Added gobrowser to smalltest workflow.

workflows/gobrowser.py

@@ -0,0 +1,221 @@
+
+import gtk
+from fluents import dataset, logger, plots, workflow, fluents, project
+import geneontology
+from scipy import array, randn, log, ones, zeros
+import networkx
+import re
+
+EVIDENCE_CODES=[('IMP', 'Inferred from mutant phenotype'),
+                ('IGI', 'Inferred from genetic interaction'),
+                ('IPI', 'Inferred from physical interaction'),
+                ('ISS', 'Inferred from sequence or structure similarity'),
+                ('IDA', 'Inferred from direct assay'),
+                ('IEP', 'Inferred on expression pattern'),
+                ('IEA', 'Inferred from electronic annotation'),
+                ('TAS', 'Traceable author statement'),
+                ('NAS', 'Non-traceable author statement'),
+                ('ND', 'No biological data available'),
+                ('RCA', 'Inferred from reviewed computational analysis'),
+                ('IC', 'Inferred by curator')]
+            
+DISTANCE_METRICS = [('resnik', 'Resnik'), 
+                    ('jiang', 'Jiang & Conrath'),
+                    ('fussimeg', 'FuSSiMeG')]
+
+GO_DATA_DIR = '/home/einarr/data'
+
+evidence = None
+go = None
+
+class GoTermView (gtk.Frame):
+
+    def __init__(self):
+        gtk.Frame.__init__(self)
+        tab = gtk.Table(2, 2, False)
+        self._table = tab
+        
+        self._name = gtk.Label('')
+        self._name.set_line_wrap(True)
+        self._name.set_alignment(0, 0)
+        name_label = gtk.Label('Name:')
+        name_label.set_alignment(0, 0)
+        tab.attach(name_label, 0, 1, 0, 1, gtk.FILL, gtk.FILL, 5, 5)
+        tab.attach(self._name, 1, 2, 0, 1, gtk.FILL|gtk.EXPAND, gtk.FILL, 5, 5)
+        
+        self._def = gtk.TextBuffer()
+        textview = gtk.TextView(self._def)
+        textview.set_wrap_mode(gtk.WRAP_WORD)
+        scrolled_window = gtk.ScrolledWindow()
+        scrolled_window.add(textview)
+        def_label = gtk.Label('Def:')
+        def_label.set_alignment(0.0, 0.0)
+        tab.attach(def_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
+        tab.attach(scrolled_window, 1, 2, 1, 2, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
+        
+        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'])
+            self._def.set_text(term['def'])
+        else:
+            self.set_label('GO Term')
+            self._name.set_text('')
+            self._def.set_text('')
+
+        
+class GeneOntologyTree (gtk.HPaned):
+    
+    def __init__(self, network):
+        gtk.HPaned.__init__(self)
+    
+        treemodel = geneontology.get_go_treestore(network)
+        self._treemodel = treemodel
+        self._tree_view = gtk.TreeView(treemodel)
+
+        self._selected_terms = set()
+
+        self._tree_view.set_fixed_height_mode(True)
+
+        # Set up context menu
+        self._context_menu = GoTermContextMenu(treemodel, self._tree_view)
+        self._tree_view.connect('popup_menu', self._popup_menu)
+        self._tree_view.connect('button_press_event', self._on_button_press)
+
+        renderer = gtk.CellRendererText()
+        go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
+        go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
+        go_column.set_fixed_width(200)
+        go_column.set_resizable(True)
+        self._tree_view.insert_column(go_column, 0)
+
+        renderer = gtk.CellRendererToggle()
+        renderer.set_property('activatable', True)
+        renderer.connect('toggled', self._toggle_selected)
+        renderer.set_active(True)
+        renderer.set_property('mode', gtk.CELL_RENDERER_MODE_ACTIVATABLE)
+        go_column = gtk.TreeViewColumn('T', renderer, active=2)
+        go_column.set_fixed_width(20)
+        go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
+        go_column.set_resizable(True)
+        self._tree_view.insert_column(go_column, 1)
+
+        renderer = gtk.CellRendererText()
