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#!/usr/bin/python3
import sys
import os
import subprocess
from parse_read import *
import numpy as np
import networkx as nx
import itertools
from pbcore.io import FastaIO
def rev_node(node):
node_id = node.split('_')[0]
return node_id + '_' + str(1-int(node.split('_')[1]))
def merge_nodes(g,in_node,out_node):
weight = str(g.edge[in_node][out_node]['length'])
if 'path' in g.node[in_node]:
path1 = g.node[in_node]['path']
weightspath1 = g.node[in_node]['weightspath']
else:
path1 = in_node
weightspath1 = ''
if 'path' in g.node[out_node]:
path2 = g.node[out_node]['path']
weightspath2 = ';' + g.node[out_node]['weightspath']
else:
path2 = out_node
weightspath2 = ''
g.node[in_node]['path'] = path1 + ';' + path2
if weightspath1 == '':
g.node[in_node]['weightspath'] = weight + weightspath2
else:
g.node[in_node]['weightspath'] = weightspath1 + ';' + weight + weightspath2
for nodeB in g.successors(out_node):
g.add_edge(in_node,nodeB,length=g.edge[out_node][nodeB]['length'])
g.node[in_node]['cut_end'] = g.node[out_node]['cut_end']
g.remove_node(out_node)
filedir = sys.argv[1]
filename = sys.argv[2]
graphml_path = sys.argv[3]
in_graph = nx.read_graphml(graphml_path)
# debug output
#for node in in_graph.nodes():
# print node
#for edge in in_graph.edges():
# print len(in_graph.edge[edge[0]][edge[1]])
reads = sorted(list(set([int(x.split("_")[0].lstrip("B")) for x in in_graph.nodes()])))
dbshow_reads = ' '.join([str(x+1) for x in reads])
DBshow_cmd = "DBshow "+ filedir+'/'+ filename+' '+dbshow_reads
stream = subprocess.Popen(DBshow_cmd.split(),
stdout=subprocess.PIPE,bufsize=1)
reads_queried = parse_read(stream.stdout)
read_dict = {}
for read_id,read in zip(reads,reads_queried):
rdlen = len(read[1])
# print read
read_dict[read_id] = read
# to simulate reads
# read_dict = {}
# for vertex in in_graph.nodes():
# read_dict[int(vertex.split('_')[0])] = ['A','A'*50000]
complement = {'A':'T','C': 'G','T':'A', 'G':'C','a':'t','t':'a','c':'g','g':'c'}
# out_graphml_name = 'test.graphml'
out_graphml_name = filedir + '/' + filename +'_draft.graphml'
# outfile = 'test.edges.list'
outfile = filedir + '/' + filename + ".edges.list"
rev_comp_contig = True
out_graph = in_graph.copy()
# first we add some info to the graph for the cutting of contigs
for vert in out_graph.nodes():
vert_id, vert_or = vert.split("_")
vert_id = vert_id.lstrip("B")
vert_len = len(read_dict[int(vert_id)][1])
out_graph.node[vert]['cut_start'] = 0
out_graph.node[vert]['cut_end'] = vert_len
# SHOULD THIS USE THE RAW MATCHES?
if out_graph.in_degree(vert) > 1:
if vert_or == '0':
out_graph.node[vert]['cut_start'] = max([out_graph.edge[x][vert]['read_b_match_start'] for x in out_graph.predecessors(vert)])
else:
out_graph.node[vert]['cut_start'] = vert_len - min([out_graph.edge[vert_id+'_0'][x]['read_a_match_start'] for x in out_graph.successors(vert_id+'_0')])
if out_graph.out_degree(vert) > 1:
if vert_or == '0':
out_graph.node[vert]['cut_end'] = min([out_graph.edge[vert][x]['read_a_match_start'] for x in out_graph.successors(vert)])
else:
out_graph.node[vert]['cut_end'] = vert_len - max([out_graph.edge[x][vert_id+'_0']['read_b_match_start'] for x in out_graph.predecessors(vert_id+'_0')])
# next we merge the nodes in out_graph to form the contigs
nodes_to_merge = [x for x in out_graph.nodes() if out_graph.in_degree(x) == 1 and out_graph.out_degree(out_graph.predecessors(x)[0]) == 1]
# print len(read_dict[41260][1])
# print len(read_dict[4697][1])
while nodes_to_merge:
cur_node = nodes_to_merge[0]
prev_node = out_graph.predecessors(cur_node)[0]
if prev_node != cur_node:
merge_nodes(out_graph,prev_node,cur_node)
else:
out_graph.node[cur_node]['path'] = out_graph.node[cur_node]['path'] + ';' + cur_node
out_graph.node[cur_node]['weightspath'] = out_graph.node[cur_node]['weightspath'] + ';' + str(out_graph.edge[prev_node][cur_node]['length'])
out_graph.node[cur_node]['cut_end'] = len(read_dict[int(cur_node.split('_')[0])][1])
nodes_to_merge.pop(0)
