def runMethodC(blastOutputFilePath, fastaFilePath, tmpDir, scoring, onto,
configMap, debug): #
p("Running Method C")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodC")
outputFilePath = os.path.join(tmpDirPath, "output.%s.txt" % (onto))
commandsi = [
"mkdir -p " + tmpDirPath, "cd " + configMap["GROUP_C_PATH"],
"./CafaWrapper3.pl %s %s %s %s" %
(blastOutputFilePath, outputFilePath, scoring, tmpDirPath)
]
commandString = ";".join(commandsi)
if debug:
print >> sys.stderr, commandString
os.chdir(currCwd)
logFile = None
logPath = os.path.join(tmpDir, "logC.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True: #s != 0:
logFile.write("Command: " + commandString)
logFile.write(str(s))
logFile.write(o)
if s != 0:
print >> sys.stderr, "!!!Error!!! " + commandString
print >> sys.stderr, str(s)
print >> sys.stderr, o
#raise
logFile.close()
predFilesContent = []
with open(outputFilePath) as f:
preds = set([])
for line in f.readlines():
line = line.rstrip()
if line.rstrip() == "" or line.startswith(
"AUTHOR") or line.startswith("MODEL") or line.startswith(
"ACCURACY") or line.startswith(
"KEYWORDS") or line.startswith("END"):
None
else:
targetId, goTerm, rel = line.rstrip().split(" ")
relFloat = max(min(float(rel), 1.00), 0.00)
rel = "%.2f" % (relFloat)
line = targetId[:63] + "\t" + goTerm + "\t" + rel
if targetId[:63] + "\t" + goTerm not in preds and goTerm.strip(
) != "" and float(rel) > 0.0:
predFilesContent.append(line)
preds.add(targetId[:63] + "\t" + goTerm)
return predFilesContent
def runMethodB(blastOutputFilePath, fastaFilePath, tmpDir, GROUP_B_K, onto, configMap):#
p("Running Method B")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodB")
if not os.path.exists(tmpDirPath):
os.mkdir(tmpDirPath)
jarPath = configMap["JAR_INSTALL_FOLDER_PATH"].rstrip("/")
outputFilePath = os.path.join(tmpDirPath, onto)
os.mkdir(outputFilePath)
commandsi = ["mkdir -p " + tmpDirPath,
"cd " + configMap["GROUP_B_PATH"],
"./knn_weighted -m weighted_knn -j %s -d %s -i %s -o %s -k %s -l %s" % (blastOutputFilePath, blastOutputFilePath, fastaFilePath, outputFilePath, GROUP_B_K, jarPath)]
commandString = ";".join(commandsi)
#print commandString
os.chdir(currCwd)
logFile=None
logPath=os.path.join(tmpDir, "logB.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s) + "\n")
logFile.write(o+ "\n")
if s != 0:
print >> sys.stderr,"!!!Error!!! " + commandString
print >> sys.stderr,str(s)
print >> sys.stderr,o
#raise
logFile.close()
outputFilePath = os.path.join(outputFilePath, os.path.basename(fastaFilePath)+".weighted_knn.predicted_leaves")
idToGoTermCount = {}
predFilesContent=[]
with open(outputFilePath) as f:
for line in f.readlines():
line = line.rstrip()
if line.startswith("AUTHOR") or line.startswith("MODEL") or line.startswith("ACCURACY") or line.startswith("KEYWORDS") or line.startswith("END"):
None
else:
currId = line.split("\t")[0][:63]
restOfLine = "\t".join(line.split("\t")[1:])
if idToGoTermCount.get(currId, 0) < 1000:
if float(restOfLine.split("\t")[1]) > 1.0:
restOfLine = restOfLine.rstrip("\n").replace("1.01", "1.00")
idToGoTermCount[currId] = idToGoTermCount.get(currId, 0) + 1
line = currId + "\t" + restOfLine
predFilesContent.append(line)
return predFilesContent
def runMethodA(blastOutputFilePath, fastaFilePath, tmpDir, GROUP_A_THRESHOLD, GROUP_A_K, iters, onto, configMap):#
p("Running Method A")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodA")
jarPath = os.path.join(configMap["JAR_INSTALL_FOLDER_PATH"], "gossip.jar")
outputFilePath = os.path.join(tmpDirPath, "output.%s.cafa.txt" % (onto))
commandsi = ["mkdir -p " + tmpDirPath,
"cd " + configMap["GROUP_A_PATH"],
"java -cp %s GOSSIPSTarter %s %s %s %s %s %s" % (jarPath, fastaFilePath, blastOutputFilePath, outputFilePath, GROUP_A_THRESHOLD, GROUP_A_K, iters)]
commandString = ";".join(commandsi)
os.chdir(currCwd)
logFile=None
logPath=os.path.join(tmpDir, "logA.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s)+"\n")
logFile.write(o+"\n")
if s != 0:
print >> sys.stderr,"!!!Error!!! " + commandString
