phed, phenotypeIndex, kinshipSnpsDataset)
print "Generating second run GW plot."
res = gwaResults.Result(srInput,
name="KW_" + phenotypeName,
phenotypeID=phenotypeIndex)
res.filterMAF()
res.negLogTransform()
srRes = gwaResults.Result(srOutput,
name="EMMA_SR_" + phenotypeName,
phenotypeID=phenotypeIndex)
srRes.filterMAF()
srRes.negLogTransform()
srPngFile = pvalFile + ".sr.png"
plotResults.plotResultWithSecondRun(res,
srRes,
pngFile=srPngFile,
ylab="$-$log$_{10}(p)$",
plotBonferroni=True)
def _runEmmaScript_(snpsDataset,
kinshipSnpsDataset,
phed,
p_i,
rFile,
chr=None,
delim=",",
missingVal="NA",
boundaries=[-1, -1],
lrt=False):
def _run_():
if len(sys.argv) == 1:
print __doc__
sys.exit(2)
long_options_list = ["rFile=","chr=", "delim=", "missingval=", "withArrayId=", "BoundaryStart=", "removeOutliers=", "addConstant=",
"logTransform", "BoundaryEnd=", "phenotypeFileType=", "help", "parallel=", "parallelAll", "LRT", "minMAF=",
"kinshipDatafile=", "phenotypeRanks", "onlyMissing","onlyOriginal96", "onlyOriginal192", "onlyBelowLatidue=",
"complement", "negate", "srInput=", "sr","srOutput=", "srPar=","srSkipFirstRun", "testRobustness",
"permutationFilter="]
try:
opts, args = getopt.getopt(sys.argv[1:], "o:c:d:m:a:h", long_options_list)
except:
traceback.print_exc()
print sys.exc_info()
print __doc__
sys.exit(2)
phenotypeRanks = False
removeOutliers = None
addConstant = -1
phenotypeFileType = 1
rFile = None
delim = ","
missingVal = "NA"
help = 0
minMAF=0.0
withArrayIds = 1
boundaries = [-1,-1]
chr=None
parallel = None
logTransform = False
negate = False
parallelAll = False
lrt = False
kinshipDatafile = None
onlyMissing = False
onlyOriginal96 = False
onlyOriginal192 = False
onlyBelowLatidue = None
complement = False
sr = False
srOutput = False
srInput = False
srSkipFirstRun = False
srTopQuantile = 0.95
srWindowSize = 30000
testRobustness = False
permutationFilter = 0.002
for opt, arg in opts:
if opt in ("-h", "--help"):
help = 1
print __doc__
elif opt in ("-a","--withArrayId"):
withArrayIds = int(arg)
elif opt in ("-o","--rFile"):
rFile = arg
elif opt in ("--phenotypeFileType"):
phenotypeFileType = int(arg)
elif opt in ("--BoundaryStart"):
boundaries[0] = int(arg)
elif opt in ("--BoundaryEnd"):
boundaries[1] = int(arg)
elif opt in ("--addConstant"):
addConstant = float(arg)
elif opt in ("--parallel"):
parallel = arg
elif opt in ("--minMAF"):
minMAF = float(arg)
elif opt in ("--parallelAll"):
parallelAll = True
elif opt in ("--onlyMissing"):
onlyMissing = True
elif opt in ("--onlyOriginal96"):
onlyOriginal96 = True
elif opt in ("--onlyOriginal192"):
onlyOriginal192 = True
elif opt in ("--onlyBelowLatidue"):
onlyBelowLatidue = float(arg)
elif opt in ("--complement"):
complement = True
elif opt in ("--logTransform"):
logTransform = True
elif opt in ("--negate"):
negate = True
elif opt in ("--removeOutliers"):
removeOutliers = float(arg)
elif opt in ("--LRT"):
lrt = True
elif opt in ("-c","--chr"):
chr = int(arg)
elif opt in ("-d","--delim"):
delim = arg
elif opt in ("-m","--missingval"):
missingVal = arg
elif opt in ("--kinshipDatafile"):
kinshipDatafile = arg
elif opt in ("--phenotypeRanks"):
phenotypeRanks = True
elif opt in ("--sr"):
sr = True
elif opt in ("--srSkipFirstRun"):
srSkipFirstRun = True
elif opt in ("--srInput"):
srInput = arg
