Added read_annotations_file()

test/fluents/annotationtest.py

@@ -0,0 +1,62 @@
+
+import unittest
+import sys
+sys.path.append('../../')
+from fluents import annotations
+
+class AnnotationsTest(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def testAddAnnotations(self):
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        assert annotations.get_dim_handler('go-terms') == h
+        assert annotations.get_dim_handler('foobar') == None
+
+    def testGetDimAnnotations(self):
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        d = {'GO:0': 'biological_process',
+             'GO:1': 'foo',
+             'GO:2': 'bar'}
+        h.add_annotations('name', d)
+        
+        ann0 = annotations.get_dim_annotations('go-terms', 'name', [])
+        assert ann0 == []
+
+        ann1 = annotations.get_dim_annotations('go-terms', 'name', ['GO:0'])
+        assert len(ann1) == 1
+        assert ann1[0] == 'biological_process'
+
+        ann2 = annotations.get_dim_annotations('go-terms', 'name', ['GO:1', 'baz'])
+        assert len(ann2) == 2
+        assert ann2 == ['foo', None]
+
+    def testDictAnnotationHandler(self):
+        h = annotations.DictAnnotationHandler()
+        annotations.set_dim_handler('go-terms', h)
+        d = {'GO:0': 'biological_process',
+             'GO:1': 'foo',
+             'GO:2': 'bar'}
+        h.add_annotations('name', d)
+        
+        ann0 = h.get_annotations('name', [])
+        assert ann0 == []
+        
+        ann1 = h.get_annotations('name', ['unexisting'])
+        assert ann1 == [None]
+        
+        ann2 = h.get_annotations('name', ['unexisting'], 42)
+        assert ann2 == [42]
+
+        assert h.get_annotation_names() == ['name']
+
+    def testReadAnnotationsFile(self):
+        ann = annotations.read_annotations_file('../data/annotations.fann')
+        assert ann != None
+        assert ann == annotations.get_dim_handler('dim1')
+
+if __name__ == '__main__':
+    unittest.main()

test/fluents/datasettest.py

@@ -0,0 +1,56 @@
+import unittest
+import sys
+sys.path.append('../..')
+from system.dataset import *
+from scipy import rand,shape, array
+
+class DatasetTest(unittest.TestCase):
+    
+    def setUp(self):
+        dim_0_ids = ('sample_a','sample_b')
+        dim_1_ids = ('gene_a','gene_b','gene_c')
+        dim_labels = ('samples','genes')
+        identifiers= [(dim_labels[0],dim_0_ids),(dim_labels[1],dim_1_ids)]
+        self.array = rand(2,3)
+        self.testdata = Dataset(self.array,identifiers)
+
+    def testCreation(self):
+        data = self.testdata
+        assert data._array == self.array
+        assert 'sample_a' in data['samples'].keys()
+        assert data['samples']['sample_b']==1
+        assert 'gene_c' in data['genes'].keys()
+        assert data['genes']['gene_c']==2
+
+    def testLookupIndicesOfIdentifiers(self):
+        data = self.testdata
+        # base case
+        self.assertEquals([0, 1, 2], data.get_indices('genes', ['gene_a', 'gene_b', 'gene_c']))
+        # "advanced" lookup
+        self.assertEquals([2, 0], data.get_indices('genes', ['gene_c', 'gene_a']))
+        # other dimension
+        self.assertEquals([0, 1], data.get_indices('samples', ['sample_a', 'sample_b']))
+
+    def testLookupIdentifiersOfIndices(self):
+        data = self.testdata
+        # base case
+        self.assertEquals(['gene_a', 'gene_b', 'gene_c'], data.get_identifiers('genes', [0, 1, 2]))
+        # "advanced" lookup
+        self.assertEquals(['gene_c', 'gene_a'], data.get_identifiers('genes', [2, 0]))
+        # handle empty matrix of indices
+        self.assertEquals([], data.get_identifiers('samples', array([])))
+        # other dimension
+        self.assertEquals(['sample_a', 'sample_b'], data.get_identifiers('samples', [0, 1]))
+        
+        
+    #def testExtraction(self):
+    #    ids = ['gene_a','gene_b']
+    #    dim_name = 'genes'
+    #    subset = self.testdata.extract_data(ids,dim_name)
+    #    assert shape(subset._data) == (2,2)
+    #    assert subset.ids[dim_name].keys() == ids
+    #    assert subset.ids[dim_name].values() == [0,1]
+
+
+if __name__ == '__main__':
+    unittest.main()