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Copy pathFilterMultiEdges.py
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207 lines (191 loc) · 10.6 KB
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from collections import Counter
import re
import glob
import sys
import numpy as np
cutoff = 1
all_barrels = []
with open("BarrelChars85.txt", "r") as barrel_list:
for line in barrel_list:
if "Barrel" not in line:
line = line.split("\t")
all_barrels.append(line[0])
graph = {} #relationship list for each node
with open("data/FiltData_E20_v6_2018_Renumb_2.txt", "r") as inData:
for line in inData:
if "dom1" not in line:
line = line.strip().split("\t")
dom1 = line[0]
dom2 = line[1]
e_value = float(line[2])
if e_value <= cutoff:
if dom1 in graph.keys():
graph[dom1].append(dom2)
else:
graph[dom1] = [dom2]
if dom2 in graph.keys():
graph[dom2].append(dom1)
else:
graph[dom2] = [dom1]
multiple_edges = [] #pairs of PDBs with multiple connections between them
stubs = []
for key in graph.keys():
if len(graph[key]) == 1:
#print(key, graph[key])
pop_from = graph[key][0]
stubs.append(key)
#print(graph[pop_from])
graph[pop_from].remove(key)
#print(graph[pop_from])
else:
#print(key, graph[key])
edges = Counter(graph[key])
for value in edges:
if edges[value] >= 2:
#find those pairs with more than one connection between them
if [value, key] in multiple_edges: continue #print("In list already")
else: multiple_edges.append([key, value])
#print(multiple_edges)
for key in stubs:
del graph[key]
#graph now only consists of pdbs with multiple connections to the same pdb
multi_edge_lines = []
with open("data/FiltData_E20_v6_2018_Renumb_2.txt", "r") as inData, open("data/NoMultiEdgesE%s_v6_2.txt"%cutoff, "w+") as all_edges, open("data/MultiEdgesE%s_v6_2.txt"%cutoff, "w+") as multi_edges, open("data/MultiEdgesE%s_v6_DontCheck_2.txt"%cutoff, "w+") as dontcheck:
for line in inData:
if "dom1" not in line:
line = line.strip().split("\t")
dom1 = line[0]
dom2 = line[1]
e_value = float(line[2])
if e_value <= cutoff:
if ([dom1, dom2] in multiple_edges or [dom2, dom1] in multiple_edges):
multi_edge_lines.append(line)
else:
all_edges.write("\t".join(line) + "\t1\n")
else:
all_edges.write(line.strip() + "\tInCyto?\n")
multi_edges.write(line.strip() + "\tInCyto?\n")
#remove the obvious near duplicates
for value in multiple_edges: #for each pair of PDBs with multiconnections:
#print(value)
edges = [] #edges relating to that pair
for line in multi_edge_lines:
if (value[0] in line and value[1] in line):
edges.append(line)
if len(edges) == 1:
print("Something went wrong ", line)
all_edges.write("\t".join(line) + "\n")
else:
kept_edges = []
#print("starting:")
#print(edges)
while len(edges) >0:
first_row = edges[0]
e_value = float(first_row[2])
pop_list = []
print_row = True
#print(len(edges), edges)
for x in range(1, len(edges)):
if edges[x][6:10] == first_row[6:10]:
if float(edges[x][2]) <= e_value:
del edges[0]
print_row = False
break
else:
pop_list.append(x)
#check if nearly identical segments
elif (abs(int(edges[x][7]) - int(first_row[7])) < 6 and abs(int(edges[x][9]) - int(first_row[9])) < 6):
#print(first_row, edges[x])
#print("ends the same", abs(int(edges[x][8]) - int(first_row[8])), abs(int(edges[x][10]) - int(first_row[10])))
if abs( abs(int(edges[x][6]) - int(first_row[6])) + abs(int(edges[x][8]) - int(first_row[8])) ) < 15:
#print("start ~same", abs(int(edges[x][7]) - int(first_row[7])), abs(int(edges[x][9]) - int(first_row[9])))
if float(edges[x][2]) <= e_value:
del edges[0]
print_row = False
break
else:
pop_list.append(x)
#check if alignment is a perfect subset
else:
#print("Ends identical ", first_row, edges[x])
