s

system/dataset.py

@@ -43,6 +43,9 @@ class Dataset:
             if len(df)!=d and df:
                 raise ValueError,"dim size and identifyer mismatch"
             
+    def __str__(self):
+        self.name = 'Arnar'
+        return self.name
     def names(self,axis=0):
         """Returns identifier names of a dimension.
         NB: sorted by values!

workflows/pca_workflow.py

@@ -54,8 +54,24 @@ class LoadAnnotationsFunction(Function):
         dialog.run()
         dialog.destroy()
 
-        ### Reading and aprsing here
+        ### Reading and parsing here
         annot = read_affy_annot(self.file)
+        i_want = 'Pathway'
+        nothing = '---'
+        ids_in_data = set(data.names('genes')) #assuming we have genes
+        sanity_check = set(annot.keys())
+        if not ids_in_data.intersection(sanity_check) == ids_in_data:
+            logger.log('debug','Some identifers in data does not exist in affy file!')
+        for affy_id,description in annot:
+            if affy_id in ids_in_data:
+                pathways = desc[i_want]:
+                    if not pathways[0][0]=='--':
+                        
+                    
+                    
+            
+            
+        
         return [self.annotations]
 
 class PCAFunction(Function):