Implemented Dataset.get_indices() and extended Dataset.get_identifiers() to convert between indices and identifiers and subsets thereof.

Also added tests.

system/dataset.py

@@ -172,13 +172,28 @@ class Dataset:
         """Returns dim names""" 
         return [dim for dim in self._dims]
 
-    def get_identifiers(self,dim):
-        """Returns identifiers aling dim, sorted by position (index)"""
+    def get_identifiers(self, dim, indices=None):
+        """Returns identifiers along dim, sorted by position (index).
+
+        You can optionally provide a list of indices to get only the
+        identifiers of a given position.
+        """
         items = self._map[dim].items()
         backitems=[ [v[1],v[0]] for v in items]
         backitems.sort()
         sorted_ids=[ backitems[i][1] for i in range(0,len(backitems))]
-        return tuple(sorted_ids)
+
+        if indices != None:
+            return [sorted_ids[index] for index in indices]
+        else:
+            return sorted_ids
+
+    def get_indices(self, dim, idents):
+        """Get indices for identifiers along dimension."""
+        reverse = {}
+        for key, value in self._map[dim].items():
+            reverse[value] = key
+        return [self._map[dim][key] for key in idents]
      
 
 class CategoryDataset(Dataset):

test/system/datasettest.py

@@ -21,6 +21,24 @@ class DatasetTest(unittest.TestCase):
         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]))
+        # other dimension
+        self.assertEquals(['sample_a', 'sample_b'], data.get_identifiers('samples', [0, 1]))
         
     #def testExtraction(self):
     #    ids = ['gene_a','gene_b']