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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
NCTCname = sys.argv[1]
filename = '/data/pacbio_assembly/pb_data/NCTC/'+NCTCname+'/'+NCTCname
graphml_path = sys.argv[2]
in_graph = nx.read_graphml(graphml_path)
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 "+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
complement = {'A':'T','C': 'G','T':'A', 'G':'C','a':'t','t':'a','c':'g','g':'c'}
def reverse_complement(string):
return "".join([complement[x] for x in reversed(string)])
def get_string(path):
#print path
ret_str = ''
for itm in path:
# print itm
read_id,rd_orientation = itm[0].split("_")
if rd_orientation == '1':
assert itm[1][0] >= itm[1][1]
# print itm
str_st = itm[1][1]
str_end = itm[1][0]
read_str = read_dict[int(read_id.lstrip("B"))][1][str_st:str_end]
else:
assert itm[1][0] <= itm[1][1]
str_st = itm[1][0]
str_end = itm[1][1]
read_str = reverse_complement(read_dict[int(read_id.lstrip("B"))][1][str_st:str_end])
# print str_st,str_end
# print read_id
# print read_dict[int(read_id)][str_st:str_end]
# print read_str
print('read len',len(read_str))
ret_str += read_str
print(len(path), len(ret_str))
return ret_str
vertices_of_interest = set([x for x in in_graph if in_graph.in_degree(x) != 1 or in_graph.out_degree(x) != 1])
read_tuples = {}
for vert in vertices_of_interest:
vert_id, vert_or = vert.split("_")
if vert_or == '1':
continue
vert_len = len(read_dict[int(vert_id)][1])
# print vert_len
read_starts = [(in_graph.edge[x][vert]['read_b_start']) for x in in_graph.predecessors(vert)]
read_ends = [(in_graph.edge[vert][x]['read_a_start']) for x in in_graph.successors(vert)]
if read_starts:
read_start = max(read_starts)
else:
read_start = 0
if read_ends:
read_end = min(read_ends)
else:
read_end = vert_len
read_tuples[vert] = (read_start,read_end)
print(read_starts, read_ends, vert)
for vert in vertices_of_interest:
vert_id, vert_or = vert.split("_")
if vert_or == '1':
read_tuples[vert] = read_tuples[vert_id+"_0"]
start_vertices = [x for x in vertices_of_interest if in_graph.in_degree(x) == 0 or in_graph.out_degree(x) > 1]
h = nx.DiGraph()
read_tuples_raw = {}
for vertex in vertices_of_interest:
successors = in_graph.successors(vertex)
if successors:
succ = successors[0]
d = in_graph.get_edge_data(vertex,succ)
read_tuples_raw[vertex] = (d['read_a_start_raw'], d['read_a_end_raw'])
else:
predecessors = in_graph.predecessors(vertex)
if not len(predecessors) == 0:
pred = predecessors[0]
d = in_graph.get_edge_data(pred,vertex)
read_tuples_raw[vertex] = (d['read_b_start_raw'], d['read_b_end_raw'])
else:
read_tuples_raw[vertex] = (0,0)
for vertex in vertices_of_interest:
h.add_node(vertex)
if vertex.split("_")[1] == '0':
path_var = [(vertex,(read_tuples[vertex][0], read_tuples[vertex][1]))]
else:
path_var = [(vertex,(read_tuples[vertex][1], read_tuples[vertex][0]))]
#print path_var
segment = get_string(path_var)
h.node[vertex]['start_read'] = path_var[0][1][0]
h.node[vertex]['end_read'] = path_var[0][1][1]
h.node[vertex]['path'] = [vertex]
h.node[vertex]['segment'] = segment
vertices_used = set([x for x in h.nodes()])
contig_no = 1
for start_vertex in vertices_of_interest:
first_out_vertices = in_graph.successors(start_vertex)
print(start_vertex, first_out_vertices)
for vertex in first_out_vertices:
predecessor = start_vertex
start_vertex_id,start_vertex_or = start_vertex.split("_")
cur_vertex = vertex
if start_vertex_or == '0':
cur_path = [(start_vertex,(read_tuples[start_vertex][1],
in_graph.edge[start_vertex][cur_vertex]['read_a_start']))]
elif start_vertex_or == '1':
cur_path = [(start_vertex,(read_tuples[start_vertex][0],
in_graph.edge[start_vertex][cur_vertex]['read_a_start']))]
while cur_vertex not in vertices_of_interest:
