#!/usr/bin/python3 import networkx as nx import random import sys from collections import Counter # This script does a random condensation of the graph down to 2000 nodes # python3 random_condensation.py ecoli.edges 2000 # It also keeps the ground truth on the graph through the condensation steps (if a json file is available) def merge_path(g,in_node,node,out_node): g.add_edge(in_node,out_node,hinge_edge = -1,false_positive = 0) g.remove_node(node) def input1(flname): print("input1") g = nx.DiGraph() with open (flname) as f: for lines in f: lines1=lines.split() #print lines1 if len(lines1) < 5: continue #print lines1 g.add_edge(lines1[0] + "_" + lines1[3], lines1[1] + "_" + lines1[4], hinge_edge=int(lines1[5])) g.add_edge(lines1[1] + "_" + str(1-int(lines1[4])), lines1[0] + "_" + str(1-int(lines1[3])),hinge_edge=int(lines1[5])) return g def input2(flname): print("input2") g = nx.DiGraph() with open (flname) as f: for lines in f: lines1=lines.split() #print lines1 g.add_edge(lines1[0], lines1[1]) return g def input3(flname): print("input3") # g = nx.DiGraph() g = nx.read_graphml(flname) def de_clip(filename, n_nodes, hinge_list,gt_file): n_iter = 5 f=open(filename) line1=f.readline() print(line1) f.close() extension = filename.split('.')[-1] if extension == 'graphml': g=input3(filename) elif len(line1.split()) !=2: g=input1(filename) else: g=input2(filename) print(nx.info(g)) degree_sequence=sorted(list(g.degree().values()),reverse=True) print(Counter(degree_sequence)) degree_sequence=sorted(list(nx.degree(g).values()),reverse=True) print(Counter(degree_sequence)) try: import ujson mapping = ujson.load(open(gt_file)) print('getting mapping') mapped_nodes=0 print(str(len(mapping))) print(str(len(g.nodes()))) for node in g.nodes(): # print node node_base=node.split("_")[0] # print node_base #print node if node_base in mapping: g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1]) g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0]) g.node[node]['chr'] = mapping[node_base][0][2] mapped_nodes+=1 else: # pass g.node[node]['aln_start'] = 0 g.node[node]['aln_end'] = 0 g.node[node]['aln_strand'] = 0 for edge in g.edges_iter(): in_node=edge[0] out_node=edge[1] # print 'akjdfakjhfakljh' if ((g.node[in_node]['aln_start'] < g.node[out_node]['aln_start'] and g.node[out_node]['aln_start'] < g.node[in_node]['aln_end']) or (g.node[in_node]['aln_start'] < g.node[out_node]['aln_end'] and g.node[out_node]['aln_end'] < g.node[in_node]['aln_end'])): g.edge[in_node][out_node]['false_positive']=0 else: g.edge[in_node][out_node]['false_positive']=1 except: raise # print "json "+filename.split('.')[0]+'.mapping.json'+" not found. exiting." print(hinge_list) print(str(mapped_nodes)+" out of " +str(len(g.nodes()))+" nodes mapped.") # for i in range(5): # merge_simple_path(g) # degree_sequence=sorted(nx.degree(g).values(),reverse=True) # print Counter(degree_sequence) in_hinges = set() out_hinges = set() num_iter=10000 iter_done=0 if hinge_list != None: print("Found hinge list.") with open(hinge_list,'r') as f: for lines in f: lines1=lines.split() if lines1[2] == '1': in_hinges.add(lines1[0]+'_0') out_hinges.add(lines1[0]+'_1') elif lines1[2] == '-1': in_hinges.add(lines1[0]+'_1') out_hinges.add(lines1[0]+'_0') print(str(len(in_hinges))+' hinges found.') for node in g.nodes(): if node in in_hinges and node in out_hinges: g.node[node]['hinge']=100 elif node in in_hinges: g.node[node]['hinge']=10 elif node in out_hinges: g.node[node]['hinge']=-10 else: g.node[node]['hinge']=0 while len(g.nodes()) > n_nodes and iter_done < num_iter : node = g.nodes()[random.randrange(len(g.nodes()))] iter_done+=1 # print iter_done if g.in_degree(node) == 1 and g.out_degree(node) == 1: base_node=node.split("_")[0] orintation = node.split("_")[1] # if orintation=='1': # node2=base_node+'_0' # else: # node2=base_node+'_1' # print node,node2 in_node = g.in_edges(node)[0][0] out_node = g.out_edges(node)[0][1] if g.node[node]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0: if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1: if in_node != node and out_node != node and in_node != out_node: bad_node=False # print g.in_edges(node) # print g.edge[g.in_edges(node)[0][0]][g.in_edges(node)[0][1]] # print g.out_edges(node) for in_edge in g.in_edges(node): if g.edge[in_edge[0]][in_edge[1]]['false_positive']==1: bad_node=True for out_edge in g.out_edges(node): if g.edge[out_edge[0]][out_edge[1]]['false_positive']==1: bad_node=True if not bad_node: #print in_node, node, out_node merge_path(g,in_node,node,out_node) # print g.edge[edge1[0]][edge1[1]]['hinge_edge'] for nd in g.nodes(): if len(nd.split("_"))==1: print(nd + " in trouble") # in_node = g.in_edges(node2)[0][0] # out_node = g.out_edges(node2)[0][1] # if g.node[node2]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0: # if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1: # if in_node != node2 and out_node != node2 and in_node != out_node: # bad_node=False # for in_edge in g.in_edges(node2): # if g.edge[in_edge]==1: # bad_node=True # for out_edge in g.out_edges(node2): # if g.edge[out_edge]==1: # bad_node=True # if not bad_node: # #print in_node, node, out_node # merge_path(g,in_node,node2,out_node) # for nd in g.nodes(): # print nd else: while len(g.nodes()) > n_nodes: node = g.nodes()[random.randrange(len(g.nodes()))] if g.in_degree(node) == 1 and g.out_degree(node) == 1: # assert g.in_degree(node2) == 1 and g.out_degree(node2) == 1 # edge_1 = g.out_edges(node)[0] # edge_2 = g.in_edges(node)[0] edge1 = g.out_edges(node)[0] edge2 = g.in_edges(node)[0] # print g.edge[edge1[0]][edge1[1]]['hinge_edge'] if (g.edge[edge1[0]][edge1[1]]['hinge_edge'] == -1 and g.edge[edge2[0]][edge2[1]]['hinge_edge'] == -1): in_node = g.in_edges(node)[0][0] out_node = g.out_edges(node)[0][1] if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1: if in_node != node and out_node != node and in_node != out_node: #print in_node, node, out_node merge_path(g,in_node,node,out_node) degree_sequence=sorted(list(nx.degree(g).values()),reverse=True) print(Counter(degree_sequence)) nx.write_graphml(g, filename.split('.')[0]+'.sparse3.graphml') print(nx.number_weakly_connected_components(g)) print(nx.number_strongly_connected_components(g)) if __name__ == "__main__": filename = sys.argv[1] try : hinge_list=sys.argv[3] print("Found hinge list.") except: hinge_list=None print("in except "+hinge_list) de_clip(filename, int(sys.argv[2]),hinge_list, sys.argv[4])