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print_csv_from_gpickle.py
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Thu, Jan 9, 05:10

print_csv_from_gpickle.py
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# LCSB EPFL 2020, Jasmin Hafner
# This script translates a gpickle graph file into a csv file suitable for Gephi import
import networkx as nx
import pickle
import timeit
import sys
import os
start_time = timeit.default_timer()
################## PARAMETERS ###################
CAR_cutoff = 0.34 # Best predictor for KEGG RPAIR of type "main"
################# OPTIONS ###################
assert 1 <= len(sys.argv) <= 2, "ERROR: only 0 or 1 arguments allowed."
if len(sys.argv) > 1 and sys.argv[1] == 'data_sources':
scopes = ['KEGG','MetaCyc','SEED', 'BiGG', 'BKMS', 'Brenda', 'MetaNetX', 'Reactome', 'Rhea', 'bioDB', 'bioATLAS', 'chemATLAS']
else:
scopes = ['bioDB', 'bioATLAS', 'chemATLAS']
################## FILE NAME ###################
input_dir_path = "../Data/"
output_folder = "../../../ATLASxAnalysis_output"
project_folder = "/CSV_files/"
if not os.path.isdir(output_folder):
os.mkdir(output_folder)
if not os.path.isdir(output_folder+project_folder):
os.mkdir(output_folder+project_folder)
output_dir_path = output_folder + project_folder
################## MAInn ###################
def main(input_dir, output_dir, scope):
rpair_file_path = input_dir + "rpairs_" + scope + "_hp.gpickle"
G = nx.Graph()
print("Load network:", scope)
G = nx.read_gpickle(rpair_file_path)
outfile = open(output_dir + 'EdgeList_' + scope + '_' + str(CAR_cutoff) + '.csv', 'w')
outfile.write('Source,Target,CAR\n')
#if CAR >= threshold -> write to table
for (u, v, c) in G.edges.data('car'):
if c > CAR_cutoff:
car = round(c, 3)
outfile.write('%d,%d,%s\n' %(u,v,str(car)))
outfile.close()
for scope in scopes:
main(input_dir_path, output_dir_path, scope)
print("Runtime:", str(timeit.default_timer() - start_time) + ' s')

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