def retrieve_components(graph_dict, tumor_type, all_cogs, radius, signif_res_neighbours): """Get the connected components and format the output.""" #inv_signif_struct_info = {v: k for k, v in signif_struct_info.items()} ttype_output = [] #neighbours = pstruct.find_neighbors(all_cogs, radius) for mystruct in graph_dict: g = graph_dict[mystruct] components = graph.connected_components(g) added_components = components """ added_components = [] for cluster in components: neighbours_in_cluster = set() for res in cluster: if res in signif_res_neighbours: neighbours_in_cluster |= signif_res_neighbours[res] added_components.append(cluster | neighbours_in_cluster) """ #print added_components tmp = [mystruct, tumor_type] for component in added_components: format_str = ';'.join('{0}:{1}:{2}'.format(n[0], n[1], n[2]) for n in component) tmp.append(format_str) ttype_output.append(tmp) return ttype_output
def retrieve_components(graph_dict, tumor_type): """Get the connected components and format the output.""" ttype_output = [] for mygene in graph_dict: g = graph_dict[mygene] components = graph.connected_components(g) tmp = [mygene, tumor_type] for component in components: format_str = ';'.join('{0}:{1}'.format(n[1], n[2]) for n in component) tmp.append(format_str) ttype_output.append(tmp) return ttype_output