# print len(nodes_to_merge)
# next we print the contigs out to the .edges.list file
contig_no = 0
# print "Writing out_graph with "+str(len(out_graph.nodes()))+" contigs/nodes"
# we keep track of the already printed nodes so that reverse complement pairs are printed together
# we don't add to printed_nodes the "border" nodes so that we still have a partition of the nodes into contigs
# printed_nodes = set()
printed_nodes = {}
# debug output
# for node in out_graph.nodes():
# print node
# print out_graph.node[node]
# for edge in out_graph.edges():
# print edge
# print out_graph.edge[edge[0]][edge[1]]
with open(outfile, 'w') as f:
for vertex in out_graph.nodes():
if rev_node(vertex) in printed_nodes:
out_graph.node[vertex]['contig_id'] = printed_nodes[rev_node(vertex)] + 1
continue
# single-node contig
if 'path' not in out_graph.node[vertex]:
out_graph.node[vertex]['contig_id'] = contig_no + 1
f.write('>Unitig%d\n'%(contig_no))
# printed_nodes = printed_nodes | set([vertex])
printed_nodes[vertex] = contig_no
contig_no += 1
# we repeat the same node twice so that the line is easily distinguishable (6 numbers)
f.write('O %s %s %s %s %d %d\n'%(vertex.split('_')[0].lstrip('B'), vertex.split('_')[1] , vertex.split('_')[0].lstrip('B'),
vertex.split('_')[1], out_graph.node[vertex]['cut_start'], out_graph.node[vertex]['cut_end']) )
f.write('>Unitig%d\n'%(contig_no))
contig_no += 1
vertex_rc = rev_node(vertex)
f.write('O %s %s %s %s %d %d\n'%(vertex_rc.split('_')[0].lstrip('B'), vertex_rc.split('_')[1] , vertex_rc.split('_')[0].lstrip('B'),
vertex_rc.split('_')[1], out_graph.node[vertex_rc]['cut_start'], out_graph.node[vertex_rc]['cut_end']) )
continue
node_list = out_graph.node[vertex]['path'].split(';')
weights_list = out_graph.node[vertex]['weightspath'].split(';')
# double-node contig
if out_graph.in_degree(vertex) != 1 and out_graph.out_degree(vertex) != 1 and len(node_list) == 2:
out_graph.node[vertex]['contig_id'] = contig_no
f.write('>Unitig%d\n'%(contig_no))
# printed_nodes = printed_nodes | set(node_list)
printed_nodes[node_list[0]] = contig_no
printed_nodes[node_list[1]] = contig_no
contig_no += 1
nodeA = node_list[0]
nodeB = node_list[1]
f.write('D %s %s %s %s %s %d %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[0], out_graph.node[vertex]['cut_start'], out_graph.node[vertex]['cut_end']) )
f.write('>Unitig%d\n'%(contig_no))
contig_no += 1
nodeA = rev_node(node_list[1])
nodeB = rev_node(node_list[0])
f.write('D %s %s %s %s %s %d %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[0], len(read_dict[int(nodeA.split('_')[0])][1]) - out_graph.node[vertex]['cut_end'], len(read_dict[int(nodeB.split('_')[0])][1]) - out_graph.node[vertex]['cut_start'] ) )
continue
# print out_graph.node[vertex]['path']
# print node_list
# print out_graph.node[vertex]['weightspath']
# print weights_list
# print len(node_list),len(weights_list)
if len(node_list) != len(weights_list)+1:
print('Something went wrong with contig '+str(contig_no))
continue
# printed_nodes = printed_nodes | set(node_list)
for curnode in node_list:
printed_nodes[curnode] = contig_no
# print 'Unitig ' +str(contig_no) + ' ('+str(len(node_list))+' nodes)'
out_graph.node[vertex]['contig_id'] = contig_no
f.write('>Unitig%d\n'%(contig_no))
contig_no += 1
# prev_vert = out_graph.node[node_list[0]]['prev_node']
# if prev_vert != '':
if out_graph.in_degree(vertex) == 1 and out_graph.predecessors(vertex)[0] != vertex:
prev_contig = out_graph.predecessors(vertex)[0]
cut_start = out_graph.node[prev_contig]['cut_end']
if 'path' in out_graph.node[prev_contig]:
nodeA = out_graph.node[prev_contig]['path'].split(';')[-1]
else:
nodeA = prev_contig
nodeB = node_list[0]
f.write('S %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'),
nodeB.split('_')[1], out_graph.edge[prev_contig][vertex]['length'], cut_start) )
if len(node_list) > 2:
nodeA = node_list[0]
nodeB = node_list[1]
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'),nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[0]) )
