Updated GO workflow. Options class test added. Reading the ontology takes too

long.

workflows/go_workflow.py

@@ -5,6 +5,23 @@ import geneontology
 from scipy import array, randn, log, ones
 import networkx
 
+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')]
+
 class GoTermView (gtk.Frame):
 
     def __init__(self):
@@ -13,8 +30,22 @@ class GoTermView (gtk.Frame):
         self._table = tab
         
         self._name = gtk.Label('')
-        tab.attach(gtk.Label('Name:'), 0, 1, 0, 1)
+        self._name.set_line_wrap(True)
-        tab.attach(self._name, 1, 2, 0, 1)
+        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)
@@ -23,9 +54,11 @@ class GoTermView (gtk.Frame):
         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):
@@ -77,6 +110,10 @@ class GoWorkflow (workflow.Workflow):
         load.add_function(LoadAnnotationsFunction())
         self.add_stage(load)
         
+        go = workflow.Stage('go', 'Gene Ontology')
+        go.add_function(GoDistanceFunction())
+        self.add_stage(go)
+
        
 class LoadGOFunction(workflow.Function): 
     def __init__(self):
@@ -90,6 +127,7 @@ class LoadGOFunction(workflow.Function):
         label.set_use_underline(True)
         fluents.app['bottom_notebook'].append_page(browser, label)
 
+
 class LoadAnnotationsFunction(workflow.Function):
 
     def __init__(self):
@@ -124,3 +162,118 @@ class LoadAnnotationsFunction(workflow.Function):
         dialog.destroy()
         return [self.annotations]
 
+
+class EvidenceCodeFrame(gtk.Frame):
+    def __init__(self):
+        gtk.Frame.__init__(self, 'Evidence Codes')
+
+        self._ec_buttons = {}
+
+        vbox = gtk.VBox(len(EVIDENCE_CODES))
+        for code, desc in EVIDENCE_CODES:
+            btn = gtk.CheckButton('%s (%s)' % (code, desc))
+            self._ec_buttons[code] = btn
+            vbox.add(btn)
+        self.add(vbox)
+
+    def set_options(self, options):
+        for code, desc in EVIDENCE_CODES:
+            self._ec_buttons[code].set_active(options[code])
+
+    def update_options(self, options):
+        for code, desc in EVIDENCE_CODES:
+            options[code] = self._ec_buttons[code].get_active()
+        return options
+
+
+class DistanceMetricFrame(gtk.Frame):
+    def __init__(self):
+        gtk.Frame.__init__(self, 'Distance Metrics')
+
+        self._metric_buttons = {}
+
+        vbox = gtk.VBox(len(DISTANCE_METRICS))
+        prev = None
+        for code, text in DISTANCE_METRICS:
+            btn = gtk.RadioButton(prev, '%s' % text)
+            self._metric_buttons[code] = btn
+            vbox.add(btn)
+            prev = btn
+        self.add(vbox)
+
+    def set_options(self, options):
+        self._metric_buttons[options['metric']].set_active(True)
+
+    def update_options(self, options):
+        for code, text in DISTANCE_METRICS:
+            if self._metric_buttons[code].get_active():
+                options['metric'] = code
+                return options
+        return options
+
+
+class GoDistanceDialog(gtk.Dialog):
+
+    def __init__(self):
+        gtk.Dialog.__init__(self, 'GO term distance matrix',
+                            None,
+                            gtk.DIALOG_MODAL | gtk.DIALOG_DESTROY_WITH_PARENT,
+                            (gtk.STOCK_OK, gtk.RESPONSE_OK,
+                             gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
+
+        self._ec_frame = EvidenceCodeFrame()
+        self._metric_frame = DistanceMetricFrame()
+        self.vbox.add(self._ec_frame)
+        self.vbox.add(self._metric_frame)
+
+    def run(self):
+        self.vbox.show_all()
+        return gtk.Dialog.run(self)
+ 
+    def set_options(self, options):
+        self._ec_frame.set_options(options)
+        self._metric_frame.set_options(options)
+
+    def update_options(self, options):
+        self._ec_frame.update_options(options)
+        self._metric_frame.update_options(options)
+        return options
+    
+    def set_editable(self, editable):
+        self._ec_frame.set_sensitive(editable)
+        self._metric_frame.set_sensitive(editable)
+
+
+class GoDistanceFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'go-dist', 'GO term distance matrix')
+        self.options = GoDistanceOptions()
+        
+    def run(self, data):
+        self.options = self.show_gui(self.options)
+
+    def show_gui(self, options, edit=True):
+        dialog = GoDistanceDialog()
+        dialog.set_options(self.options)
+        dialog.show_all()
+        dialog.set_editable(edit)
+        response = dialog.run()
+        dialog.hide()
+        if response == gtk.RESPONSE_OK:
+            return dialog.update_options(self.options)
+        else:
+            return options
+
+
+class Options(dict):
+    def __init__(self):
+        dict.__init__(self)
+
+
+class GoDistanceOptions(Options):
+    def __init__(self):
+        Options.__init__(self)
+        for code, desc in EVIDENCE_CODES:
+            self[code] = True
+        self['metric'] = 'fussimeg'
+