def _walkCreate(koEntry, lvItem): item = QTreeWidgetItem(lvItem) id = "path:" + org_code + koEntry.title[:5] if koEntry.title[:5] in path_ids: p = kegg_pathways.get_entry(id) if p is None: # In case the genesets still have obsolete entries name = koEntry.title else: name = p.name genes, p_value, ref = self.pathways[id] item.setText(0, name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id if p is not None else None else: if id in allPathways: text = kegg_pathways.get_entry(id).name else: text = koEntry.title item.setText(0, text) if id in allPathways: item.pathway_id = id elif "path:map" + koEntry.title[:5] in allRefPathways: item.pathway_id = "path:map" + koEntry.title[:5] else: item.pathway_id = None for child in koEntry.entries: if child in allClasses: _walkCreate(child, item)
def _walkCreate(koEntry, lvItem): item = QTreeWidgetItem(lvItem) id = "path:" + org_code + koEntry.title[:5] if koEntry.title[:5] in path_ids: p = kegg_pathways.get_entry(id) if p is None: # In case the genesets still have obsolete entries name = koEntry.title else: name = p.name genes, p_value, ref = self.pathways[id] item.setText(0, name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id if p is not None else None else: if id in allPathways: text = kegg_pathways.get_entry(id).name else: text = koEntry.title item.setText(0, text) if id in allPathways: item.pathway_id = id elif "path:map" + koEntry.title[:5] in allRefPathways: item.pathway_id = "path:map" + koEntry.title[:5] else: item.pathway_id = None for child in koEntry.entries: if child in allClasses: _walkCreate(child, item)
def UpdateListView(self): self.bestPValueItem = None self.listView.clear() if not self.data: return allPathways = self.org.pathways() allRefPathways = kegg.pathways("map") items = [] kegg_pathways = kegg.KEGGPathways() org_code = self.organismCodes[min(self.organismIndex, len(self.organismCodes) - 1)] if self.showOrthology: self.koOrthology = kegg.KEGGBrite("ko00001") self.listView.setRootIsDecorated(True) path_ids = set([s[-5:] for s in self.pathways.keys()]) def _walkCollect(koEntry): num = koEntry.title[:5] if koEntry.title else None if num in path_ids: return ([koEntry] + reduce(lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], [])) else: c = reduce(lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], []) return c + (c and [koEntry] or []) allClasses = reduce(lambda li1, li2: li1 + li2, [_walkCollect(c) for c in self.koOrthology], []) def _walkCreate(koEntry, lvItem): item = QTreeWidgetItem(lvItem) id = "path:" + org_code + koEntry.title[:5] if koEntry.title[:5] in path_ids: p = kegg_pathways.get_entry(id) if p is None: # In case the genesets still have obsolete entries name = koEntry.title else: name = p.name genes, p_value, ref = self.pathways[id] item.setText(0, name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id if p is not None else None else: if id in allPathways: text = kegg_pathways.get_entry(id).name else: text = koEntry.title item.setText(0, text) if id in allPathways: item.pathway_id = id elif "path:map" + koEntry.title[:5] in allRefPathways: item.pathway_id = "path:map" + koEntry.title[:5] else: item.pathway_id = None for child in koEntry.entries: if child in allClasses: _walkCreate(child, item) for koEntry in self.koOrthology: if koEntry in allClasses: _walkCreate(koEntry, self.listView) self.listView.update() else: self.listView.setRootIsDecorated(False) pathways = self.pathways.items() pathways = sorted(pathways, key=lambda item: item[1][1]) for id, (genes, p_value, ref) in pathways: item = QTreeWidgetItem(self.listView) item.setText(0, kegg_pathways.get_entry(id).name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id items.append(item) self.bestPValueItem = items and items[0] or None self.listView.expandAll() for i in range(4): self.listView.resizeColumnToContents(i) if self.bestPValueItem: index = self.listView.indexFromItem(self.bestPValueItem) self.listView.selectionModel().select( index, QItemSelectionModel.ClearAndSelect )
def UpdateListView(self): self.bestPValueItem = None self.listView.clear() if not self.data: return allPathways = self.org.pathways() allRefPathways = kegg.pathways("map") items = [] kegg_pathways = kegg.KEGGPathways() org_code = self.organismCodes[min(self.organismIndex, len(self.organismCodes) - 1)] if self.showOrthology: self.koOrthology = kegg.KEGGBrite("ko00001") self.listView.setRootIsDecorated(True) path_ids = set([s[-5:] for s in self.pathways.keys()]) def _walkCollect(koEntry): num = koEntry.title[:5] if koEntry.title else None if num in path_ids: return ([koEntry] + reduce(lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], [])) else: c = reduce(lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], []) return c + (c and [koEntry] or []) allClasses = reduce(lambda li1, li2: li1 + li2, [_walkCollect(c) for c in self.koOrthology], []) def _walkCreate(koEntry, lvItem): item = QTreeWidgetItem(lvItem) id = "path:" + org_code + koEntry.title[:5] if koEntry.title[:5] in path_ids: p = kegg_pathways.get_entry(id) if p is None: # In case the genesets still have obsolete entries name = koEntry.title else: name = p.name genes, p_value, ref = self.pathways[id] item.setText(0, name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id if p is not None else None else: if id in allPathways: text = kegg_pathways.get_entry(id).name else: text = koEntry.title item.setText(0, text) if id in allPathways: item.pathway_id = id elif "path:map" + koEntry.title[:5] in allRefPathways: item.pathway_id = "path:map" + koEntry.title[:5] else: item.pathway_id = None for child in koEntry.entries: if child in allClasses: _walkCreate(child, item) for koEntry in self.koOrthology: if koEntry in allClasses: _walkCreate(koEntry, self.listView) self.listView.update() else: self.listView.setRootIsDecorated(False) pathways = self.pathways.items() pathways = sorted(pathways, key=lambda item: item[1][1]) for id, (genes, p_value, ref) in pathways: item = QTreeWidgetItem(self.listView) item.setText(0, kegg_pathways.get_entry(id).name) item.setText(1, "%.5f" % p_value) item.setText(2, "%i of %i" % (len(genes), len(self.genes))) item.setText(3, "%i of %i" % (ref, len(self.referenceGenes))) item.pathway_id = id items.append(item) self.bestPValueItem = items and items[0] or None self.listView.expandAll() for i in range(4): self.listView.resizeColumnToContents(i) if self.bestPValueItem: index = self.listView.indexFromItem(self.bestPValueItem) self.listView.selectionModel().select( index, QItemSelectionModel.ClearAndSelect)