Updated GO workflow.

workflows/geneontology.py

@@ -1,3 +1,5 @@
+import gobject
+import gtk
 import networkx
 import re
 
@@ -38,15 +40,18 @@ class GeneOntology(networkx.XDiGraph):
     def link_ontology(self, linkattr, obsolete=False):
         for node in self.nodes():
             for link in node[linkattr]:
-                self.add_edge(node, self.by_id[link], linkattr)
+                self.add_edge(self.by_id[link], node, linkattr)
 
     def get_bp(self):
+        """Returns the root node of the biological_process tree"""
         return self.by_id['GO:0008150']
 
     def get_cc(self):
+        """Returns the root node of the cellular_component tree"""
         return self.by_id['id: GO:0005575']
 
     def get_mf(self):
+        """Returns the root node of the molecular_function tree"""
         return self.by_id['GO:0003674']
 
 
@@ -106,7 +111,7 @@ def read_gene_ontology(fd):
             section = s
             if s == 'Term':
                 term = GOTerm()
-                print "[Term]"
+#                print "[Term]"
             else:
                 term = None
                 print "ignoring: %s" %s
@@ -116,7 +121,7 @@ def read_gene_ontology(fd):
 #                print "    %s: %s" % (k, v)
             else:
                 print "no term: ignoring: %s" %line
-        print '.',
+#        print '.',
         line = fd.readline()
 
     if term:
@@ -127,6 +132,68 @@ def read_gene_ontology(fd):
 def read_default_go():
     f = open("/usr/share/gene-ontology/gene_ontology.obo")
     go = read_gene_ontology(f)
-
+    go.link_ontology('is_a')
     f.close()
     return go
+
+def _add_subgraphs(treestore, ontology, parent, nodes):
+    for n in nodes:
+        i = treestore.insert(parent, 0, (n['id'], n['name'], n))
+        _add_subgraphs(treestore, ontology, i, ontology.successors(n))
+
+def get_go_treestore(ontology):
+    ts = gtk.TreeStore(gobject.TYPE_STRING,   ## ID
+                       gobject.TYPE_STRING,   ## Name
+                       gobject.TYPE_PYOBJECT) ## Node
+    _add_subgraphs(ts, ontology, None, [ontology.get_bp()])
+    return ts
+
+class NetworkTreeModel(gtk.GenericTreeModel):
+        
+    def __init__(self, network, root):
+        gtk.GenericTreeModel.__init__(self) 
+        self._network = network
+        self._root = root
+
+    def on_get_flags(self):
+        return 0
+
+    def on_get_n_columns(self):
+        return 1
+
+    def on_get_column_type(self, index):
+        if index==0:
+            return gobject.TYPE_STRING
+
+    def on_get_iter(self, path):
+        node = self._root
+        for p in path[1:]:
+            children = self._network.predecessors(node)
+            node = children[p]
+        return node
+
+    def on_get_path(self, rowref):
+        pass
+
+    def on_get_value(self, rowref, column):
+        print 'get_value'
+        return rowref['id']
+
+    def on_iter_next(self, rowref):
+        pass
+
+    def on_iter_children(self, parent):
+        pass
+
+    def on_iter_has_child(self, rowref):
+        pass
+
+    def on_iter_n_children(self, rowref):
+        pass
+
+    def on_iter_nth_child(self, parent, n):
+        pass
+
+    def on_iter_parent(self, child):
+        pass
+    

workflows/go_workflow.py

@@ -1,6 +1,6 @@
 import gtk
 from fluents import dataset, logger, plots, workflow, fluents
-#import geneontology
+import geneontology
 #import gostat
 from scipy import array, randn, log, ones
 import networkx
@@ -9,20 +9,59 @@ class GoTermView (gtk.Frame):
 
     def __init__(self):
         gtk.Frame.__init__(self)
-        self.set_label('GO Term')
+        tab = gtk.Table(2, 2, False)
+        self._table = tab
+        
+        self._name = gtk.Label('')
+        tab.attach(gtk.Label('Name:'), 0, 1, 0, 1)
+        tab.attach(self._name, 1, 2, 0, 1)
+        
+        self.add(tab)
+        self.set_go_term(None)
+
+    def set_go_term(self, term):
+        if term:
+            self.set_label(term['id'])
+            self._name.set_text(term['name'])
+        else:
+            self.set_label('GO Term')
+            self._name.set_text('')
 
         
 class GeneOntologyTree (gtk.HPaned):
     
-    def __init__(self):
+    def __init__(self, network):
         gtk.HPaned.__init__(self)
-        self._tree_view = gtk.TreeView()
+    
+        treemodel = geneontology.get_go_treestore(network)
+        self._treemodel = treemodel
+        self._tree_view = gtk.TreeView(treemodel)
+
+        renderer = gtk.CellRendererText()
+        go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
+        self._tree_view.insert_column(go_column, 0)
+
+        renderer = gtk.CellRendererText()
+        go_column = gtk.TreeViewColumn('Name', renderer, text=1)
+        self._tree_view.insert_column(go_column, 1)
+
         self._desc_view = GoTermView()
 
-        self.add1(self._tree_view)
+        self._tree_view.connect('cursor-changed', self._on_cursor_changed)
+
+        scrolled_window = gtk.ScrolledWindow()
+        scrolled_window.add(self._tree_view)
+        self.add1(scrolled_window)
         self.add2(self._desc_view)
         self.show_all()
 
+    def _on_cursor_changed(self, tree):
+        path, col = self._tree_view.get_cursor()
+        current = self._treemodel.get_iter(path)
+        term = self._treemodel.get_value(current, 2)
+        self._desc_view.set_go_term(term)        
+        
+
 class GoWorkflow (workflow.Workflow):
 
     name = 'Gene Ontology'
@@ -44,7 +83,9 @@ class LoadGOFunction(workflow.Function):
         workflow.Function.__init__(self, 'load-go', 'Load Gene Ontology')
 
     def run(self):
-        browser = GeneOntologyTree()
+        global go
+        go = geneontology.read_default_go()
+        browser = GeneOntologyTree(go)
         label = gtk.Label('_Gene Ontology')
         label.set_use_underline(True)
         fluents.app['bottom_notebook'].append_page(browser, label)