if int(edges[x][3]) < int(first_row[3]):
if len(first_row[10].split(edges[x][10][5:-5])) == 2 and len(first_row[11].split(edges[x][11][5:-5])) == 2:
#print(first_row, edges[x])
pop_list.append(x)
elif int(edges[x][3]) > int(first_row[3]):
if len(edges[x][10].split(first_row[10][5:-5])) == 2 and len(edges[x][11].split(first_row[11][5:-5])) == 2:
#print(first_row, edges[x])
del edges[0]
print_row = False
break
#check if alignment is a perfect subset
else:
#print("Starts identical ", first_row, edges[x])
if int(edges[x][3]) < int(first_row[3]):
if len(first_row[10].split(edges[x][10][5:-5])) == 2 and len(first_row[11].split(edges[x][11][5:-5])) == 2:
#print(first_row, edges[x])
pop_list.append(x)
elif int(edges[x][3]) > int(first_row[3]):
if len(edges[x][10].split(first_row[10][5:-5])) == 2 and len(edges[x][11].split(first_row[11][5:-5])) == 2:
#print(first_row, edges[x])
del edges[0]
print_row = False
break
#if value[1] == "1pho_A" and value[0] == "2wjr_A": print(pop_list, print_row)
for y in reversed(pop_list): del edges[y]
if print_row == True:
#all_edges.write("\t".join(first_row) + "\n")
kept_edges.append(first_row)
del edges[0]
#print("Final edges: ")
#print(kept_edges)
if len(kept_edges) == 1:
all_edges.write("\t".join(kept_edges[0]) + "\t1\n")
else:
keep_row = kept_edges[0]
for x in range(1,len(kept_edges)):
if float(kept_edges[x][2]) < float(keep_row[2]):
keep_row = kept_edges[x]
if len(kept_edges) == 2:
if (int(kept_edges[1][7]) < int(kept_edges[0][6])+10) or (int(kept_edges[1][6]) > int(kept_edges[0][7])-10) or (int(kept_edges[1][9]) < int(kept_edges[0][8])+10) or (int(kept_edges[1][8]) > int(kept_edges[0][9])-10):
for value in kept_edges:
if value == keep_row:
dontcheck.write("\t".join(value) + "\t1\n")
else:
dontcheck.write("\t".join(value) + "\t0\n")
elif (abs(int(kept_edges[1][7]) - int(kept_edges[0][7])) < 10 and abs(int(kept_edges[1][8]) - int(kept_edges[0][8])) < 10 and abs(int(kept_edges[1][6]) - int(kept_edges[0][6])) > 25 and abs(int(kept_edges[1][9]) - int(kept_edges[0][9])) > 25):
for value in kept_edges:
if value == keep_row:
dontcheck.write("\t".join(value) + "\t1\n")
else:
dontcheck.write("\t".join(value) + "\t0\n")
elif (abs(int(kept_edges[1][7]) - int(kept_edges[0][7])) > 25 and abs(int(kept_edges[1][8]) - int(kept_edges[0][8])) > 25 and abs(int(kept_edges[1][6]) - int(kept_edges[0][6])) < 10 and abs(int(kept_edges[1][9]) - int(kept_edges[0][9])) < 10):
for value in kept_edges:
if value == keep_row:
dontcheck.write("\t".join(value) + "\t1\n")
else:
dontcheck.write("\t".join(value) + "\t0\n")
elif (abs(int(kept_edges[1][7]) - int(kept_edges[0][7])) < 6 and abs(int(kept_edges[1][9]) - int(kept_edges[0][9])) > 25) or (abs(int(kept_edges[1][7]) - int(kept_edges[0][7])) > 25 and abs(int(kept_edges[1][9]) - int(kept_edges[0][9])) < 6):
for value in kept_edges:
if value == keep_row:
dontcheck.write("\t".join(value) + "\t1\n")
else:
dontcheck.write("\t".join(value) + "\t0\n")
elif (abs(int(kept_edges[1][6]) - int(kept_edges[0][6])) < 6 and abs(int(kept_edges[1][8]) - int(kept_edges[0][8])) > 25) or (abs(int(kept_edges[1][6]) - int(kept_edges[0][6])) > 25 and abs(int(kept_edges[1][8]) - int(kept_edges[0][8])) < 6):
for value in kept_edges:
if value == keep_row:
dontcheck.write("\t".join(value) + "\t1\n")
else:
dontcheck.write("\t".join(value) + "\t0\n")
else:
for value in kept_edges:
if value == keep_row:
multi_edges.write("\t".join(value) + "\t1\n")
else:
multi_edges.write("\t".join(value) + "\t0\n")
else:
for value in kept_edges:
if value == keep_row:
multi_edges.write("\t".join(value) + "\t1\n")
else:
multi_edges.write("\t".join(value) + "\t0\n")