def createNetwork(network_file, filename, colname, output):
logfc = pd.read_csv(filename, sep="\t", header=0, index_col=0)
logfc = logfc[~logfc.index.duplicated(keep='first')]
raw_network = Network(network_file, "\t")
for n in raw_network.getNodes():
try:
raw_network.getNode(n).logFC = logfc.loc[n, colname]
except:
continue
# logFC file has been filtered by p-value to be less than <0.05, then node without logFC value (0 logFC) should be removed
raw_network.removeNonDiffNode()
raw_network.filterNetwork()
raw_network.printNetworkTofile(set(), file(output, "w"))
return raw_network
def main():
# Config class
config = Config.Config('config/config.yaml')
# Logger class
logger = Logger.Logger(config.get('log'))
# Start the logger
logger.run()
# Network class
network = Network.Network({
'ip_file': config.get('ip.file')
}, logger)
# GoDaddy class
godaddy = GoDaddy.GoDaddy({
'username': config.get('godaddy.username'),
'password': config.get('godaddy.password'),
'hostname': config.get('godaddy.hostname'),
'type': config.get('godaddy.type'),
}, logger, network)
# Get the public IP
ip = network.getPublicIP()
if network.checkIpCache(ip) != 1:
godaddy.updateDNS(ip)
else:
print("Everything is all good, mate")
from lib import Network
netApi = Network.NetworkApi(
'0RNK9UsKTgCCRWSQJg6sdzdYp7JlWs9J',
'IIOunDfkI9bMolM2cJdwUx0IPTPPehzY'
)
# Gets list of all Network Files
networkFileList = netApi.listNetworks()
for networkFile in networkFileList:
if networkFile['name'] !== 'Default.csv.json': # Don't delete the default Network
print(
netApi.deleteNetwork(networkFile['id'])
)
## Script filter network generated from FIMO
## accept a parameter that is the folder of the network files
import sys
import os
import shutil
sys.path.append("..")
import numpy as np
import pandas as pd
from lib.Network import *
from lib.GeneralUtil import *
from lib.johnson import *
folder = sys.argv[1]
files = os.listdir(folder)
for f in files:
raw_network = Network(folder + "/" + f, "\t")
raw_network.filterNetwork()
fout = file(folder + "/filtered_" + f, "w")
raw_network.printNetworkTofile(set(), fout)
fout.close()
# Load test case
alg = Algebra.Allen(False)
tf = ReadFile.TestFile("test cases/ia_test_instances_10.txt")
# alg = Algebra.Allen(True)
# tf = ReadFile.TestFile("test cases/30x500_m_3_allen.csp.txt")
skip = 0
overall = timeit.default_timer()
# statprof.start()
# try:
for graph in tf.processNext():
if skip > 0:
skip -= 1
continue
net = Network.QCSP(alg, *graph[0]) # First row is always header
graph = graph[1:] # remove header
# create list for very first A-Closure call
initialConstraints = []
for A, B, rel in graph:
net.addConstraint(A, B, rel)
if rel != net.algebra.Universal:
initialConstraints.append([A, B])
print("processing: '%s'" % net.description)
refinementCounter = 0
pre = timeit.default_timer()
valid = Search(net).refinementV2(initialConstraints,
net.listOfNontractableConstraints(0))
print("%d Iterations" % refinementCounter)
print(" > '%s' is %s (%f s)" %