add lots of tests

tests/test_anglerfish/test_demux/test_adaptor.py

@@ -1,15 +1,13 @@
 import re
 
-import pytest
-
-from anglerfish.demux import adaptor as adaptor_to_test
+from anglerfish.demux import adaptor as to_test
 
 
 def test_has_match():
     assert (
-        adaptor_to_test.has_match(re.compile("pattern"), "thereisapatterninthisstring") is True
+        to_test.has_match(re.compile("pattern"), "thereisapatterninthisstring") is True
     )
-    assert adaptor_to_test.has_match(re.compile("pattern"), "nothinghere") is False
+    assert to_test.has_match(re.compile("pattern"), "nothinghere") is False
 
 
 def test_validate_adaptors():
@@ -19,7 +17,7 @@ def test_validate_adaptors():
             "i7": "CAGT<N><U9>GGAA",
         },
     }
-    assert adaptor_to_test.validate_adaptors(valid_adaptors_dict) is None
+    assert to_test.validate_adaptors(valid_adaptors_dict) is None
 
     invalid_adaptors_dict = {
         "falseq_umi": {
@@ -28,21 +26,159 @@ def test_validate_adaptors():
         },
     }
     try:
-        adaptor_to_test.validate_adaptors(invalid_adaptors_dict)
+        to_test.validate_adaptors(invalid_adaptors_dict)
     except UserWarning as e:
         assert e
     else:
         raise AssertionError("UserWarning not raised")
 
 
 def test_load_adaptors():
-    adaptors = adaptor_to_test.load_adaptors()
+    adaptors = to_test.load_adaptors()
     assert adaptors
     assert isinstance(adaptors, list)
     for adaptor in adaptors:
-        assert isinstance(adaptor, adaptor_to_test.Adaptor)
+        assert isinstance(adaptor, to_test.Adaptor)
 
