Add attributes to RegulatoryModule class to cover available data

tests/test_eukaryote_schema.py

@@ -501,12 +501,29 @@ def test_constructor(self):
         promoter = eukaryote_schema.RegulatoryElementLocus(polymer=dna1, start=6, end=8)
         enhancer = eukaryote_schema.RegulatoryElementLocus(polymer=dna1, start=2, end=4)
 
+        tf = eukaryote_schema.ProteinSpeciesType(id='tf')
+
         reg_module1 = eukaryote_schema.RegulatoryModule(gene=gene1, 
-            regulatory_elements=[promoter, enhancer])
-        reg_module2 = eukaryote_schema.RegulatoryModule(gene=gene2, 
-            regulatory_elements=[enhancer])
+            regulatory_element=promoter, binding_factor=tf, 
+            type=eukaryote_schema.RegulationType.proximal, 
+            direction=eukaryote_schema.RegulatoryDirection.positive)
+        reg_module2 = eukaryote_schema.RegulatoryModule(gene=gene1, 
+            regulatory_element=enhancer, binding_factor=tf, 
+            type=eukaryote_schema.RegulationType.distal, 
+            direction=eukaryote_schema.RegulatoryDirection.negative)
+        reg_module3 = eukaryote_schema.RegulatoryModule(id='rm3', name='reg_module3', 
+            gene=gene2, regulatory_element=enhancer)
 
         self.assertEqual(reg_module1.gene, gene1)
-        self.assertEqual(reg_module1.regulatory_elements, [promoter, enhancer])
-        self.assertEqual(reg_module2.gene, gene2)
-        self.assertEqual(reg_module2.regulatory_elements, [enhancer])
+        self.assertEqual(reg_module1.regulatory_element, promoter)
+        self.assertEqual(reg_module1.binding_factor, tf)
+        self.assertEqual(reg_module1.type.value, 1)
+        self.assertEqual(reg_module1.direction.value, 1)
+        self.assertEqual(reg_module2.gene, gene1)
+        self.assertEqual(reg_module2.regulatory_element, enhancer)
+        self.assertEqual(reg_module2.binding_factor, tf)
+        self.assertEqual(reg_module2.type.value, 2)
+        self.assertEqual(reg_module2.direction.value, -1)
+        self.assertEqual(reg_module3.id, 'rm3')
+        self.assertEqual(reg_module3.name, 'reg_module3')
+        self.assertEqual(set([i.gene for i in enhancer.regulatory_modules]), set([gene1, gene2]))

wc_kb/eukaryote_schema.py

@@ -29,13 +29,26 @@ class RegulatoryElementType(enum.Enum):
 
 
 class ActivityLevel(enum.Enum):
+    """ Activity level of regulatory element"""
     active = 1
     poised = 2
     repressed = 3
     inactive = 4
     na = 5
 
 
+class RegulationType(enum.Enum):
+    """ Type of regulation between a regulatory element and a gene """
+    proximal = 1
+    distal = 2
+
+
+class RegulatoryDirection(enum.Enum):
+    """ The direction of regulation """
+    positive = 1
+    negative = -1
+
+
 #####################
 #####################
 # Locus types
@@ -50,7 +63,7 @@ class GeneLocus(core.PolymerLocus):
 
     Related attributes:
         rna (:obj:`list` of :obj:`PreRnaSpeciesType`): rna
-        regulatory_modules (:obj:`RegulatoryModule`): regulatory_modules
+        regulatory_modules (:obj:`list` of `RegulatoryModule`): regulatory_modules
     """
     symbol = obj_model.StringAttribute()
     type = obj_model.EnumAttribute(core.GeneType)
@@ -108,30 +121,41 @@ class RegulatoryElementLocus(core.PolymerLocus):
     motif_features = obj_model.ManyToManyAttribute('ProteinSpeciesType', related_name='regulatory_elements')
 
     class Meta(obj_model.Model.Meta):
-        attribute_order = ('id', 'polymer', 'name', 'type', 'activity', 
+        attribute_order = ('id', 'polymer', 'name', 'type', 'activity', 'strand', 
                            'start', 'end', 'bound_start', 'bound_end', 'motif_features', 
                            'comments', 'references', 'database_references')
 
 
 class RegulatoryModule(obj_model.Model):
     """ Knowledge about regulatory modules
 
-    Attributes:        
+    Attributes:
+        id (:obj:`str`): identifier
+        name (:obj:`str`): name        
         gene (:obj:`GeneLocus`): gene
-        regulatory_elements (:obj:`list` of :obj:`RegulatoryElementLocus`): regulatory elements
+        regulatory_element (:obj:`RegulatoryElementLocus`): regulatory element
+        binding_factor (:obj:`ProteinSpeciesType`): binding factor
+        type (:obj:`RegulationType`): type of regulation (proximal or distal)
+        direction (:obj:`RegulatoryDirection`): direction of regulation
         comments (:obj:`str`): comments
         references (:obj:`list` of :obj:`Reference`): references
         database_references (:obj:`list` of :obj:`DatabaseReference`): database references
     """
-    gene = obj_model.OneToOneAttribute(GeneLocus, related_name='regulatory_modules')
-    regulatory_elements = obj_model.ManyToManyAttribute(
+    id = obj_model.SlugAttribute(primary=True, unique=True)
+    name = obj_model.StringAttribute()
+    gene = obj_model.ManyToOneAttribute(GeneLocus, related_name='regulatory_modules')
+    regulatory_element = obj_model.ManyToOneAttribute(
         RegulatoryElementLocus, related_name='regulatory_modules')
+    binding_factor = obj_model.ManyToOneAttribute('ProteinSpeciesType', related_name='regulatory_modules')
+    type = obj_model.EnumAttribute(RegulationType)
+    direction = obj_model.EnumAttribute(RegulatoryDirection)
     comments = obj_model.LongStringAttribute()
     references = obj_model.ManyToManyAttribute(core.Reference, related_name='regulatory_modules')
     database_references = core.DatabaseReferenceAttribute(related_name='regulatory_modules')    
 
     class Meta(obj_model.Model.Meta):
-        attribute_order = ('gene', 'regulatory_elements', 'comments', 'references', 'database_references')
+        attribute_order = ('id', 'name', 'gene', 'regulatory_element', 'binding_factor', 'type', 
+                            'direction', 'comments', 'references', 'database_references')
 
 
 #####################
@@ -314,10 +338,11 @@ class ProteinSpeciesType(core.PolymerSpeciesType):
     Attributes:
         uniprot (:obj:`str`): uniprot id
         transcript (:obj:`TranscriptSpeciesType`): transcript
-        coding_regions (:obj:1list` of :obj:`CdsLocus`): CDS Loci
+        coding_regions (:obj:`list` of :obj:`CdsLocus`): CDS Loci
 
     Related attributes:
-        regulatory_elements (:obj:`RegulatoryElementLocus`): protein binding sites    
+        regulatory_elements (:obj:`list` of `RegulatoryElementLocus`): potential binding sites
+        regulatory_modules (:obj:`list` of `RegulatoryModule`): regulatory DNA binding sites    
     """
 
     uniprot = obj_model.StringAttribute()