successor = in_graph.successors(cur_vertex)[0]
start_point = in_graph.edge[predecessor][cur_vertex]['read_b_start']
end_point = in_graph.edge[cur_vertex][successor]['read_a_start']
cur_path.append((cur_vertex,(start_point,end_point)))
vertices_used.add(cur_vertex)
predecessor = cur_vertex
cur_vertex = successor
stop_vertex_id, stop_vertex_or = cur_vertex.split("_")
if stop_vertex_or == '0':
cur_path.append((cur_vertex,(in_graph.edge[predecessor][cur_vertex]['read_b_start'],
read_tuples[cur_vertex][0])))
elif stop_vertex_or == '1':
cur_path.append((cur_vertex,(in_graph.edge[predecessor][cur_vertex]['read_b_start'],
read_tuples[cur_vertex][1])))
node_name = str(contig_no)
h.add_node(node_name)
contig_no += 1
# print cur_path
node_path = [x[0] for x in cur_path]
h.node[node_name]['path'] = node_path
h.node[node_name]['start_read'] = path_var[0][1][0]
h.node[node_name]['end_read'] = path_var[-1][1][1]
h.node[node_name]['segment'] = get_string(cur_path)
h.add_edges_from([(start_vertex,node_name),(node_name,cur_vertex)])
# paths.append(cur_path)
#print read_tuples
while set(in_graph.nodes())-vertices_used:
vert = list(set(in_graph.nodes())-vertices_used)[0]
vert_id,vert_or = vert.split("_")
if vert_or == '0':
read_start = min( min([(in_graph.edge[x][vert]['read_b_start']) for x in in_graph.predecessors(vert)]),
max([(in_graph.edge[vert][x]['read_a_start']) for x in in_graph.successors(vert)]))
read_end = max( min([(in_graph.edge[x][vert]['read_b_start']) for x in in_graph.predecessors(vert)]),
max([(in_graph.edge[vert][x]['read_a_start']) for x in in_graph.successors(vert)]))
vertRC = vert_id+"_1"
else:
read_start = max( min([(in_graph.edge[x][vert]['read_b_start']) for x in in_graph.predecessors(vert)]),
max([(in_graph.edge[vert][x]['read_a_start']) for x in in_graph.successors(vert)]))
read_end = min( min([(in_graph.edge[x][vert]['read_b_start']) for x in in_graph.predecessors(vert)]),
max([(in_graph.edge[vert][x]['read_a_start']) for x in in_graph.successors(vert)]))
vertRC = vert_id+"_0"
successor_start = in_graph.successors(vert)[0]
d = in_graph.get_edge_data(vert,successor_start)
read_tuples_raw[vert] = (d['read_a_start_raw'], d['read_a_end_raw'])
successor_start = in_graph.successors(vertRC)[0]
d = in_graph.get_edge_data(vertRC,successor_start)
read_tuples_raw[vertRC] = (d['read_a_start_raw'], d['read_a_end_raw'])
h.add_node(vert)
node_path = [vert]
h.node[vert]['path'] = node_path
h.node[vert]['start_read'] = read_start
h.node[vert]['end_read'] = read_end
h.node[vert]['segment'] = get_string([(vert,(read_start, read_end))])
vertices_used.add(vert)
first_out_vertices = in_graph.successors(vert)
for vertex in first_out_vertices:
predecessor = vert
cur_vertex = vertex
cur_path = []
while cur_vertex != vert:
successor = in_graph.successors(cur_vertex)[0]
start_point = in_graph.edge[predecessor][cur_vertex]['read_b_start']
end_point = in_graph.edge[cur_vertex][successor]['read_a_start']
cur_path.append((cur_vertex,(start_point,end_point)))
vertices_used.add(cur_vertex)
predecessor = cur_vertex
cur_vertex = successor
node_name = str(contig_no)
h.add_node(node_name)
contig_no += 1
# print cur_path
node_path = [x[0] for x in cur_path]
h.node[node_name]['path'] = node_path
h.node[node_name]['start_read'] = path_var[0][1][0]
h.node[node_name]['end_read'] = path_var[-1][1][1]
h.node[node_name]['segment'] = get_string(cur_path)
h.add_edges_from([(vert,node_name),(node_name,vert)])
if vertRC not in vertices_used:
h.add_node(vertRC)
h.node[vertRC]['segment'] = get_string([(vertRC,(read_end, read_start))])
h.node[vertRC]['path'] = [vertRC]
h.node[vertRC]['start_read'] = read_end
h.node[vertRC]['end_read'] = read_start
vertices_used.add(vertRC)
first_out_vertices = in_graph.successors(vertRC)
for vertex in first_out_vertices:
predecessor = vertRC
cur_vertex = vertex
cur_path = []
while cur_vertex != vertRC:
successor = in_graph.successors(cur_vertex)[0]
start_point = in_graph.edge[predecessor][cur_vertex]['read_b_start']
end_point = in_graph.edge[cur_vertex][successor]['read_a_start']
cur_path.append((cur_vertex,(start_point,end_point)))
vertices_used.add(cur_vertex)
predecessor = cur_vertex
cur_vertex = successor
node_name = str(contig_no)
h.add_node(node_name)
contig_no += 1
# print cur_path
node_path = [x[0] for x in cur_path]
h.node[node_name]['path'] = node_path
h.node[node_name]['start_read'] = path_var[0][1][0]
h.node[node_name]['end_read'] = path_var[-1][1][1]
h.node[node_name]['segment'] = get_string(cur_path)
print(len(cur_path))
h.add_edges_from([(vertRC,node_name),(node_name,vertRC)])
outfile = '/data/pacbio_assembly/pb_data/NCTC/'+NCTCname+'/'+NCTCname + ".edges.list"
vert_to_merge = [x for x in h.nodes() if len(h.successors(x)) == 1 and len(h.predecessors(h.successors(x)[0])) == 1 and
len(nx.node_connected_component(h.to_undirected(), x)) > 2]
while True:
vert_to_merge = [x for x in h.nodes() if len(h.successors(x)) == 1 and len(h.predecessors(h.successors(x)[0])) == 1 and
len(nx.node_connected_component(h.to_undirected(), x)) > 2]
if not vert_to_merge:
break
vert = vert_to_merge[0]
#print vert,
succ = h.successors(vert)[0]
preds = h.predecessors(vert)
h.node[succ]['segment'] = h.node[vert]['segment'] + h.node[succ]['segment']
h.node[succ]['path'] = h.node[vert]['path'] + h.node[succ]['path'][1:]
for pred in preds:
#print pred, succ
h.add_edges_from([(pred,succ)])
h.remove_edge(pred,vert)
h.remove_edge(vert,succ)
h.remove_node(vert)
for i, vert in enumerate(h.nodes()):
print(i,len(h.node[vert]['path']))
with open(outfile, 'w') as f:
for i,node in enumerate(h.nodes()):
#print node
#print h.node[node]
path = h.node[node]['path']
f.write('>Unitig%d\n'%(i))
if len(path) == 1:
#print path[0]
f.write(' '.join([path[0].split('_')[0], path[0].split('_')[1], str(read_tuples_raw[path[0]][0]), str(read_tuples_raw[path[0]][1])]) + '\n')
for j in range(len(path)-1):
nodeA = path[j].lstrip("B")
nodeB = path[j+1].lstrip("B")
d = in_graph.get_edge_data(path[j],path[j+1])
f.write('%s %s %s %s %d %d %d %d %d\n'%(nodeA.split('_')[0],nodeA.split('_')[1] , nodeB.split('_')[0],
nodeB.split('_')[1], -d['read_a_start_raw'] + d['read_a_end_raw'] - d['read_b_start_raw'] + d['read_b_end_raw'],
d['read_a_start_raw'], d['read_a_end_raw'], d['read_b_start_raw'], d['read_b_end_raw']))
out_graphml_name = '/data/pacbio_assembly/pb_data/NCTC/'+NCTCname+'/'+NCTCname+'_draft.graphml'
gfaname = '/data/pacbio_assembly/pb_data/NCTC/'+NCTCname+'/'+NCTCname+'_draft_python.gfa'
consensus_name = sys.argv[3]
consensus_contigs = []
try:
with open(consensus_name) as f:
for line in f:
if line[0] != '>':
consensus_contigs.append(line.strip())
except:
pass
for i, vert in enumerate(h.nodes()):
print(i,len(h.node[vert]['path']), len(h.node[vert]['segment']), len(consensus_contigs[i]))
with open(gfaname,'w') as f:
f.write("H\tVN:Z:1.0\n")
for i,vert in enumerate(h.nodes()):
if len(consensus_contigs) > 0:
seg = consensus_contigs[i]
else:
seg = h.node[vert]['segment']
seg_line = "S\t"+vert+"\t"+seg + '\n'
f.write(seg_line)
for edge in h.edges():
edge_line = "L\t"+edge[0]+"\t+\t"+edge[1]+"\t+\t0M\n"
f.write(edge_line)
#last = h.nodes()[-1]
#print h.node[last]
#path_last = h.node[last]['path']
#for i in range(len(path_last)-1):
# read_a = path_last[i]
# read_b = path_last[i+1]
# print read_a, read_b, in_graph.edge[read_a][read_b]
for i,node in enumerate(h.nodes()):
h.node[node]['path'] = ';'.join(h.node[node]['path'])
nx.write_graphml(h,out_graphml_name)
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