-    adaptors_raw = adaptor_to_test.load_adaptors(raw = True)
+    adaptors_raw = to_test.load_adaptors(raw=True)
     assert isinstance(adaptors_raw, dict)
     for adaptor in adaptors_raw:
         assert isinstance(adaptors_raw[adaptor], dict)
+
+
+class TestAdaptorPart:
+    """Explicit combinatorial testing, ugly but effective and readable."""
+
+    def test_simple(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG", name="simple", index_seq=None
+        )
+        assert adaptor_part.sequence_token == "ATCG"
+        assert adaptor_part.name == "simple"
+        assert adaptor_part.index_seq is None
+        assert adaptor_part.has_index is False
+        assert adaptor_part.len_index == 0
+        assert adaptor_part.has_umi is False
+        assert adaptor_part.len_umi == 0
+        assert adaptor_part.len_before_index is None
+        assert adaptor_part.len_after_index is None
+        assert adaptor_part.len_umi_before_index is None
+        assert adaptor_part.len_umi_after_index is None
+        assert adaptor_part.len_total == 4
+        assert adaptor_part.len_constant == 4
+        assert adaptor_part.get_mask(insert_Ns=True) == "ATCG"
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCG"
+
+    def test_unknown_index(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG<N>ATC", name="unknown_index", index_seq=None
+        )
+        assert adaptor_part.sequence_token == "ATCG<N>ATC"
+        assert adaptor_part.name == "unknown_index"
+        assert adaptor_part.index_seq is None
+        assert adaptor_part.has_index is True
+        assert adaptor_part.len_index is None
+        assert adaptor_part.has_umi is False
+        assert adaptor_part.len_umi == 0
+        assert adaptor_part.len_before_index == 4
+        assert adaptor_part.len_after_index == 3
+        assert adaptor_part.len_umi_before_index == 0
+        assert adaptor_part.len_umi_after_index == 0
+        assert adaptor_part.len_total is None
+        assert adaptor_part.len_constant == 7
+        try:
+            adaptor_part.get_mask(insert_Ns=True)
+        except UserWarning as e:
+            assert e
+        else:
+            raise AssertionError("UserWarning not raised")
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
+
+    def test_known_index(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG<N>ATC", name="known_index", index_seq="GGG"
+        )
+        assert adaptor_part.sequence_token == "ATCG<N>ATC"
+        assert adaptor_part.name == "known_index"
+        assert adaptor_part.index_seq == "GGG"
+        assert adaptor_part.has_index is True
+        assert adaptor_part.len_index == 3
+        assert adaptor_part.has_umi is False
+        assert adaptor_part.len_umi == 0
+        assert adaptor_part.len_before_index == 4
+        assert adaptor_part.len_after_index == 3
+        assert adaptor_part.len_umi_before_index == 0
+        assert adaptor_part.len_umi_after_index == 0
+        assert adaptor_part.len_total == 10
+        assert adaptor_part.len_constant == 7
+        assert adaptor_part.get_mask(insert_Ns=True) == "ATCGNNNATC"
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
+
+    def test_unknown_index_umi(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG<N><U5>ATC", name="unknown_index_umi", index_seq=None
+        )
+        assert adaptor_part.sequence_token == "ATCG<N><U5>ATC"
+        assert adaptor_part.name == "unknown_index_umi"
+        assert adaptor_part.index_seq is None
+        assert adaptor_part.has_index is True
+        assert adaptor_part.len_index is None
+        assert adaptor_part.has_umi is True
+        assert adaptor_part.len_umi == 5
+        assert adaptor_part.len_before_index == 4
+        assert adaptor_part.len_after_index == 8
+        assert adaptor_part.len_umi_before_index == 0
+        assert adaptor_part.len_umi_after_index == 5
+        assert adaptor_part.len_total is None
+        assert adaptor_part.len_constant == 7
+        try:
+            adaptor_part.get_mask(insert_Ns=True)
+        except UserWarning as e:
+            assert e
+        else:
+            raise AssertionError("UserWarning not raised")
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
+
+    def test_known_index_umi(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG<N><U5>ATC", name="known_index_umi", index_seq="GGG"
+        )
+        assert adaptor_part.sequence_token == "ATCG<N><U5>ATC"
+        assert adaptor_part.name == "known_index_umi"
+        assert adaptor_part.index_seq == "GGG"
+        assert adaptor_part.has_index is True
+        assert adaptor_part.len_index == 3
+        assert adaptor_part.has_umi is True
+        assert adaptor_part.len_umi == 5
+        assert adaptor_part.len_before_index == 4
+        assert adaptor_part.len_after_index == 8
+        assert adaptor_part.len_umi_before_index == 0
+        assert adaptor_part.len_umi_after_index == 5
+        assert adaptor_part.len_total == 15
+        assert adaptor_part.len_constant == 7
+        assert adaptor_part.get_mask(insert_Ns=True) == "ATCGNNNNNNNNATC"
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
+
+    def test_umi_known_index(self):
+        adaptor_part = to_test.AdaptorPart(
+            sequence_token="ATCG<U5><N>ATC", name="umi_known_index", index_seq="GGG"
+        )
+        assert adaptor_part.sequence_token == "ATCG<U5><N>ATC"
+        assert adaptor_part.name == "umi_known_index"
+        assert adaptor_part.index_seq == "GGG"
+        assert adaptor_part.has_index is True
+        assert adaptor_part.len_index == 3
+        assert adaptor_part.has_umi is True
+        assert adaptor_part.len_umi == 5
+        assert adaptor_part.len_before_index == 9
+        assert adaptor_part.len_after_index == 3
+        assert adaptor_part.len_umi_before_index == 5
+        assert adaptor_part.len_umi_after_index == 0
+        assert adaptor_part.len_total == 15
+        assert adaptor_part.len_constant == 7
+        assert adaptor_part.get_mask(insert_Ns=True) == "ATCGNNNNNNNNATC"
+        assert adaptor_part.get_mask(insert_Ns=False) == "ATCGATC"
+
+class TestAdaptor:
+
+    raise AssertionError("WIP")