elif opt in ("--srOutput"):
srOutput = arg
elif opt in ("--srPar"):
vals = arg.split(",")
srTopQuantile = float(vals[0])
srWindowSize = int(vals[1])
elif opt in ("--testRobustness"):
testRobustness = True
elif opt in ("--permutationFilter"):
permutationFilter = float(arg)
else:
if help==0:
print "Unkown option!!\n"
print __doc__
sys.exit(2)
if len(args)<3 and not parallel:
if help==0:
print "Arguments are missing!!\n"
print __doc__
sys.exit(2)
print "Emma is being set up with the following parameters:"
print "output:",rFile
print "phenotypeRanks:",phenotypeRanks
print "withArrayId:",withArrayIds
print "phenotypeFileType:",phenotypeFileType
print "parallel:",parallel
print "parallelAll:",parallelAll
print "minMAF:",minMAF
print "LRT:",lrt
print "delim:",delim
print "missingval:",missingVal
print "kinshipDatafile:",kinshipDatafile
print "chr:",chr
print "boundaries:",boundaries
print "onlyMissing:",onlyMissing
print "onlyOriginal96:",onlyOriginal96
print "onlyOriginal192:",onlyOriginal192
print "onlyBelowLatidue:",onlyBelowLatidue
print "complement:",complement
print "negate:",negate
print "logTransform:",logTransform
print "addConstant:",addConstant
print "removeOutliers:",removeOutliers
print "sr:",sr
print "srSkipFirstRun:",srSkipFirstRun
print "srInput:",srInput
print "srOutput:",srOutput
print "srTopQuantile:",srTopQuantile
print "srWindowSize:",srWindowSize
print "testRobustness:",testRobustness
print "permutationFilter:",permutationFilter
def runParallel(phenotypeIndex,phed):
#Cluster specific parameters
print phenotypeIndex
phenName = phed.getPhenotypeName(phenotypeIndex)
outFileName = resultDir+"Emma_"+parallel+"_"+phenName
shstr = """#!/bin/csh
#PBS -l walltime=100:00:00
#PBS -l mem=8g
#PBS -q cmb
"""
shstr += "#PBS -N E"+phenName+"_"+parallel+"\n"
shstr += "set phenotypeName="+parallel+"\n"
shstr += "set phenotype="+str(phenotypeIndex)+"\n"
shstr += "(python "+emmadir+"Emma.py -o "+outFileName+" "
if onlyOriginal96:
shstr+=" --onlyOriginal96 "
elif onlyOriginal192:
shstr+=" --onlyOriginal192 "
if onlyBelowLatidue:
shstr+=" --onlyBelowLatidue="+str(onlyBelowLatidue)+" "
if logTransform:
shstr += " --logTransform "
if negate:
shstr += " --negate "
if removeOutliers:
shstr += " --removeOutliers="+str(removeOutliers)+" "
if phenotypeRanks:
shstr += " --phenotypeRanks "
if testRobustness:
shstr+=" --testRobustness "
shstr+=" --permutationFilter="+str(permutationFilter)+" "
if sr:
shstr += " --sr "
if not srOutput:
output = resultDir+"Emma_"+parallel+"_"+phenName+".sr.pvals"
shstr += " --srOutput="+str(output)+" "
if srSkipFirstRun:
if not srInput:
output = resultDir+"Emma_"+parallel+"_"+phenName+".pvals"
shstr += " --srInput="+str(output)+" "
shstr += " --srSkipFirstRun "
shstr += " --srPar="+str(srTopQuantile)+","+str(srWindowSize)+" "
shstr += " -a "+str(withArrayIds)+" "
if kinshipDatafile:
shstr += " --kinshipDatafile="+str(kinshipDatafile)+" "
shstr += " --addConstant="+str(addConstant)+" "
shstr += snpsDataFile+" "+phenotypeDataFile+" "+str(phenotypeIndex)+" "
shstr += "> "+outFileName+"_job"+".out) >& "+outFileName+"_job"+".err\n"
f = open(parallel+".sh",'w')
f.write(shstr)
f.close()
#Execute qsub script
os.system("qsub "+parallel+".sh ")
snpsDataFile = args[0]
phenotypeDataFile = args[1]
if parallel: #Running on the cluster..
