Move self-tests for Bio.PDB.PSEA to unit tests (#3980)

Authored-by: Valentin Vareskic <valentin.vareskic@gmail.com>

.gitignore

@@ -125,3 +125,4 @@ Doc/api/*.rst
 
 #Ignore virtual environment file
 .env
+venv/

Bio/PDB/PSEA.py

@@ -103,16 +103,3 @@ class PSEA:
     def get_seq(self):
         """Return secondary structure string."""
         return self.ss_seq
-
-
-if __name__ == "__main__":
-
-    import sys
-    from Bio.PDB import PDBParser
-
-    # Parse PDB file
-    p = PDBParser()
-    s = p.get_structure("X", sys.argv[1])
-
-    # Annotate structure with PSEA secondary structure info
-    PSEA(s[0], sys.argv[1])

Tests/test_PDB_PSEA.py

@@ -0,0 +1,126 @@
+# Copyright 2022 by Valentin Vareskic (valentin.vareskic@gmail.com).
+# All rights reserved. This code is part of the Biopython distribution
+# and governed by its license.  Please see the LICENSE file that should
+# have been included as part of this package.
+
+"""Tests for PDB PSEA."""
+
+import os
+import unittest
+from subprocess import getoutput
+
+from Bio import MissingExternalDependencyError
+from Bio.PDB import PDBParser
+from Bio.PDB.PSEA import run_psea, psea, psea2HEC, PSEA
+
+
+os.environ["LANG"] = "C"
+
+
+cmd_output = getoutput("psea -h")
+if not cmd_output.startswith("o---"):
+    raise MissingExternalDependencyError(
+        "Download and install psea from "
+        "ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. "
+        "Make sure that psea is on path"
+    )
+
+
+def remove_sea_files():
+    for file in os.listdir():
+        if file.endswith(".sea"):
+            os.remove(file)
+
+
+class TestPDBPSEA(unittest.TestCase):
+    def tearDown(self):
+        remove_sea_files()
+
+    def test_run_psea(self):
+        psae_run = run_psea("PDB/1A8O.pdb")
+        self.assertEqual(psae_run, "1A8O.sea")
+
+    def test_psea(self):
+        psae_run = psea("PDB/2BEG.pdb")
+        self.assertEqual(psae_run, "ccccbbbbbbbccccbbbbbbbbbbc")
+
+    def test_psea_2HEC(self):
+        seq = psea("PDB/2BEG.pdb")
+        psae_run = psea2HEC(seq)
+        self.assertEqual(
+            psae_run,
+            [
+                "C",
+                "C",
+                "C",
+                "C",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "C",
+                "C",
+                "C",
+                "C",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "C",
+            ],
+        )
+
+
+class TestPSEA(unittest.TestCase):
+    def tearDown(self):
+        remove_sea_files()
+
+    def test_get_seq(self):
+        p = PDBParser()
+        s = p.get_structure("X", "PDB/2BEG.pdb")
+        psea_class = PSEA(s[0], "PDB/2BEG.pdb")
+        self.assertEqual(
+            psea_class.get_seq(),
+            [
+                "C",
+                "C",
+                "C",
+                "C",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "C",
+                "C",
+                "C",
+                "C",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "E",
+                "C",
+            ],
+        )
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity=2)
+    unittest.main(testRunner=runner)