metastudent 2.0.1-1 / usr / lib / python2.7 / dist-packages / metastudentPkg / runMethods.py

'''
Created on Mar 17, 2012

@author: hampt
'''

import os
import commands
from Logger import Logger
from BlastWrapper import blastallParameters, createBlastPGPCommand
from metastudentPkg.commons import p, splitBigFastaFile
import sys
import shlex
import subprocess
import time


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

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