phed = phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter='\t') #Get Phenotype data
if parallelAll:
for phenotypeIndex in phed.phenIds:
if onlyMissing:
phenName = phed.getPhenotypeName(phenotypeIndex)
pvalFile = resultDir+"Emma_"+parallel+"_"+phenName+".pvals"
res = None
try:
res = os.stat(pvalFile)
except Exception:
print "File",pvalFile,"does not exist."
if res and res.st_size>0:
print "File",pvalFile,"already exists, and is non-empty."
if sr:
srInput = resultDir+"Emma_"+parallel+"_"+phenName+".sr.pvals"
srRes = None
try:
srRes = os.stat(srInput)
except Exception:
print "File",srInput,"does not exist."
if srRes and srRes.st_size>0:
print "File",srInput,"already exists, and is non-empty."
else:
runParallel(phenotypeIndex,phed)
else:
print "Setting up the run."
runParallel(phenotypeIndex,phed)
else:
runParallel(phenotypeIndex,phed)
else:
phenotypeIndex = int(args[2])
runParallel(phenotypeIndex,phed)
return
else:
phenotypeIndex = int(args[2])
print "phenotypeIndex:",phenotypeIndex
print "\nStarting program now!\n"
snpsds = dataParsers.parseCSVData(snpsDataFile, format=1, deliminator=delim, missingVal=missingVal, withArrayIds=withArrayIds)
#Load phenotype file
phed = phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter='\t') #Get Phenotype data
numAcc = len(snpsds[0].accessions)
#Removing outliers
if removeOutliers:
print "Remoing outliers"
phed.naOutliers(phenotypeIndex,removeOutliers)
#If onlyOriginal96, then remove all other phenotypes..
if onlyOriginal96:
print "Filtering for the first 96 accessions"
original_96_ecotypes = phenotypeData._getFirst96Ecotypes_()
original_96_ecotypes = map(str,original_96_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_96_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_96_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyOriginal192:
print "Filtering for the first 192 accessions"
original_192_ecotypes = phenotypeData._getFirst192Ecotypes_()
original_192_ecotypes = map(str,original_192_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_192_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_192_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyBelowLatidue:
print "Filtering for the accessions which orginate below latitude",onlyBelowLatidue
eiDict = phenotypeData._getEcotypeIdInfoDict_()
print eiDict
keepEcotypes = []
for acc in phed.accessions:
acc = int(acc)
if eiDict.has_key(acc) and eiDict[acc][2] and eiDict[acc][2]<onlyBelowLatidue:
keepEcotypes.append(str(acc))
elif eiDict.has_key(acc) and eiDict[acc][2]==None:
keepEcotypes.append(str(acc))
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
sys.stdout.write("Finished prefiltering phenotype accessions.\n")
sys.stdout.flush()
phenotype = phed.getPhenIndex(phenotypeIndex)
accIndicesToKeep = []
phenAccIndicesToKeep = []
#Checking which accessions to keep and which to remove .
for i in range(0,len(snpsds[0].accessions)):
acc1 = snpsds[0].accessions[i]
for j in range(0,len(phed.accessions)):
acc2 = phed.accessions[j]
if acc1==acc2 and phed.phenotypeValues[j][phenotype]!='NA':
accIndicesToKeep.append(i)
phenAccIndicesToKeep.append(j)
break
print "\nFiltering accessions in genotype data:"
#Filter accessions which do not have the phenotype value (from the genotype data).
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.removeAccessionIndices(accIndicesToKeep)
print ""
print numAcc-len(accIndicesToKeep),"accessions removed from genotype data, leaving",len(accIndicesToKeep),"accessions in all."
print "\nNow filtering accessions in phenotype data:"
phed.removeAccessions(phenAccIndicesToKeep) #Removing accessions that don't have genotypes or phenotype values
print "Verifying number of accessions: len(phed.accessions)==len(snpsds[0].accessions) is",len(phed.accessions)==len(snpsds[0].accessions)
if len(phed.accessions)!=len(snpsds[0].accessions):
raise Exception
#Filtering monomorphic
print "Filtering monomorphic SNPs"
for snpsd in snpsds:
print "Removed", str(snpsd.filterMonoMorphicSnps()),"Snps"
#Remove minor allele frequencies
if minMAF!=0:
sys.stdout.write("Filterting SNPs with MAF<"+str(minMAF)+".")
