* fluent: General cleanup.

workflows/go_workflow.py

@@ -2,6 +2,9 @@ import gtk
 import logger
 from annotations import Annotations
 from workflow import *
+import geneontology
+import gostat
+from scipy import array
 
 class EinarsWorkflow (Workflow):
 
@@ -19,7 +22,7 @@ class EinarsWorkflow (Workflow):
 
         go = Stage('go', 'Gene Ontology Data')
         go.add_function(LoadAnnotationsFunction())
-        go.add_function(Function('godist', 'GO Distances'))
+        go.add_function(GODistanceFunction())
         self.add_stage(go)
 
         regression = Stage('regression', 'Regression')
@@ -37,6 +40,7 @@ class LoadAnnotationsFunction(Function):
     def load_file(self, filename):
         f = open(filename)
         self.annotations = Annotations('genes', 'go-terms')
+        logger.log('notice', 'Loading annotation file: %s' % filename)
 
         for line in f.readlines():
             val = line.split(' \t')
@@ -61,3 +65,21 @@ class LoadAnnotationsFunction(Function):
         dialog.destroy()
         return [self.annotations]
 
+class GODistanceFunction(Function):
+
+    def __init__(self):
+        Function.__init__(self, 'go_diatance', 'GO Distances')
+        self.output = None
+
+    def run(self, data):
+        logger.log('debug', 'datatype: %s' % type(data))
+        if not type(data) == Annotations:
+            return None
+
+        logger.log('debug', 'dimensions: %s' % data.dimensions)
+        
+        genes = data.get_ids('genes')
+        gene_distances = array((len(genes), len(genes)))
+
+        return gene_distances
+