Updated GO workflow. Options class test added. Reading the ontology takes too
long.
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@ -5,6 +5,23 @@ import geneontology
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from scipy import array, randn, log, ones
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import networkx
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EVIDENCE_CODES=[('IMP', 'Inferred from mutant phenotype'),
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('IGI', 'Inferred from genetic interaction'),
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('IPI', 'Inferred from physical interaction'),
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('ISS', 'Inferred from sequence or structure similarity'),
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('IDA', 'Inferred from direct assay'),
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('IEP', 'Inferred on expression pattern'),
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('IEA', 'Inferred from electronic annotation'),
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('TAS', 'Traceable author statement'),
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('NAS', 'Non-traceable author statement'),
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('ND', 'No biological data available'),
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('RCA', 'Inferred from reviewed computational analysis'),
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('IC', 'Inferred by curator')]
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DISTANCE_METRICS = [('resnik', 'Resnik'),
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('jiang', 'Jiang & Conrath'),
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('fussimeg', 'FuSSiMeG')]
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class GoTermView (gtk.Frame):
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def __init__(self):
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@ -13,8 +30,22 @@ class GoTermView (gtk.Frame):
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self._table = tab
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self._name = gtk.Label('')
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tab.attach(gtk.Label('Name:'), 0, 1, 0, 1)
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tab.attach(self._name, 1, 2, 0, 1)
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self._name.set_line_wrap(True)
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self._name.set_alignment(0, 0)
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name_label = gtk.Label('Name:')
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name_label.set_alignment(0, 0)
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tab.attach(name_label, 0, 1, 0, 1, gtk.FILL, gtk.FILL, 5, 5)
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tab.attach(self._name, 1, 2, 0, 1, gtk.FILL|gtk.EXPAND, gtk.FILL, 5, 5)
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self._def = gtk.TextBuffer()
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textview = gtk.TextView(self._def)
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textview.set_wrap_mode(gtk.WRAP_WORD)
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scrolled_window = gtk.ScrolledWindow()
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scrolled_window.add(textview)
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def_label = gtk.Label('Def:')
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def_label.set_alignment(0.0, 0.0)
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tab.attach(def_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
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tab.attach(scrolled_window, 1, 2, 1, 2, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
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self.add(tab)
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self.set_go_term(None)
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@ -23,9 +54,11 @@ class GoTermView (gtk.Frame):
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if term:
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self.set_label(term['id'])
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self._name.set_text(term['name'])
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self._def.set_text(term['def'])
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else:
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self.set_label('GO Term')
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self._name.set_text('')
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self._def.set_text('')
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class GeneOntologyTree (gtk.HPaned):
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@ -77,6 +110,10 @@ class GoWorkflow (workflow.Workflow):
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load.add_function(LoadAnnotationsFunction())
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self.add_stage(load)
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go = workflow.Stage('go', 'Gene Ontology')
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go.add_function(GoDistanceFunction())
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self.add_stage(go)
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class LoadGOFunction(workflow.Function):
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def __init__(self):
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@ -90,6 +127,7 @@ class LoadGOFunction(workflow.Function):
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label.set_use_underline(True)
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fluents.app['bottom_notebook'].append_page(browser, label)
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class LoadAnnotationsFunction(workflow.Function):
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def __init__(self):
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@ -124,3 +162,118 @@ class LoadAnnotationsFunction(workflow.Function):
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dialog.destroy()
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return [self.annotations]
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class EvidenceCodeFrame(gtk.Frame):
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def __init__(self):
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gtk.Frame.__init__(self, 'Evidence Codes')
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self._ec_buttons = {}
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vbox = gtk.VBox(len(EVIDENCE_CODES))
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for code, desc in EVIDENCE_CODES:
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btn = gtk.CheckButton('%s (%s)' % (code, desc))
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self._ec_buttons[code] = btn
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vbox.add(btn)
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self.add(vbox)
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def set_options(self, options):
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for code, desc in EVIDENCE_CODES:
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self._ec_buttons[code].set_active(options[code])
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def update_options(self, options):
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for code, desc in EVIDENCE_CODES:
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options[code] = self._ec_buttons[code].get_active()
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return options
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class DistanceMetricFrame(gtk.Frame):
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def __init__(self):
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gtk.Frame.__init__(self, 'Distance Metrics')
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self._metric_buttons = {}
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vbox = gtk.VBox(len(DISTANCE_METRICS))
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prev = None
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for code, text in DISTANCE_METRICS:
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btn = gtk.RadioButton(prev, '%s' % text)
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self._metric_buttons[code] = btn
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vbox.add(btn)
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prev = btn
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self.add(vbox)
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def set_options(self, options):
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self._metric_buttons[options['metric']].set_active(True)
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def update_options(self, options):
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for code, text in DISTANCE_METRICS:
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if self._metric_buttons[code].get_active():
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options['metric'] = code
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return options
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return options
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class GoDistanceDialog(gtk.Dialog):
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def __init__(self):
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gtk.Dialog.__init__(self, 'GO term distance matrix',
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None,
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gtk.DIALOG_MODAL | gtk.DIALOG_DESTROY_WITH_PARENT,
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(gtk.STOCK_OK, gtk.RESPONSE_OK,
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gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
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self._ec_frame = EvidenceCodeFrame()
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self._metric_frame = DistanceMetricFrame()
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self.vbox.add(self._ec_frame)
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self.vbox.add(self._metric_frame)
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def run(self):
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self.vbox.show_all()
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return gtk.Dialog.run(self)
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def set_options(self, options):
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self._ec_frame.set_options(options)
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self._metric_frame.set_options(options)
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def update_options(self, options):
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self._ec_frame.update_options(options)
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self._metric_frame.update_options(options)
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return options
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def set_editable(self, editable):
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self._ec_frame.set_sensitive(editable)
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self._metric_frame.set_sensitive(editable)
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class GoDistanceFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'go-dist', 'GO term distance matrix')
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self.options = GoDistanceOptions()
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def run(self, data):
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self.options = self.show_gui(self.options)
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def show_gui(self, options, edit=True):
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dialog = GoDistanceDialog()
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dialog.set_options(self.options)
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dialog.show_all()
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dialog.set_editable(edit)
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response = dialog.run()
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dialog.hide()
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if response == gtk.RESPONSE_OK:
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return dialog.update_options(self.options)
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else:
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return options
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class Options(dict):
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def __init__(self):
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dict.__init__(self)
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class GoDistanceOptions(Options):
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def __init__(self):
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Options.__init__(self)
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for code, desc in EVIDENCE_CODES:
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self[code] = True
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self['metric'] = 'fussimeg'
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