laydi/workflows/go_workflow.py

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)
        tab = gtk.Table(2, 2, False)
        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.add(tab)
        self.set_go_term(None)

    def set_go_term(self, term):
        if term:
            self.set_label(term['id'])
            self._name.set_text(term['name'])
        else:
            self.set_label('GO Term')
            self._name.set_text('')

        
class GeneOntologyTree (gtk.HPaned):
    
    def __init__(self, network):
        gtk.HPaned.__init__(self)
    
        treemodel = geneontology.get_go_treestore(network)
        self._treemodel = treemodel
        self._tree_view = gtk.TreeView(treemodel)

        renderer = gtk.CellRendererText()
        go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
        self._tree_view.insert_column(go_column, 0)

        renderer = gtk.CellRendererText()
        go_column = gtk.TreeViewColumn('Name', renderer, text=1)
        self._tree_view.insert_column(go_column, 1)

        self._desc_view = GoTermView()

        self._tree_view.connect('cursor-changed', self._on_cursor_changed)

        scrolled_window = gtk.ScrolledWindow()
        scrolled_window.add(self._tree_view)
        self.add1(scrolled_window)
        self.add2(self._desc_view)
        self.show_all()

    def _on_cursor_changed(self, tree):
        path, col = self._tree_view.get_cursor()
        current = self._treemodel.get_iter(path)
        term = self._treemodel.get_value(current, 2)
        self._desc_view.set_go_term(term)        
        

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):
        global go
        go = geneontology.read_default_go()
        browser = GeneOntologyTree(go)
        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]