Added categorygetter for PhenotypeDataset.

test/workflows/affy_workflowtest.py

@@ -75,6 +75,17 @@ CEL\tsex\tage\tinfected
                            ['02-05-34', 'F', '9', 'N'],
                            ['02-05-35', 'M', '8', 'I']], dataset.get_phenotype_table())
 
+    def testGetCategories(self):
+        cel_data = """\
+CEL\tsex\tage\tinfected
+02-05-33\tF\t8\tI
+02-05-34\tF\t9\tN
+02-05-35\tM\t8\tI
+"""
+        dataset = PhenotypeDataset(cel_data)
+
+        self.assertEquals(set(['F', 'M', 'I', 'N']), set(dataset.get_categories()))
+
 
 
 if __name__=='__main__':

workflows/affy_workflow.py

@@ -231,6 +231,7 @@ class PhenotypeDataset(dataset.Dataset):
         col_names = rows[0][1:]
         phenotypes = []
         categories = {}
+        self._categories = set()
 
         for col_name, column in zip(col_names, columns[1:]):
             try:
@@ -247,8 +248,8 @@ class PhenotypeDataset(dataset.Dataset):
 
                     entries[entry].append(i)
                     
-
                 for key in keys:
+                    self._categories.add(key)
                     z = zeros(len(column))
                     for i in entries[key]:
                         z[i] = 1
@@ -269,6 +270,14 @@ class PhenotypeDataset(dataset.Dataset):
                                                        ('phenotypes', phenotypes)],
                                  shape=(len(cel_names),len(phenotypes)), name="Phenotype Data")
             
-
     def get_phenotype_table(self):
+        """Get string based table of phenotypes as read from file."""
         return self._table
+
+    def get_categories(self):
+        """Get categories of factors.
+
+        If factor 'sick' had possibilites Y/N, and 'sex' M/F, the
+        categories would be Y, N, M and F.
+        """
+        return self._categories