+        go_column = gtk.TreeViewColumn('Name', renderer, text=1)
+        go_column.set_fixed_width(200)
+        go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
+        go_column.set_resizable(True)
+        self._tree_view.insert_column(go_column, 2)
+
+        self._desc_view = GoTermView()
+
+        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, 3)
+        self._desc_view.set_go_term(term)        
+        
+
+    ##
+    ## GTK Callback functions
+    ##
+    def _popup_menu(self, *rest):
+        self.menu.popup(None, None, None, 0, 0)
+
+    def _on_button_press(self, widget, event):
+        path = widget.get_path_at_pos(int(event.x), int(event.y))
+        iter = None
+
+        if path:
+            iter = self._treemodel.get_iter(path[0])
+            obj = self._treemodel.get_value(iter, 3)
+        else:
+            obj = None
+
+        self._context_menu.set_current_term(obj, iter)
+
+        if event.button == 3:
+            self._context_menu.popup(None, None, None, event.button, event.time)
+
+    def _toggle_selected(self, renderer, path):
+        iter = self._treemodel.get_iter(path)
+        
+        selected = self._treemodel.get_value(iter, 2)
+        id = self._treemodel.get_value(iter, 0)
+
+        self._treemodel.set_value(iter, 2, not selected)
+
+        if selected:
+            self._selected_terms.remove(id)
+        else:
+            self._selected_terms.add(id)
+
+
+class GoTermContextMenu (gtk.Menu):
+    """Context menu for GO terms in the gene ontology browser"""
+
+    def __init__(self, treemodel, treeview):
+        self._treemodel = treemodel
+        self._treeview = treeview
+        self._current_term = None
+        self._current_iter = None
+
+        gtk.Menu.__init__(self)
+
+        # Popuplate tree
+        self._expand_item = i = gtk.MenuItem('Expand')
+        i.connect('activate', self._on_expand_subtree, treemodel, treeview)
+        self.append(i)
+        i.show()
+
+        self._collapse_item = i = gtk.MenuItem('Collapse')
+        i.connect('activate', self._on_collapse_subtree, treemodel, treeview)
+        self.append(i)
+        i.show()
+
+        self._select_subtree_item = i = gtk.MenuItem('Select subtree')
+        i.connect('activate', self._on_select_subtree, treemodel, treeview)
+        self.append(i)
+        i.show()
+
+    def set_current_term(self, term, it):
+        self._current_term = term
+        self._current_iter = it
+
+    def _on_expand_subtree(self, item, treemodel, treeview):
+        path = treemodel.get_path(self._current_iter)
+        treeview.expand_row(path, True)
+
+    def _on_collapse_subtree(self, item, treemodel, treeview):
+        treeview.collapse_row(treemodel.get_path(self._current_iter))
+
+    def _on_select_subtree(self, item, treemodel, treeview):
+        logger.log('notice', 'Selecting subtree from GO id: %s (%s)' %
+                   (self._current_term['id'], self._current_term['name']))
+        ids = [x['id'] for x in networkx.bfs(go, self._current_term)]
+        project.project.set_selection('go-terms', set(ids))
+
+
+class LoadGOFunction(workflow.Function): 
+    def __init__(self):
+        workflow.Function.__init__(self, 'load-go', 'Load Gene Ontology')
+
+    def run(self):
+        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)
+

workflows/smalltest.py

@@ -3,6 +3,7 @@ import webbrowser
 
 from fluents import logger, plots,workflow,dataset
 from fluents.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
+import gobrowser, geneontology
 import scipy
 
 
@@ -40,6 +41,10 @@ class SmallTestWorkflow(workflow.Workflow):
         query.add_function(KEGGQuery())
         self.add_stage(query)
         
+        go = workflow.Stage('go', 'Gene Ontology')
+        go.add_function(gobrowser.LoadGOFunction())
+        self.add_stage(go)
+
         # EXTRA PLOTS
         #plt = workflow.Stage('net', 'Network')
         #plt.add_function(nx_analyser.KeggNetworkAnalyser())