test case for non existing unitprot

README.md

@@ -45,7 +45,7 @@ options:
 
 You can provide the optional argument `--pdbpath` if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB.
 
-For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and the generate the PDB shown in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
+For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and generates the PDB shown in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
 
 ```
 wget https://files.rcsb.org/download/7UPI.pdb

missense/missense.py

@@ -462,7 +462,7 @@ def create_parser() -> argparse.ArgumentParser:
     parser.add_argument(
         "--tsv",
         type=str,
-        help="You can provide the path to the tsv file if you want to skip the downloading part.",
+        help="You can provide the path to the tsv file if you want to skip the download.",
         default=None
     )
 
@@ -579,6 +579,10 @@ def _run(uniprot_id: str,
 
     pos_to_val = get_data_tuple(uniprot_id=uniprot_id, tsv_path=tsvpath)
 
+    if len(pos_to_val) == 0:
+        print(f"Could not find any data in the AlphaMissense database for uniprot id {uniprot_id}")
+        sys.exit(1)
+
     out_fig_pth = os.path.join(output_path, f"{uniprot_id}.pdf")
     img_raw_data = make_and_save_plot(pos_to_val, out_fig_pth, maxacid)
     print(f"Save plot to {out_fig_pth}")

tests/test_run.py

@@ -35,6 +35,20 @@ def test_pdf_and_and_are_generated(self):
             self.assertEqual(True, os.path.exists(os.path.join(tmpdirname,"Q9UQ13.pdf")))
             self.assertEqual(True, os.path.exists(os.path.join(tmpdirname, "Q9UQ13-edit.pdb")))
 
+    def test_pdf_and_and_are_generated_non_existing_uniprot(self):
+
+        shutil.copyfile(os.path.join(os.path.dirname(__file__), "../resources/tests/Q9UQ13/alpha.tsv"),
+                        os.path.join(tempfile.gettempdir(), "alpha.tsv"))
+
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            with self.assertRaises(SystemExit):
+                ms._run(uniprot_id="Q9UQ13234234",
+                        output_path=tmpdirname,
+                        maxacid=200,
+                        pdbpath=None,
+                        tsvpath=None
+                        )
+
     def test_pdf_and_and_are_generated_tsv_by_path(self):
 
         with tempfile.TemporaryDirectory() as tmpdirname: