367 lines
12 KiB
Python
367 lines
12 KiB
Python
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import gtk
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from fluents import dataset, logger, plots, workflow, fluents, project
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import geneontology
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from scipy import array, randn, log, ones, zeros
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import networkx
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import re
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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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GO_DATA_DIR = '/home/einarr/data'
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evidence = None
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go = None
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class GoTermView (gtk.Frame):
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def __init__(self):
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gtk.Frame.__init__(self)
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tab = gtk.Table(2, 2, False)
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self._table = tab
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self._name = gtk.Label('')
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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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def set_go_term(self, term):
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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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def __init__(self, network):
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gtk.HPaned.__init__(self)
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treemodel = geneontology.get_go_treestore(network)
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self._treemodel = treemodel
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self._tree_view = gtk.TreeView(treemodel)
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self._selected_terms = set()
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self._tree_view.set_fixed_height_mode(True)
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# Set up context menu
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self._context_menu = GoTermContextMenu(treemodel, self._tree_view)
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self._tree_view.connect('popup_menu', self._popup_menu)
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self._tree_view.connect('button_press_event', self._on_button_press)
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renderer = gtk.CellRendererText()
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go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_fixed_width(200)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 0)
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renderer = gtk.CellRendererToggle()
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renderer.set_property('activatable', True)
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renderer.connect('toggled', self._toggle_selected)
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renderer.set_active(True)
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renderer.set_property('mode', gtk.CELL_RENDERER_MODE_ACTIVATABLE)
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go_column = gtk.TreeViewColumn('T', renderer, active=2)
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go_column.set_fixed_width(20)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 1)
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renderer = gtk.CellRendererText()
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go_column = gtk.TreeViewColumn('Name', renderer, text=1)
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go_column.set_fixed_width(200)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 2)
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self._desc_view = GoTermView()
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self._tree_view.connect('cursor-changed', self._on_cursor_changed)
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scrolled_window = gtk.ScrolledWindow()
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scrolled_window.add(self._tree_view)
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self.add1(scrolled_window)
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self.add2(self._desc_view)
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self.show_all()
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def _on_cursor_changed(self, tree):
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path, col = self._tree_view.get_cursor()
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current = self._treemodel.get_iter(path)
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term = self._treemodel.get_value(current, 3)
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self._desc_view.set_go_term(term)
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##
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## GTK Callback functions
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##
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def _popup_menu(self, *rest):
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self.menu.popup(None, None, None, 0, 0)
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def _on_button_press(self, widget, event):
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path = widget.get_path_at_pos(int(event.x), int(event.y))
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iter = None
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if path:
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iter = self._treemodel.get_iter(path[0])
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obj = self._treemodel.get_value(iter, 3)
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else:
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obj = None
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self._context_menu.set_current_term(obj, iter)
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if event.button == 3:
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self._context_menu.popup(None, None, None, event.button, event.time)
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def _toggle_selected(self, renderer, path):
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iter = self._treemodel.get_iter(path)
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selected = self._treemodel.get_value(iter, 2)
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id = self._treemodel.get_value(iter, 0)
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self._treemodel.set_value(iter, 2, not selected)
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if selected:
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self._selected_terms.remove(id)
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else:
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self._selected_terms.add(id)
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class GoTermContextMenu (gtk.Menu):
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"""Context menu for GO terms in the gene ontology browser"""
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def __init__(self, treemodel, treeview):
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self._treemodel = treemodel
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self._treeview = treeview
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self._current_term = None
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self._current_iter = None
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gtk.Menu.__init__(self)
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# Popuplate tree
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self._expand_item = i = gtk.MenuItem('Expand')
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i.connect('activate', self._on_expand_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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self._collapse_item = i = gtk.MenuItem('Collapse')
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i.connect('activate', self._on_collapse_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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self._select_subtree_item = i = gtk.MenuItem('Select subtree')
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i.connect('activate', self._on_select_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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def set_current_term(self, term, it):
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self._current_term = term
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self._current_iter = it
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def _on_expand_subtree(self, item, treemodel, treeview):
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path = treemodel.get_path(self._current_iter)
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treeview.expand_row(path, True)
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def _on_collapse_subtree(self, item, treemodel, treeview):
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treeview.collapse_row(treemodel.get_path(self._current_iter))
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def _on_select_subtree(self, item, treemodel, treeview):
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logger.log('notice', 'Selecting subtree from GO id: %s (%s)' %
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(self._current_term['id'], self._current_term['name']))
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ids = [x['id'] for x in networkx.bfs(go, self._current_term)]
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project.project.set_selection('go-terms', set(ids))
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class LoadGOFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'load-go', 'Load Gene Ontology')
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def run(self):
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global go
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if go:
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return
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go = geneontology.read_default_go()
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browser = GeneOntologyTree(go)
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label = gtk.Label('_Gene Ontology')
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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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workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
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self.annotations = None
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def run(self):
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global evidence
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f = open(GO_DATA_DIR + '/goa-condensed')
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ev_codes = f.readline().split()
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go_terms = []
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lines = f.readlines()
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m = zeros((len(lines), len(ev_codes)))
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for i, l in enumerate(lines):
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values = l.split()
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go_terms.append(values[0])
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for j, v in enumerate(values[1:]):
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m[i,j] = float(v.strip())
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d = dataset.Dataset(m,
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[['go-terms', go_terms], ['evidence', ev_codes]],
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name='GO evidence')
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evidence = d
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return [d]
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class GOWeightDialog(gtk.Dialog):
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def __init__(self):
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gtk.Dialog.__init__(self, 'GO Gene List Influence',
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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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table = gtk.Table(2, 2)
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sim_lbl = gtk.Label('Similarity threshold: ')
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table.attach(sim_lbl, 0, 1, 0, 1)
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adjustment = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
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sim_spin = gtk.SpinButton(adjustment, 0.0, 2)
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table.attach(sim_spin, 1, 2, 0, 1)
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rank_lbl = gtk.Label('Rank threshold: ')
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table.attach(rank_lbl, 0, 1, 1, 2)
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rank_adj = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
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rank_spin = gtk.SpinButton(rank_adj, 0.0, 2)
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table.attach(rank_spin, 1, 2, 1, 2)
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sim_lbl.show()
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sim_spin.show()
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rank_lbl.show()
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rank_spin.show()
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table.show()
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self.vbox.add(table)
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self._sim_spin = sim_spin
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self._rank_spin = rank_spin
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def set_options(self, options):
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self._sim_spin.set_value(options['similarity_threshold'])
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self._rank_spin.set_value(options['rank_threshold'])
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def set_editable(self, editable):
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self._sim_spin.set_sensitive(editable)
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self._rank_spin.set_sensitive(editable)
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def update_options(self, options):
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options['similarity_threshold'] = self._sim_spin.get_value()
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options['rank_threshold'] = self._rank_spin.get_value()
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class GOWeightFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'load-go-ann', 'GO Influence')
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self.options = GOWeightOptions()
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def run(self, genelist, similarity):
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## Show dialog box
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self.show_gui(self.options)
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## assure that data is "correct", i.e., that we can perform
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## the desired operations.
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common_dims = genelist.common_dims(similarity)
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if len(common_dims) == 0:
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logger.log('error', 'No common dimension in the selected datasets.')
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elif len(common_dims) > 1:
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logger.log('error', "More than one common dimension in the " +
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"selected datasets. Don't know what to do.")
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gene_dim = common_dims[0]
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logger.log('debug', 'Assuming genes are in dimension: %s' % gene_dim)
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## Do the calculations.
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d = {}
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def show_gui(self, options, edit=True):
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dialog = GOWeightDialog()
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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 TTestOptionsDialog(workflow.OptionsDialog):
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def __init__(self, data, options):
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workflow.OptionsDialog.__init__(self, data, options,
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['X', 'Categories'])
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class TTestFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 't-test', 't-test')
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self.options = TTestOptions()
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def run(self, x, categories):
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self.show_gui(x, categories)
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def show_gui(self, x, categories):
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dlg = TTestOptionsDialog([x, categories], self.options)
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dlg.run()
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class TTestOptions(workflow.Options):
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def __init__(self):
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workflow.Options.__init__(self)
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class GOWeightOptions(workflow.Options):
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def __init__(self):
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workflow.Options.__init__(self)
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self['similarity_threshold'] = 0.0
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self['rank_threshold'] = 0.0
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