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

long.
This commit is contained in:
Einar Ryeng 2006-10-26 16:51:42 +00:00
parent 438dbd358b
commit fb77ddb549

View File

@ -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'