Merge pull request #669 from biolink/go-site-887-gorule-0000005-some-…

…codes-are-not-allowed-for-protein-binding-or-binding

For #887

ontobio/io/qc.py

@@ -36,6 +36,8 @@
 iss_eco = ecomapping.coderef_to_ecoclass("ISS")
 isa_eco = ecomapping.coderef_to_ecoclass("ISA")
 iso_eco = ecomapping.coderef_to_ecoclass("ISO")
+ism_eco = ecomapping.coderef_to_ecoclass("ISM")
+rca_eco = ecomapping.coderef_to_ecoclass("RCA")
 
 # TestResult = collections.namedtuple("TestResult", ["result_type", "message", "result"])
 class TestResult(object):
@@ -187,6 +189,16 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
         fails = ((annotation_obj_id == "GO:0005488" or annotation_obj_id == "GO:0005515") and annotation.negated)
         return self._result(not fails)
 
+class GoRule05(GoRule):
+
+    def __init__(self):
+        super().__init__("GORULE:0000005", "IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'", FailMode.SOFT)
+
+    def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
+        evidence = str(annotation.evidence.type)
+        annotation_obj_id = str(annotation.object.id)
+        fails = ((annotation_obj_id == "GO:0005488" or annotation_obj_id == "GO:0005515") and evidence in [iea_eco, iss_eco, iso_eco, ism_eco, isa_eco, iba_eco, rca_eco])
+        return self._result(not fails)
 
 class GoRule06(GoRule):
 
@@ -915,6 +927,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
 
 GoRules = enum.Enum("GoRules", {
     "GoRule02": GoRule02(),
+    "GoRule05": GoRule05(),    
     "GoRule06": GoRule06(),
     "GoRule07": GoRule07(),
     "GoRule08": GoRule08(),

tests/test_qc.py

@@ -93,7 +93,29 @@ def test_go_rule02():
     assoc.object.id = Curie.from_str("GO:0003674")
     test_result = qc.GoRule02().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.PASS
-
+
+def test_go_rule_05():
+    fail_terms = ["GO:0005488", "GO:0005515"]
+    fail_codes = ["IEA", "ISS", "ISO", "ISM", "ISA", "IBA", "RCA"]
+    for term in fail_terms:
+        for code in fail_codes:
+            assoc = make_annotation(goid=term, evidence=code).associations[0]
+            test_result = qc.GoRule05().test(assoc, all_rules_config(ontology=ontology))
+            assert test_result.result_type == qc.ResultType.WARNING
+
+    assoc = make_annotation(goid="GO:0034655", evidence="IEA").associations[0]
+    test_result = qc.GoRule05().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.PASS
+
+
+    assoc = make_annotation(goid="GO:0005488", evidence="HEP").associations[0]
+    test_result = qc.GoRule05().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.PASS
+
+    assoc = make_annotation(goid="GO:0034655", evidence="HEP").associations[0]
+    test_result = qc.GoRule05().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.PASS    
+
 def test_go_rule_06():
 
     assoc = make_annotation(goid="GO:0005575", evidence="HEP", aspect="C").associations[0]
@@ -769,7 +791,7 @@ def test_all_rules():
     assoc = gafparser.to_association(a).associations[0]
 
     test_results = qc.test_go_rules(assoc, config).all_results
-    assert len(test_results.keys()) == 24
+    assert len(test_results.keys()) == 25
     assert test_results[qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
     assert test_results[qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS