Add ploidy attribute to DNA species type

KarrLab · Nov 25, 2018 · be574a7 · be574a7
1 parent e5834e7
commit be574a7
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/tests/fixtures/core.xlsx b/tests/fixtures/core.xlsx
diff --git a/tests/fixtures/eukaryote_core.xlsx b/tests/fixtures/eukaryote_core.xlsx
diff --git a/tests/test_core.py b/tests/test_core.py
@@ -167,12 +167,13 @@ def get_seq(self): return Bio.Seq.Seq(
 class DnaSpeciesTypeTestCase(unittest.TestCase):
     def test(self):
         dna = core.DnaSpeciesType(id='dna1', name='dna1', seq=Bio.Seq.Seq('ACGTACGT', alphabet=Bio.Alphabet.DNAAlphabet()),
-                                  circular=False, double_stranded=False)
+                                  circular=False, double_stranded=False, ploidy=2)
 
         self.assertEqual(dna.id, 'dna1')
         self.assertEqual(dna.name, 'dna1')
         self.assertEqual(dna.circular, False)
         self.assertEqual(dna.double_stranded, False)
+        self.assertEqual(dna.ploidy, 2)
 
         L = dna.get_len()
         self.assertEqual(dna.get_empirical_formula(),

diff --git a/wc_kb/core.py b/wc_kb/core.py
@@ -1258,7 +1258,7 @@ class PolymerSpeciesType(SpeciesType):
     double_stranded = obj_model.BooleanAttribute()
 
     class Meta(obj_model.Model.Meta):
-        attribute_order = ('id', 'name', 'circular', 'double_stranded',
+        attribute_order = ('id', 'name', 'circular', 'double_stranded', 
                            'half_life', 'comments', 'references', 'database_references')
 
     @abc.abstractmethod
@@ -1559,10 +1559,11 @@ class DnaSpeciesType(PolymerSpeciesType):
     """
 
     seq = obj_model.extra_attributes.BioSeqAttribute(verbose_name='Sequence')
+    ploidy = obj_model.IntegerAttribute(min=0)
 
     class Meta(obj_model.Model.Meta):
-        attribute_order = ('id', 'name', 'seq', 'circular',
-                           'double_stranded', 'half_life', 'comments', 'references', 'database_references')
+        attribute_order = ('id', 'name', 'seq', 'circular', 'double_stranded', 
+            'ploidy', 'half_life', 'comments', 'references', 'database_references')
         verbose_name = 'DNA species type'
 
     def get_seq(self, start=None, end=None):