Removed obsolete module annotations.

system/annotations.py

@@ -1,93 +0,0 @@
-
-from sets import Set as set
-set.update = set.union_update
-import dataset
-import scipy
-
-
-class AnnotationsException(Exception):
-    pass
-
-class Annotations:
-    def __init__(self, *dimensions):
-        """ Initializes a new Annotation with the given dimension labels.
-        dimensions is a list of dimension labels.
-        """ 
-        if len(dimensions) != 2:
-            msg = 'Annotations only supports two dimensions.'
-            raise AnnotationsException(msg)
-
-        self.dimensions = {}
-        for d in dimensions:
-            self.dimensions[d] = {}
-
-    def add_annotations(self, dim, id, ann_dim, annotations):
-        """ Adds new annotations.
-        dim: the dimension in which the new data should be added.
-        id: the identifier that should be annotated.
-        ann_dim: the dimension of the annotations to id.
-        annotations: the new annotations to id.
-        Returns the total set of annotations to id.
-        """
-        if not self.has_dimension(dim):
-            msg = 'Annotations object does not contain dimension %s' % dim
-            raise AnnotationsException(msg)
-
-        if not self.has_dimension(ann_dim):
-            msg = 'Annotations object does not contain dimension %s' % ann_dim
-            raise AnnotationsException(msg)
-
-        for a in annotations:
-            if not self.dimensions[ann_dim].has_key(a):
-                self.dimensions[ann_dim][a] = set()
-            self.dimensions[ann_dim][a].add(id)
-
-        if not self.dimensions[dim].has_key(id):
-            self.dimensions[dim][id] = set()
-        self.dimensions[dim][id].update(annotations)
-
-        return self.dimensions[dim][id]
-        
-    def get_annotations(self, dim, id, ann_dim):
-        """Returns all annotations to id.
-        dim: the dimension where id can be found.
-        id: the id to retrieve annotations for.
-        """
-        if not self.has_dimension(dim):
-            msg = 'Annotations object does not contain dimension %s' % dim
-            raise AnnotationsException(msg)
-
-        if self.dimensions[dim].has_key(id):
-            return self.dimensions[dim][id]
-        return set()
-
-    def has_dimension(self, dim):
-        """ Retuns true if the Annotations object indexes dim.
-        """
-        return self.dimensions.has_key(dim)
-
-    def to_dataset(self,dim):
-        """ Returns a dataset representation of annotations.
-        """
-        if self.has_dimension(dim):
-            num_dim1 = len(set(self.dimensions[dim])) #number of unique genes
-            all_genes = set(self.dimensions[dim])
-            all_categories = set()
-            for cat in self.dimensions[dim].values():
-                all_categories.update(cat)
-            num_dim1 = len(all_genes) #number of unique genes
-            num_dim2 = len(all_categories) #number of unique categories
-            gene_list=[]
-            cat_list=[]
-        matrix = scipy.zeros((num_dim1,num_dim2),'bwu')
-        for i,gene in enumerate(all_genes):
-            gene_list.append(gene)
-            for j,cat in enumerate(all_categories):
-                cat_list.append(cat)
-                matrix[i,j] = 1
-        def_list = [['genes',gene_list],['go',cat_list]]
-
-        return dataset.Dataset(matrix,def_list)
-        
-        
-    

workflows/go_workflow.py

@@ -1,16 +1,16 @@
 import gtk
 from system import dataset, logger, plots, workflow
-from system.annotations import Annotations
 #import geneontology
 #import gostat
 from scipy import array,randn,log
 import cPickle
 
-class EinarsWorkflow (workflow.Workflow):
+class GOWorkflow (workflow.Workflow):
 
-    name = 'Test Workflow'
+    name = 'Gene Ontology Workflow'
     ident = 'go'
     description = 'Gene Ontology Workflow. This workflow currently serves as a general testing workflow.'
+
     def __init__(self, app):
         workflow.Workflow.__init__(self, app)
 
@@ -26,7 +26,6 @@ class EinarsWorkflow (workflow.Workflow):
         self.add_stage(preproc)
 
         go = workflow.Stage('go', 'Gene Ontology Data')
-        go.add_function(LoadAnnotationsFunction())
         go.add_function(GODistanceFunction())
         self.add_stage(go)
 
@@ -42,8 +41,6 @@ class EinarsWorkflow (workflow.Workflow):
         save.add_function(DatasetSaveFunction())
         self.add_stage(save)
         
-        logger.log('debug', '\tEinar\'s workflow is now active')
-
 class LoadAnnotationsFunction(workflow.Function):
 
     def __init__(self):