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laydi/workflows/go_workflow.py

86 lines
2.6 KiB
Python

import gtk
from fluents import dataset, logger, plots, workflow, fluents
#import geneontology
#import gostat
from scipy import array, randn, log, ones
import networkx
class GoTermView (gtk.Frame):
def __init__(self):
gtk.Frame.__init__(self)
self.set_label('GO Term')
class GeneOntologyTree (gtk.HPaned):
def __init__(self):
gtk.HPaned.__init__(self)
self._tree_view = gtk.TreeView()
self._desc_view = GoTermView()
self.add1(self._tree_view)
self.add2(self._desc_view)
self.show_all()
class GoWorkflow (workflow.Workflow):
name = 'Gene Ontology'
ident = 'go'
description = 'Gene Ontology Workflow. For tree distance measures based '\
+ 'on the GO tree.'
def __init__(self, app):
workflow.Workflow.__init__(self, app)
load = workflow.Stage('load', 'Load GO Annotations')
load.add_function(LoadGOFunction())
load.add_function(LoadAnnotationsFunction())
self.add_stage(load)
class LoadGOFunction(workflow.Function):
def __init__(self):
workflow.Function.__init__(self, 'load-go', 'Load Gene Ontology')
def run(self):
browser = GeneOntologyTree()
label = gtk.Label('_Gene Ontology')
label.set_use_underline(True)
fluents.app['bottom_notebook'].append_page(browser, label)
class LoadAnnotationsFunction(workflow.Function):
def __init__(self):
workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
self.annotations = None
def load_file(self, filename):
f = open(filename)
self.annotations = Annotations('genes', 'go-terms')
logger.log('notice', 'Loading annotation file: %s' % filename)
for line in f.readlines():
val = line.split(' \t')
if len(val) > 1:
val = [v.strip() for v in val]
retval.add_annotations('genes', val[0],
'go-terms', set(val[1:]))
def on_response(self, dialog, response):
if response == gtk.RESPONSE_OK:
logger.log('notice', 'Reading file: %s' % dialog.get_filename())
self.load_file(dialog.get_filename())
def run(self):
btns = ('Open', gtk.RESPONSE_OK, \
'Cancel', gtk.RESPONSE_CANCEL)
dialog = gtk.FileChooserDialog('Open GO Annotation File',
buttons=btns)
dialog.connect('response', self.on_response)
dialog.run()
dialog.destroy()
return [self.annotations]