Move regulatory feature type from core to eukaryote schema

KarrLab · Nov 28, 2018 · e4962fb · e4962fb
1 parent 0d9f7ab
commit e4962fb
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Showing 3 changed files with 30 additions and 13 deletions.
diff --git a/tests/test_eukaryote_schema.py b/tests/test_eukaryote_schema.py
@@ -16,6 +16,24 @@
 import unittest
 
 
+class TestCore(unittest.TestCase):
+
+    def test_RegulatoryElementType(self):
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.promoter.value, 1)
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.promoter_flanking_region.value, 2)
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.enhancer.value, 3)
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.CTCF_binding_site.value, 4)
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.TF_binding_site.value, 5)
+        self.assertEqual(eukaryote_schema.RegulatoryElementType.open_chromatin_region.value, 6)
+
+    def test_ActivityLevel(self):
+        self.assertEqual(eukaryote_schema.ActivityLevel.active.value, 1)
+        self.assertEqual(eukaryote_schema.ActivityLevel.poised.value, 2)
+        self.assertEqual(eukaryote_schema.ActivityLevel.repressed.value, 3)
+        self.assertEqual(eukaryote_schema.ActivityLevel.inactive.value, 4)
+        self.assertEqual(eukaryote_schema.ActivityLevel.na.value, 5)
+
+
 class CellTestCase(unittest.TestCase):
     def test_constructor(self):
         cell = core.Cell(taxon=9606)
@@ -382,12 +400,12 @@ def test_constructor(self):
 class RegulatoryElementLocusTestCase(unittest.TestCase):
     def test_constructor(self):
         promoter = eukaryote_schema.RegulatoryElementLocus(id='p1', name='promoter1', 
-            type=core.RegulatoryElementType.promoter, 
+            type=eukaryote_schema.RegulatoryElementType.promoter, 
             activity=eukaryote_schema.ActivityLevel.active, 
             strand=core.PolymerStrand.positive, start=2, end=10)
         self.assertEqual(promoter.id, 'p1')
         self.assertEqual(promoter.name, 'promoter1')
-        self.assertEqual(promoter.type, core.RegulatoryElementType.promoter)
+        self.assertEqual(promoter.type, eukaryote_schema.RegulatoryElementType.promoter)
         self.assertEqual(promoter.activity, eukaryote_schema.ActivityLevel.active)
         self.assertEqual(promoter.strand, core.PolymerStrand.positive)
         self.assertEqual(promoter.start, 2)

diff --git a/wc_kb/core.py b/wc_kb/core.py
@@ -63,16 +63,6 @@ class GeneType(enum.Enum):
     tRna = 3
 
 
-class RegulatoryElementType(enum.Enum):
-    """ Type of regulatory element """
-    promoter = 1
-    promoter_flanking_region = 2
-    enhancer = 3
-    CTCF_binding_site = 4
-    TF_binding_site = 5
-    open_chromatin_region = 6
-
-
 class ComplexType(enum.Enum):
     """ Type of complex """
     tRnaSynthClassII = 0

diff --git a/wc_kb/eukaryote_schema.py b/wc_kb/eukaryote_schema.py
@@ -16,6 +16,15 @@
 #####################
 # Enumeration classes
 
+class RegulatoryElementType(enum.Enum):
+    """ Type of regulatory element """
+    promoter = 1
+    promoter_flanking_region = 2
+    enhancer = 3
+    CTCF_binding_site = 4
+    TF_binding_site = 5
+    open_chromatin_region = 6
+
 
 class ActivityLevel(enum.Enum):
     active = 1
@@ -81,7 +90,7 @@ class RegulatoryElementLocus(core.PolymerLocus):
     Related attributes:
         regulatory_modules (:obj:`list` of :obj:`RegulatoryModule`): regulatory_modules
     """
-    type = obj_model.EnumAttribute(core.RegulatoryElementType)
+    type = obj_model.EnumAttribute(RegulatoryElementType)
     activity = obj_model.EnumAttribute(ActivityLevel)
 
     class Meta(obj_model.Model.Meta):