Fix NameError: add default PidentComments

my_tests/test_pidentcomments.py

@@ -0,0 +1,21 @@
+import math
+from my_tests.pidentcomments import pident_comment, DEFAULT, PERFECT, IMPERFECT
+
+def test_defaults_and_branches():
+    assert "No alignment" in pident_comment(None, 3)
+    assert "aligns perfectly" in pident_comment(100, 1)
+    assert "does not align perfectly" in pident_comment(99.9, 1)
+    # With 0 targets we fall back to DEFAULT
+    assert "No alignment" in pident_comment(0, 0)
+
+def test_never_raises_on_weird_inputs():
+    for pair in [("x","y"), ([],{}), (object(),object()), (-1,-1)]:
+        out = pident_comment(*pair)
+        assert isinstance(out, str)
+        assert "No alignment" in out
+
+def test_constants_are_strings():
+    for s in (DEFAULT, PERFECT, IMPERFECT):
+        assert isinstance(s, str)
+
+

scripts/puppy-primers

@@ -984,10 +984,21 @@ elif args.primers_type == "group":
             unintendedComment = "UNINTENDED AMPLIFICATION:\nWARNING - This gene amplifies unintended species in the defined community!"
 
         ## Comments about percentage identity of alignments:
-        if pidentSum == 100 * numTargets:
-            PidentComments = "ALIGNMENTS %ID:\nThis gene aligns perfectly (100% ID) to each target gene."
-        elif pidentSum < 100 * numTargets:
-            PidentComments = "ALIGNMENTS %ID:\nThis gene does not align perfectly (100% ID) to at least one target gene."
+        PidentComments = "ALIGNMENTS %ID:\nNo alignment information available."
+
+        if isinstance(pidentSum, (int, float)) and isinstance(numTargets, (int, float)):
+            if not pidentSum or not numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nNo alignment information available."
+                )
+            elif pidentSum == 100 * numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nThis gene aligns perfectly (100% ID) to each target gene."
+                )
+            elif pidentSum < 100 * numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nThis gene does not align perfectly (100% ID) to at least one target gene."
+                )
 
         ## Comments about alignments query coverage:
         if qcovSum == 1 * numTargets: