def mergeG2():
fin = open("%s/FSUBTEST/2/GFileMap.txt" % params.JADER_OUT)
fout = open("%s/FSUBTEST/2/G2.txt" % params.JADER_OUT, "w")
dDrug2Se = dict()
while True:
line = fin.readline()
if line == "":
break
line = line.strip()
parts = line.split("\t")
hashFile = parts[0]
f = open("%s/FSUBTEST/2/%s" % (params.JADER_OUT, hashFile))
while True:
l = f.readline()
if l == "":
break
parts = l.strip().split("_")
drug = parts[0]
se = parts[1].split("\t")[0]
ses = utils.get_insert_key_dict(dDrug2Se, drug, [])
ses.append(se)
# print(drug, ses)
f.close()
for k, v in dDrug2Se.items():
fout.write("%s\t%s\n" % (k, ",".join(v)))
fout.close()
def plotDrugLength2NSEs():
import numpy as np
dDrugLength2NSes = dict()
fin = open("%s/JADER2AllSeList.txt" % params.JADER_OUT)
while True:
line = fin.readline()
if line == "":
break
parts = line.strip().split("$")
drugCombs = parts[0].split(":")[0]
nDrug = len(drugCombs.split(","))
nSe = int(parts[1])
seLengths = utils.get_insert_key_dict(dDrugLength2NSes, nDrug, [])
seLengths.append(nSe)
x = dDrugLength2NSes.keys()
xmax = max(x)
x = [i for i in range(1, xmax + 1)]
y = np.zeros(xmax)
for k, v in dDrugLength2NSes.items():
# avg = sum(v) / len(v)
y[k-1] = np.median(v)
import matplotlib.pyplot as plt
plt.scatter(x,y)
plt.xlabel("DrugComb length")
plt.ylabel("Median SEs")
plt.tight_layout()
plt.savefig("%s/%s.png" % (params.FIG_DIR, "JADERAvgSEDrugCombLength"))
def exportReactionsFile():
fin = codecs.open("%s/reactions.txt" % CAD_FOLDER_INP)
fout = open("%s/Reactions1.txt" % params.CAD_OUT, "w")
dId2Ses = dict()
while True:
line = fin.readline()
if line == "":
break
ios = io.StringIO(line.strip().lower())
vv = list(csv.reader(ios, delimiter='$'))[0]
# print( vv)
sId = vv[1]
seName = vv[5]
isInValid = False
for invalidSe in invalidSes:
if seName.__contains__(invalidSe):
isInValid = True
break
if isInValid:
continue
seList = utils.get_insert_key_dict(dId2Ses, sId, set())
seList.add(seName)
# print(cId, currentDrugs)
fin.close()
for k,v in dId2Ses.items():
fout.write("%s$%s\n" % (k, ",".join(list(v))))
fout.close()
def exportSubG2():
fin = open("%s/JADER.txt" % params.JADER_OUT)
foutDict = dict()
dlen2SeCount = dict()
nA = 0
print("Reading...")
while True:
line = fin.readline()
if line == "":
break
nA += 1
print("\r%s" % nA, end="")
parts = line.strip().split("$")
drugCmb = parts[0]
ses = parts[1]
drugs = drugCmb.split(",")
nD = len(drugs)
drugs = sorted(drugs)
sortNames = ",".join(drugs)
fO = utils.get_dict(foutDict, nD, -1)
if fO == -1:
fO = open("%s/SUB/G%s" % (params.JADER_OUT, nD), "w")
foutDict[nD] = fO
fO.write("%s$%s\n" % (sortNames, ses))
if len(drugs) > 2 and len(drugs) <= 20:
for i in range(len(drugs)):
for j in range(i + 1, len(drugs)):
d1 = drugs[i]
d2 = drugs[j]
pair = "%s,%s" % (d1, d2)
try:
f2 = foutDict[2]
except:
f2 = open("%s/SUB/G%s" % (params.JADER_OUT, 2), "w")
foutDict[2] = f2
f2.write("%s$%s\n" % (pair, ses))
len2SeCount = utils.get_insert_key_dict(dlen2SeCount, nD, dict())
sess = ses.split(",")
for se in sess:
utils.add_dict_counter(len2SeCount, se)
for k, v in foutDict.items():
v.close()
d2 = dict()
for k, v in dlen2SeCount.items():
kvs = utils.sort_dict(v)
ks = []
for kv in kvs:
kk, _ = kv
ks.append(kk)
d2[k] = ks
utils.save_obj(d2, "%s/SUB/drugSize2CommonSEs" % params.JADER_OUT)
def exportDrugCom2Side():
fin = open("%s/JADER.txt" % params.JADER_OUT)
fout = open("%s/JADER2AllSeList.txt" % params.JADER_OUT, "w")
dDrugComb2Se = dict()
dDrugCombCount = dict()
dDrugCom2Lenght = dict()
drugCont = dict()
seCount = dict()
cc = 0
while True:
line = fin.readline()
if line == "":
break
cc += 1
line = line.strip()
parts = line.split("$")
drugCom = parts[0]
dDrugCom2Lenght[drugCom] = len(drugCom.split(","))
ses = parts[1].split(",")
utils.add_dict_counter(dDrugCombCount, drugCom, 1)
for drug in drugCom.split(","):
utils.add_dict_counter(drugCont, drug, 1)
sesComb = utils.get_insert_key_dict(dDrugComb2Se, drugCom, dict())
for se in ses:
utils.add_dict_counter(sesComb, se, 1)
utils.add_dict_counter(seCount, se)
kvs = utils.sort_dict(dDrugCombCount)
for kv in kvs:
k, v = kv
seCountKv = utils.sort_dict(dDrugComb2Se[k])
sString = []
for seCountx in seCountKv:
se,count = seCountx
sString.append("%s:%s"% (se, count))
fout.write("%s:%s$%s$%s\n" % (k, v, len(sString), ",".join(sString)))
fout.close()
utils.save_obj(seCount, "%s/JADERSeCountFX" % params.JADER_OUT)
utils.save_obj(dDrugCom2Lenght, "%s/DrugCombLength" % params.JADER_OUT)
print(len(drugCont), len(seCount))
def exportSub():
fin = open("%s/FDrug2SeList_19814.txt" % params.FADER_OUT)
foutDict = dict()
dlen2SeCount = dict()
nA = 0
print("Reading...")
while True:
line = fin.readline()
if line == "":
break
nA += 1
print("\r%s" % nA, end="")
parts = line.strip().split("$")
drugCmb = parts[0]
ses = parts[1]
drugs = drugCmb.split(",")
nD = len(drugs)
sortNames = ",".join(sorted(drugs))
fO = utils.get_dict(foutDict, nD, -1)
if fO == -1:
fO = open("%s/SUB/%s" % (params.FADER_OUT, nD), "w")
foutDict[nD] = fO
fO.write("%s$%s\n" % (sortNames, ses))
len2SeCount = utils.get_insert_key_dict(dlen2SeCount, nD, dict())
sess = ses.split(",")
for se in sess:
utils.add_dict_counter(len2SeCount, se)
for k, v in foutDict.items():
v.close()
d2 = dict()
for k, v in dlen2SeCount.items():
kvs = utils.sort_dict(v)
ks = []
for kv in kvs:
kk, _ = kv
ks.append(kk)
d2[k] = ks
utils.save_obj(d2, "%s/SUB/drugSize2CommonSEs" % params.FADER_OUT)
def exportPolySEs():
drugDesMap = utils.load_obj("%s/DrugBank/DrugMorganDes" % params.DATA_DIR)
seDict = dict()
dComb2Se = dict()
fin = open("%s/FTest/FileMap.txt" % params.FADER_OUT)
hashFiles = fin.readlines()
ln = min(N_FILE, len(hashFiles))
hashFiles = hashFiles[:ln]
for hashId in hashFiles:
parts = hashId.strip().split("\t")
hashId = parts[0]
ses = parts[1].split("__")
for se in ses:
utils.get_update_dict_index(seDict, se)
path = "%s/FTest/%s" % (params.FADER_OUT, hashId)
print("Reading... ", path)
polySes = open(path).readlines()
for polySe in polySes:
polySe = polySe.strip().split("_")
drugComb = polySe[0]
seParts = polySe[1].split("\t")
se = seParts[0]
if seParts[1] == 'inf':
pass
drugs = drugComb.split(",")
isValidComb = True
# print(drugs)
for drug in drugs:
if drug not in drugDesMap:
isValidComb = False
break
if isValidComb:
# print(drugComb)
sel = utils.get_insert_key_dict(dComb2Se, drugComb, [])
sel.append(se)
fout = open("%s/PolySes.txt" % params.FADER_OUT, "w")