print >> sys.stderr,str(s)
print >> sys.stderr,o
#raise
logFile.close()
outputFilePath = outputFilePath+".cafa"
outputFile = open(outputFilePath)
preds = set([])
predFilesContent=[]
for line in outputFile:
if line.startswith("AUTHOR") or line.startswith("MODEL") or line.startswith("ACCURACY") or line.startswith("KEYWORDS") or line.startswith("END"):
None
else:
targetId, goTerm, rel = line.rstrip().split("\t")
targetId = targetId[1:].split("(")[0][:63]
relFloat = max(min(float(rel), 1.00), 0.00)
rel = "%.2f" % (relFloat)
line = targetId + "\t" + goTerm + "\t" + rel
if targetId + "\t" + goTerm not in preds and goTerm.strip() != "":
predFilesContent.append(line)
preds.add(targetId + "\t" + goTerm)
return predFilesContent
def runMethodC(blastOutputFilePath, fastaFilePath, tmpDir, scoring, onto, configMap, debug):#
p("Running Method C")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodC")
outputFilePath = os.path.join(tmpDirPath, "output.%s.txt" % (onto))
commandsi = ["mkdir -p " + tmpDirPath,
"cd " + configMap["GROUP_C_PATH"],
"./CafaWrapper3.pl %s %s %s %s" % (blastOutputFilePath, outputFilePath, scoring, tmpDirPath)]
commandString = ";".join(commandsi)
if debug:
print >> sys.stderr, commandString
os.chdir(currCwd)
logFile=None
logPath=os.path.join(tmpDir, "logC.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString)
logFile.write(str(s))
logFile.write(o)
if s != 0:
print >> sys.stderr, "!!!Error!!! " + commandString
print >> sys.stderr,str(s)
print >> sys.stderr,o
#raise
logFile.close()
predFilesContent = []
with open(outputFilePath) as f:
preds = set([])
for line in f.readlines():
line=line.rstrip()
if line.rstrip() == "" or line.startswith("AUTHOR") or line.startswith("MODEL") or line.startswith("ACCURACY") or line.startswith("KEYWORDS") or line.startswith("END"):
None
else:
targetId, goTerm, rel = line.rstrip().split(" ")
relFloat = max(min(float(rel), 1.00), 0.00)
rel = "%.2f" % (relFloat)
line = targetId[:63] + "\t" + goTerm + "\t" + rel
if targetId[:63] + "\t" + goTerm not in preds and goTerm.strip() != "" and float(rel) > 0.0:
predFilesContent.append(line)
preds.add(targetId[:63] + "\t" + goTerm)
return predFilesContent
def runBlast(inputFilePath, blastDatabasePath, outputFilePath, tmpDir, eValue,
iters, configMap):
fastaSplits = splitBigFastaFile(inputFilePath, tmpDir,
configMap["FASTA_SPLIT_SIZE"])
for i, fastaSplit in enumerate(fastaSplits):
blastParas = blastallParameters()
blastParas.setBlastExePath(configMap["BLASTPGP_EXE_PATH"])
blastParas.setBlastDatabasePath(blastDatabasePath)
blastParas.setEValue(eValue)
blastParas.setJ(iters)
blastParas.setB(1000)
blastParas.setV(1000)
blastParas.setInputFilePath(fastaSplit)
blastParas.setOutputFilePath(fastaSplit + ".blast")
blastCommand = createBlastPGPCommand(blastParas)
#print blastCommand
# executeCommandInSGELocalAsync(blastCommand, "blast_%d" % i, tmpDir)
#
# executeCommandInSGELocalAsyncJoin()
s, o = commands.getstatusoutput(blastCommand)
if s != 0:
Logger.log("!!!Error!!! " + blastCommand)
Logger.log(s)
Logger.log(o)
raise Exception
p("Merging Blast Output")
# allRoundSplits = ["" for bla in range(int(NUMBER_OF_ITERATIONS))]
bigOutputFile = open(outputFilePath, 'w')
for fastaSplit in fastaSplits:
blastFile = open(fastaSplit + ".blast")
blastOutput = "\n" + blastFile.read()
blastFile.close()
bigOutputFile.write(blastOutput)
bigOutputFile.close()
def runBlast(inputFilePath, blastDatabasePath, outputFilePath, tmpDir, eValue, iters, configMap):
fastaSplits = splitBigFastaFile(inputFilePath, tmpDir, configMap["FASTA_SPLIT_SIZE"])
for i, fastaSplit in enumerate(fastaSplits):
blastParas = blastallParameters()
blastParas.setBlastExePath(configMap["BLASTPGP_EXE_PATH"])
blastParas.setBlastDatabasePath(blastDatabasePath)
blastParas.setEValue(eValue)
blastParas.setJ(iters)
blastParas.setB(1000)
blastParas.setV(1000)
blastParas.setInputFilePath(fastaSplit)
blastParas.setOutputFilePath(fastaSplit+".blast")
blastCommand = createBlastPGPCommand(blastParas)
#print blastCommand
