diff --git a/workflows/go_workflow.py b/workflows/go_workflow.py index 6a65a46..7515ab6 100644 --- a/workflows/go_workflow.py +++ b/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) - tab.attach(self._name, 1, 2, 0, 1) + 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) @@ -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): @@ -76,6 +109,10 @@ class GoWorkflow (workflow.Workflow): load.add_function(LoadGOFunction()) 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): @@ -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' +