2.0"
 
 description = "A toolbox for gene expression-based prediction of metabolic alterations"
 keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"]

src/gemcat/cli.py

@@ -14,7 +14,7 @@
 import cobra
 from pandas import DataFrame, Series, read_csv
 
-from .io import load_json_cobra, load_sbml_cobra
+from .io import load_json_cobra, load_mat_cobra, load_sbml_cobra
 from .workflows import workflow_standard
 
 
@@ -33,7 +33,7 @@ def not_implemented(whatever: Any):
     "xml": load_sbml_cobra,
     "json": load_json_cobra,
     "csv": not_implemented,
-    "mat": not_implemented,
+    "mat": load_mat_cobra,
 }
 
 

src/gemcat/io.py

@@ -41,10 +41,7 @@ def load_json_cobra(json_file: Union[str, Path]) -> cobra.Model:
     :return: Model object created from the COBRA model
     :rtype: Model
     """
-    if isinstance(json_file, Path):
-        json_file = json_file.as_posix()
-    cobra_model = cobra.io.load_json_model(json_file)
-
+    cobra_model = cobra.io.load_json_model(str(json_file))
     return cobra_model
 
 
@@ -56,10 +53,19 @@ def load_sbml_cobra(sbml_file: Union[str, Path]) -> cobra.Model:
     :return: Model object created from the COBRA model
     :rtype: Model
     """
-    if isinstance(sbml_file, Path):
-        sbml_file = sbml_file.as_posix()
-    cobra_model = cobra.io.read_sbml_model(sbml_file)
+    cobra_model = cobra.io.read_sbml_model(str(sbml_file))
+    return cobra_model
 
+
+def load_mat_cobra(mat_file: Union[str, Path]) -> cobra.Model:
+    """
+    Loads a Pagerank-based Model from a COBRA SBML file.
+    :param mat_file: Path to json SBML file
+    :type mat_file: Union[str, Path]
+    :return: COBRA model object
+    :rtype: Model
+    """
+    cobra_model = cobra.io.load_matlab_model(str(mat_file))
     return cobra_model
 
 

tests/test_cli.py

@@ -81,45 +81,31 @@ def test_cli_293_xml():
 
 
 @pytest.mark.slow
-def test_cli_paper_uc_ns():
-    args = MockNamespace(
-        expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"),
-        expressioncolumn="foldchange",
-        baseline=str(expression_path / "prot_uc_vs_healthy.csv"),
-        baselinecolumn="base",
-        genefill=None,
-        modelfile=str(model_path / "Recon3D.json"),
-        outfile="./temp_outfile.csv",
-    )
-    result, outfile = cli.cli_standard(args)
-    assert isinstance(result, Series)
-    assert len(result) > 1000
-    assert outfile.stem == "temp_outfile"
-    assert outfile.suffix == ".csv"
-    expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0]
-    assert allclose(expected.values, result.values, atol=0.3)
-
-
-@pytest.mark.slow
-def test_cli_paper_uc_wf():
-    args = MockNamespace(
-        expressionfile=str(expression_path / "prot_uc_vs_healthy.csv"),
-        expressioncolumn="foldchange",
-        baseline=str(expression_path / "prot_uc_vs_healthy.csv"),
-        baselinecolumn="base",
-        genefill=None,
-        modelfile=str(model_path / "Recon3D.json"),
-        outfile="./temp_outfile.csv",
+def test_cli_293_mat():
+    out_file = Path("./temp_outfile.csv")
+    run(
+        [
+            "gemcat",
+            str(model_path / "Recon3D_301.mat"),
+            str(expression_path / "prot_uc_vs_healthy.csv"),
+            "-e",
+            "foldchange",
+            "-o",
+            str(out_file),
+            "-g",
+            "1.0",
+        ],
+        shell=False,
     )
-    result, _ = cli.cli_standard(args)
-    assert isinstance(result, Series)
-    assert len(result) > 1000
-    expected = read_csv(results_path / "uc.csv", sep=",", index_col=0).iloc[:, 0]
-    assert allclose(expected.values, result.values, atol=0.3)
+    assert out_file.is_file()
+    received = read_csv(out_file, sep=",", index_col=0).iloc[:, 0]
+    out_file.unlink()
+    assert len(received > 1000)
+    assert received.isna().sum() == 0
 
 
 @pytest.mark.slow
-def test_cli_paper_uc_term():
+def test_cli_uc_json():
     out_file = Path("./temp_outfile.csv")
     run(
         [