# executeCommandInSGELocalAsync(blastCommand, "blast_%d" % i, tmpDir)
#
# executeCommandInSGELocalAsyncJoin()
s, o = commands.getstatusoutput(blastCommand)
if s != 0:
Logger.log("!!!Error!!! " + blastCommand)
Logger.log(s)
Logger.log(o)
raise Exception
p("Merging Blast Output")
# allRoundSplits = ["" for bla in range(int(NUMBER_OF_ITERATIONS))]
bigOutputFile = open(outputFilePath,'w')
for fastaSplit in fastaSplits:
blastFile = open(fastaSplit+".blast")
blastOutput = "\n" + blastFile.read()
blastFile.close()
bigOutputFile.write(blastOutput)
bigOutputFile.close()
def runMethodA(blastOutputFilePath, fastaFilePath, tmpDir, GROUP_A_THRESHOLD,
GROUP_A_K, iters, onto, configMap): #
p("Running Method A")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodA")
jarPath = os.path.join(configMap["JAR_INSTALL_FOLDER_PATH"], "gossip.jar")
outputFilePath = os.path.join(tmpDirPath, "output.%s.cafa.txt" % (onto))
commandsi = [
"mkdir -p " + tmpDirPath, "cd " + configMap["GROUP_A_PATH"],
"java -cp %s GOSSIPSTarter %s %s %s %s %s %s" %
(jarPath, fastaFilePath, blastOutputFilePath, outputFilePath,
GROUP_A_THRESHOLD, GROUP_A_K, iters)
]
commandString = ";".join(commandsi)
os.chdir(currCwd)
logFile = None
logPath = os.path.join(tmpDir, "logA.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True: #s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s) + "\n")
logFile.write(o + "\n")
if s != 0:
print >> sys.stderr, "!!!Error!!! " + commandString
print >> sys.stderr, str(s)
print >> sys.stderr, o
#raise
logFile.close()
outputFilePath = outputFilePath + ".cafa"
outputFile = open(outputFilePath)
preds = set([])
predFilesContent = []
for line in outputFile:
if line.startswith("AUTHOR") or line.startswith(
"MODEL") or line.startswith("ACCURACY") or line.startswith(
"KEYWORDS") or line.startswith("END"):
None
else:
targetId, goTerm, rel = line.rstrip().split("\t")
targetId = targetId[1:].split("(")[0][:63]
relFloat = max(min(float(rel), 1.00), 0.00)
rel = "%.2f" % (relFloat)
line = targetId + "\t" + goTerm + "\t" + rel
if targetId + "\t" + goTerm not in preds and goTerm.strip() != "":
predFilesContent.append(line)
preds.add(targetId + "\t" + goTerm)
return predFilesContent
def runMethodB(blastOutputFilePath, fastaFilePath, tmpDir, GROUP_B_K, onto,
configMap): #
p("Running Method B")
currCwd = os.getcwd()
tmpDirPath = os.path.join(tmpDir, "methodB")
if not os.path.exists(tmpDirPath):
os.mkdir(tmpDirPath)
jarPath = configMap["JAR_INSTALL_FOLDER_PATH"].rstrip("/")
outputFilePath = os.path.join(tmpDirPath, onto)
os.mkdir(outputFilePath)
commandsi = [
"mkdir -p " + tmpDirPath, "cd " + configMap["GROUP_B_PATH"],
"./knn_weighted -m weighted_knn -j %s -d %s -i %s -o %s -k %s -l %s" %
(blastOutputFilePath, blastOutputFilePath, fastaFilePath,
outputFilePath, GROUP_B_K, jarPath)
]
commandString = ";".join(commandsi)
#print commandString
os.chdir(currCwd)
logFile = None
logPath = os.path.join(tmpDir, "logB.txt")
if not os.path.exists(logPath):
logFile = open(logPath, 'w')
else:
logFile = open(logPath, 'a')
s, o = commands.getstatusoutput(commandString)
if True: #s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s) + "\n")
logFile.write(o + "\n")
if s != 0:
print >> sys.stderr, "!!!Error!!! " + commandString
print >> sys.stderr, str(s)
print >> sys.stderr, o
#raise
logFile.close()
outputFilePath = os.path.join(
outputFilePath,
os.path.basename(fastaFilePath) + ".weighted_knn.predicted_leaves")
idToGoTermCount = {}
predFilesContent = []
with open(outputFilePath) as f:
for line in f.readlines():
line = line.rstrip()
if line.startswith("AUTHOR") or line.startswith(
"MODEL") or line.startswith("ACCURACY") or line.startswith(
"KEYWORDS") or line.startswith("END"):
None
else:
currId = line.split("\t")[0][:63]
restOfLine = "\t".join(line.split("\t")[1:])
if idToGoTermCount.get(currId, 0) < 1000:
if float(restOfLine.split("\t")[1]) > 1.0:
restOfLine = restOfLine.rstrip("\n").replace(
"1.01", "1.00")
idToGoTermCount[currId] = idToGoTermCount.get(currId,
0) + 1
line = currId + "\t" + restOfLine
predFilesContent.append(line)
return predFilesContent