for drugComb, ses in dComb2Se.items():
fout.write("%s\t%s\n" % (drugComb, ",".join(ses)) )
fout.close()
def exportPolySE():
fin = open("%s/%s" % (OUT_DIR, "ttStatsRe"))
dDrugPair2Se = dict()
while True:
line = fin.readline()
if line == "":
break
line = line.strip()
parts = line.split("\t")
drugPairs = parts[0]
se = parts[1]
seList = utils.get_insert_key_dict(dDrugPair2Se, drugPairs, [])
seList.append(se)
fin.close()
fin = open("%s/Data/DrugBank/DrugBankNames.txt" % params.C_DIR)
dName2Inchi = dict()
while True:
line = fin.readline()
if line == "":
break
line = line.strip()
parts = line.split("||")
drugName = parts[0]
inchi = parts[3]
dName2Inchi[drugName] = inchi
fin.close()
fout = open("%s/%s" % (OUT_DIR, "CPolySE"), "w")
for dp, ses in dDrugPair2Se.items():
d1, d2 = dp.split(",")
i1, i2 = utils.get_dict(dName2Inchi, d1,
-1), utils.get_dict(dName2Inchi, d2, -1)
if i1 == -1 or i2 == -1:
continue
if len(i1) < 2 or len(i2) < 2:
continue
fout.write("%s|%s|%s|%s|%s\n" % (d1, d2, i1, i2, ",".join(ses)))
fout.close()
def merger():
fin = open("%s/ReportDrug1.txt" % params.CAD_OUT)
fout = open("%s/ReportDrug2.txt" % params.CAD_OUT, "w")
dCout = dict()
nError = 0
cc = 0
dId2Drugs = dict()
while True:
line = fin.readline()
if line == "":
break
line = line.strip()
parts = line.split("$")
id = parts[0]
drugs = parts[1].split(",")
drugSet = utils.get_insert_key_dict(dId2Drugs, id, set())
for drug in drugs:
drugSet.add(drug)
fin.close()
for k, v in dId2Drugs.items():
fout.write("%s$%s\n" % (k, ",".join(sorted(list(v)))))
fout.close()
def filterDrugMatching2():
salts = set()
saltStrings = open("%s/rawMatching/Salt.txt" %
params.OUTPUT_DIR).readlines()
for line in saltStrings:
salts.add(line.strip())
fin = open("%s/rawMatching/MatchingDrug2.txt" % params.OUTPUT_DIR)
d = dict()
while True:
line = fin.readline()
if line == "":
break
line = line.strip()
parts = line.split("||")
match2 = utils.get_insert_key_dict(d, parts[0], set())
mD = parts[-1]
if mD in salts and not parts[0].startswith('hydro'):
continue
if parts[0].__contains__('sodium chloride'):
if mD == 'chloride ion' or mD == 'chlorine':
continue
match2.add(parts[-1])
fin.close()
fout1 = open("%s/rawMatching/MatchingDrug2_1.txt" % params.OUTPUT_DIR, "w")
fout2 = open("%s/rawMatching/MatchingDrug2_2.txt" % params.OUTPUT_DIR, "w")
for k, v in d.items():
v = list(v)
if len(v) == 1:
fout1.write("%s||%s\n" % (k, v[0]))
else:
fout2.write("%s||%s\n" % (k, ",".join(v)))
fout1.close()
fout2.close()
def exportIndicationFile():
fin = codecs.open("%s/report_drug_indication.txt" % CAD_FOLDER_INP)
fout = open("%s/Indications1.txt" % params.CAD_OUT, "w")
dId2Ses = dict()
while True:
line = fin.readline()
if line == "":
break
ios = io.StringIO(line.strip().lower())
vv = list(csv.reader(ios, delimiter='$'))[0]
# print( vv)
sId = vv[1]
indcName = vv[4]
indcList = utils.get_insert_key_dict(dId2Ses, sId, set())
indcList.add(indcName)
# print(cId, currentDrugs)
fin.close()
for k,v in dId2Ses.items():
fout.write("%s$%s\n" % (k, ",".join(list(v))))
fout.close()
def exportBySE(seNames, pathIn, dirOut, pathInfo):
fin = open(pathIn)
dCombCount = dict()
dCombSe = dict()
dSe = dict()
nA = 0
print("Reading...")
if not type(seNames) == set:
seNames = set(seNames)
print(seNames)
while True:
line = fin.readline()
if line == "":
break
nA += 1
parts = line.strip().split("$")
drugCmb = parts[0]
ses = parts[1]
ses = set(ses.split(","))
for se in seNames:
dCombCountx = utils.get_insert_key_dict(dCombCount, se, dict())
utils.add_dict_counter(dCombCountx, drugCmb)
if se in ses:
dComSEx = utils.get_insert_key_dict(dCombSe, se, dict())
utils.add_dict_counter(dSe, se)
utils.add_dict_counter(dComSEx, drugCmb)
fin.close()
print("Cal Contingency table...")
dContigenTable = dict()
for se in seNames:
dCombCountx = dCombCount[se]
dComSEx = utils.get_dict(dCombSe, se, dict())
nSe = utils.get_dict(dSe, se, 0)
if nSe == 0:
continue
for drugComb, nComb in dCombCountx.items():
ar = np.zeros((2, 2))
nCombSe = utils.get_dict(dComSEx, drugComb, 0)
if nCombSe == 0:
# print("SKIP")
continue
ar[0, 0] = nCombSe
ar[1, 0] = nComb - nCombSe
ar[0, 1] = nSe - nCombSe
ar[1, 1] = nA - (nComb + nSe - nCombSe)
nName = "%s_%s" % (drugComb, se)
dContigenTable[nName] = ar
producers = []
consumers = []
queue = Queue(params.K_FOLD)
counter = Value('i', 0)
counter2 = Value('i', 0)
inputList = list(dContigenTable.items())
nInputList = len(inputList)
nDPerWorker = int(nInputList / params.N_DATA_WORKER)
# assert 'g-csf' in allDrugNames
for i in range(params.N_DATA_WORKER):
startInd = i * nDPerWorker
endInd = (i + 1) * nDPerWorker
endInd = min(endInd, nInputList)
if i == params.N_DATA_WORKER - 1:
endInd = nInputList
data = inputList[startInd:endInd]
producers.append(Process(target=producer, args=(queue, data)))
sname = "__".join(list(seNames))
seNameString = "%s" % hash(sname)
fFileNameMap = open(pathInfo, "a")
fFileNameMap.write("%s\t%s\n" % (seNameString, sname))
fFileNameMap.close()
fout = open("%s/%s" % (dirOut, seNameString), "w")
p = Process(target=consumer, args=(queue, counter, counter2, fout, []))
p.daemon = True
consumers.append(p)
print("Start Producers...")
for p in producers:
p.start()
print("Start Consumers...")
for p in consumers:
p.start()
for p in producers:
p.join()
print("Finish Producers")
queue.put(None)
while True:
if counter.value == 0:
time.sleep(0.01)
continue
else:
break
fout.flush()
fout.close()
def exportAllDict1():
dDict1 = dict()
# Perfect matching:
fin = open("%s/rawMatching/MatchingDrug1.txt" % params.OUTPUT_DIR, "r")
while True:
line = fin.readline()
if line == "":
break
parts = line.strip().split("||")
t = utils.get_insert_key_dict(dDict1, parts[0], set())
t.add(parts[1])
fin.close()
# Salt:
fin = open("%s/rawMatching/Salt.txt" % params.OUTPUT_DIR)
lines = fin.readlines()
salts = set()
for salt in lines:
salt = salt.strip()
if salt.__contains__("#"):
continue
salts.add(salt)
# Partial matching:
dHardDrug, _, _ = loadDrugBankNames()
fin = open("%s/rawMatching/MatchingDrug2.txt" % params.OUTPUT_DIR)
lines = fin.readlines()
fin.close()
for line in lines:
line = line.strip()
parts = line.split("||")
if parts[1] in salts:
continue
drugBankName = dHardDrug[parts[1]]
jaderName = parts[0]
t = utils.get_insert_key_dict(dDict1, jaderName, set())
t.add(drugBankName)
# Typos
fin = open("%s/typosMatching/MatchingDrugTypos.txt" % params.OUTPUT_DIR)
lines = fin.readlines()
fin.close()
for line in lines:
line = line.strip()
if line.__contains__("#"):
continue
parts = line.split("||")
t = utils.get_insert_key_dict(dDict1, parts[0], set())
t.add(parts[-1])
fout = open("%s/finalMap/DrugMap1.txt" % params.OUTPUT_DIR, "w")
fout2 = open("%s/finalMap/DrugMap2.txt" % params.OUTPUT_DIR, "w")
for k, v in dDict1.items():
v = list(v)
if len(v) == 1:
fout.write("%s||%s\n" % (k, v[0]))
else:
fout2.write("%s||%s\n" % (k, "|".join(v)))
fout.close()
fout2.close()