else:
nodeA = node_list[0]
nodeB = node_list[1]
f.write('S %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[0], out_graph.node[vertex]['cut_start']) )
for i in range(1,len(weights_list)-1):
nodeA = node_list[i]
nodeB = node_list[i+1]
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[i]) )
if out_graph.out_degree(vertex) == 1 and out_graph.successors(vertex)[0] != vertex:
if len(node_list) > 2:
nodeA = node_list[len(weights_list)-1]
nodeB = node_list[len(weights_list)]
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[-1]) )
next_contig = out_graph.successors(vertex)[0]
# we end this contig where the next one begins
cut_end = out_graph.node[next_contig]['cut_start']
nodeA = node_list[len(weights_list)]
if 'path' in out_graph.node[next_contig]:
nodeB = out_graph.node[next_contig]['path'].split(';')[0]
else:
nodeB = next_contig
f.write('E %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'),nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'),
nodeB.split('_')[1], out_graph.edge[vertex][next_contig]['length'], cut_end) )
else:
nodeA = node_list[len(weights_list)-1]
nodeB = node_list[len(weights_list)]
f.write('E %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'),nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[-1], out_graph.node[vertex]['cut_end']) )
# if we want reverse complement contigs, we print them next to each other
if rev_comp_contig == False:
continue
f.write('>Unitig%d\n'%(contig_no))
contig_no += 1
if out_graph.out_degree(vertex) == 1 and out_graph.successors(vertex)[0] != vertex:
next_contig = out_graph.successors(vertex)[0]
nodeB = rev_node(node_list[len(weights_list)])
if 'path' in out_graph.node[next_contig]:
nodeA = rev_node(out_graph.node[next_contig]['path'].split(';')[0])
else:
nodeA = rev_node(next_contig)
# we start this contig where the previous (rc: next) one ended
cut_start = len(read_dict[int(nodeA.split('_')[0])][1]) - out_graph.node[next_contig]['cut_start']
f.write('S %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'),
nodeB.split('_')[1], out_graph.edge[vertex][next_contig]['length'], cut_start) )
if len(node_list) > 2:
nodeA = rev_node(node_list[len(weights_list)])
nodeB = rev_node(node_list[len(weights_list)-1])
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[-1]) )
else:
nodeA = rev_node(node_list[len(weights_list)])
nodeB = rev_node(node_list[len(weights_list)-1])
f.write('S %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[-1], len(read_dict[int(nodeA.split('_')[0])][1]) - out_graph.node[vertex]['cut_end']) )
for i in range(len(weights_list)-1,1,-1):
nodeA = rev_node(node_list[i])
nodeB = rev_node(node_list[i-1])
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[i-1]) )
if out_graph.in_degree(vertex) == 1 and out_graph.predecessors(vertex)[0] != vertex:
if len(node_list) > 2:
nodeA = rev_node(node_list[1])
nodeB = rev_node(node_list[0])
f.write('T %s %s %s %s %s\n'%(nodeA.split('_')[0].lstrip('B'), nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1], weights_list[0]) )
prev_contig = out_graph.predecessors(vertex)[0]
nodeA = rev_node(node_list[0])
if 'path' in out_graph.node[prev_contig]:
nodeB = rev_node(out_graph.node[prev_contig]['path'].split(';')[-1])
else:
nodeB = rev_node(prev_contig)
cut_end = len(read_dict[int(nodeB.split('_')[0])][1]) - out_graph.node[prev_contig]['cut_end']
f.write('E %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'),nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'),
nodeB.split('_')[1], out_graph.edge[prev_contig][vertex]['length'], cut_end) )
else:
nodeB = rev_node(node_list[0])
nodeA = rev_node(node_list[1])
f.write('E %s %s %s %s %s %d\n'%(nodeA.split('_')[0].lstrip('B'),nodeA.split('_')[1] , nodeB.split('_')[0].lstrip('B'), nodeB.split('_')[1],
weights_list[0], len(read_dict[int(nodeB.split('_')[0])][1]) - out_graph.node[vertex]['cut_start']) )
print("Number of contigs: "+str(contig_no))
nx.write_graphml(out_graph,out_graphml_name)
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