Implemented PhenotypeDataset with tests.

test/workflows/affy_workflowtest.py

@@ -0,0 +1,81 @@
+import unittest
+import sys
+
+sys.path.append("../..")
+from workflows.affy_workflow import PhenotypeDataset
+
+class PhenotypeDatasetTest(unittest.TestCase):
+    def testEmptyData(self):
+        # we have a list of cel-files, but no categories
+        cel_data = """\
+CEL
+02-05-33
+03-07-38
+"""
+        dataset = PhenotypeDataset(cel_data)
+        self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
+        self.assertEquals(['02-05-33', '03-07-38'], dataset.get_identifiers('CEL'))
+        self.assertEquals([], dataset.get_identifiers('phenotypes'))
+
+    def testFloatData(self):
+        cel_data = """\
+CEL\tage
+02-05-33\t8
+03-07-38\t9
+"""
+        dataset = PhenotypeDataset(cel_data)
+        self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
+        self.assertEquals(['age'], dataset.get_identifiers('phenotypes'))
+        self.assertEquals([[8],
+                           [9]], dataset.asarray().tolist())
+
+    def testCategoryData(self):
+        """Categories expand to one numeric column for each category choice."""
+        cel_data = """\
+CEL\tsick
+02-05-33\tyes
+03-07-38\tno
+04-93-33\tyes
+08-32-33\tmaybe
+"""
+        dataset = PhenotypeDataset(cel_data)
+        self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
+        self.assertEquals(['sick-yes', 'sick-no', 'sick-maybe'], dataset.get_identifiers('phenotypes'))
+        self.assertEquals([[1, 0, 0],
+                           [0, 1, 0],
+                           [1, 0, 0],
+                           [0, 0, 1]], dataset.asarray().tolist())
+
+    def testMultipleCategoriesAndFloats(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(['sex-F', 'sex-M', 'age', 'infected-I', 'infected-N'],
+                          dataset.get_identifiers('phenotypes'))
+
+        self.assertEquals([[1, 0, 8, 1, 0],
+                           [1, 0, 9, 0, 1],
+                           [0, 1, 8, 1, 0]], dataset.asarray().tolist())
+
+    def testGetPhenotypeTable(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([['CEL', 'sex', 'age', 'infected'],
+                           ['02-05-33', 'F', '8', 'I'],
+                           ['02-05-34', 'F', '9', 'N'],
+                           ['02-05-35', 'M', '8', 'I']], dataset.get_phenotype_table())
+
+
+
+if __name__=='__main__':
+    unittest.main()