From 4eefaad0e69718682b9fbe904548d025ea887240 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 31 May 2024 09:09:58 +0000
Subject: [PATCH] add tests and safeguard

---
 anglerfish/demux/adaptor.py                   |  4 ++
 .../test_demux/test_adaptor.py                | 54 +++++++++++++++++--
 2 files changed, 55 insertions(+), 3 deletions(-)

diff --git a/anglerfish/demux/adaptor.py b/anglerfish/demux/adaptor.py
index 041c729..4d9db5a 100644
--- a/anglerfish/demux/adaptor.py
+++ b/anglerfish/demux/adaptor.py
@@ -76,6 +76,10 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.len_index = len(index_seq) if index_seq else None
 
         else:
+            if self.index_seq is not None:
+                raise UserWarning(
+                    "Index sequence specified, but no index token found in adaptor sequence."
+                )
             self.has_index = False
             self.len_index = 0
 
diff --git a/tests/test_anglerfish/test_demux/test_adaptor.py b/tests/test_anglerfish/test_demux/test_adaptor.py
index ccc301e..8745d8a 100644
--- a/tests/test_anglerfish/test_demux/test_adaptor.py
+++ b/tests/test_anglerfish/test_demux/test_adaptor.py
@@ -48,11 +48,22 @@ def test_load_adaptors():
 
 class TestAdaptorPart:
     """Explicit combinatorial testing, ugly but effective and readable.
-    
+
     Here-in are contained test cases for a variety of instantiated AdaptorPart objects.
     All attributes and methods are tested for correctness.
     """
 
+    def test_should_fail(self):
+        """Specifying an index on an adaptor without an index should raise a UserWarning."""
+        try:
+            to_test.AdaptorPart(
+                sequence_token="ATCG", name="should_fail", index_seq="AAA"
+            )
+        except UserWarning as e:
+            assert e
+        else:
+            raise AssertionError("UserWarning not raised")
+
     def test_simple(self):
         adaptor_part = to_test.AdaptorPart(
             sequence_token="ATCG", name="simple", index_seq=None
@@ -183,6 +194,43 @@ def test_umi_known_index(self):
         assert adaptor_part.get_mask(insert_Ns=True) == "ATCGNNNNNNNNATC"
         assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
 
+
 class TestAdaptor:
-    
-    raise AssertionError("WIP")
\ No newline at end of file
+    def test_adaptor(self):
+        adaptors = {
+            "simple_and_index_umi": {
+                "i5": "AAA",
+                "i7": "AAA<N><U4>CCC",
+            }
+        }
+
+        adaptor = to_test.Adaptor(
+            "simple_and_index_umi", adaptors, i5_index=None, i7_index="TTT"
+        )
+        assert adaptor.name == "simple_and_index_umi"
+        assert isinstance(adaptor.i5, to_test.AdaptorPart)
+        assert isinstance(adaptor.i7, to_test.AdaptorPart)
+        assert (
+            adaptor.get_fastastring(insert_Ns=True)
+            == "\n".join(
+                [
+                    ">simple_and_index_umi_i5",
+                    "AAA",
+                    ">simple_and_index_umi_i7",
+                    "AAANNNNNNNCCC",
+                ]
+            )
+            + "\n"
+        )
+        assert (
+            adaptor.get_fastastring(insert_Ns=False)
+            == "\n".join(
+                [
+                    ">simple_and_index_umi_i5",
+                    "AAA",
+                    ">simple_and_index_umi_i7",
+                    "AAACCC",
+                ]
+            )
+            + "\n"
+        )