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.filterMinMAF(minMAF)
#Removing SNPs which are outside of boundaries.
if chr:
print "\nRemoving SNPs which are outside of boundaries."
snpsds[chr-1].filterRegion(boundaries[0],boundaries[1])
snpsds = [snpsds[chr-1]]
#Ordering accessions in genotype data to fit phenotype data.
print "Ordering genotype data accessions."
accessionMapping = []
i = 0
for acc in phed.accessions:
if acc in snpsds[0].accessions:
accessionMapping.append((snpsds[0].accessions.index(acc),i))
i += 1
#print zip(accessionMapping,snpsds[0].accessions)
print "len(snpsds[0].snps)",len(snpsds[0].snps)
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.orderAccessions(accessionMapping)
print "\nGenotype data has been ordered."
#Converting format to 01
newSnpsds = []
sys.stdout.write("Converting data format")
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
newSnpsds.append(snpsd.getSnpsData(missingVal=missingVal))
print ""
print "Checking kinshipfile:",kinshipDatafile
if kinshipDatafile: #Is there a special kinship file?
kinshipSnpsds = dataParsers.parseCSVData(kinshipDatafile, format=1, deliminator=delim, missingVal=missingVal, withArrayIds=withArrayIds)
accIndicesToKeep = []
#Checking which accessions to keep and which to remove (genotype data).
sys.stdout.write("Removing accessions which do not have a phenotype value for "+phed.phenotypeNames[phenotype]+".")
sys.stdout.flush()
for i in range(0,len(kinshipSnpsds[0].accessions)):
acc1 = kinshipSnpsds[0].accessions[i]
for j in range(0,len(phed.accessions)):
acc2 = phed.accessions[j]
if acc1==acc2 and phed.phenotypeValues[j][phenotype]!='NA':
accIndicesToKeep.append(i)
break
print accIndicesToKeep
for snpsd in kinshipSnpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.removeAccessionIndices(accIndicesToKeep)
print ""
print numAcc-len(accIndicesToKeep),"accessions removed from kinship genotype data, leaving",len(accIndicesToKeep),"accessions in all."
print "Ordering kinship data accessions."
accessionMapping = []
i = 0
for acc in snpsds[0].accessions:
if acc in kinshipSnpsds[0].accessions:
accessionMapping.append((kinshipSnpsds[0].accessions.index(acc),i))
i += 1
print zip(accessionMapping,snpsds[0].accessions)
print "len(snpsds[0].snps)",len(snpsds[0].snps)
for snpsd in kinshipSnpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.orderAccessions(accessionMapping)
print "Kinship genotype data has been ordered."
newKinshipSnpsds = []
sys.stdout.write("Converting data format")
for snpsd in kinshipSnpsds:
sys.stdout.write(".")
sys.stdout.flush()
newKinshipSnpsds.append(snpsd.getSnpsData(missingVal=missingVal)) #This data might have NAs
print ""
kinshipSnpsds = newKinshipSnpsds
else:
kinshipSnpsds = newSnpsds
print "Found kinship data."
#Ordering accessions according to the order of accessions in the genotype file
# accessionMapping = []
# i = 0
# for acc in snpsds[0].accessions:
# if acc in phed.accessions:
# accessionMapping.append((phed.accessions.index(acc),i))
# i += 1
# phed.orderAccessions(accessionMapping)
#Negating phenotypic values
if negate:
phed.negateValues(phenotypeIndex)
#Adding a constant.
if addConstant!=-1:
if addConstant==0:
addConstant = math.sqrt(phed.getVariance(phenotypeIndex))/10
addConstant = addConstant - phed.getMinValue(phenotypeIndex)
print "Adding a constant to phenotype:",addConstant
phed.addConstant(phenotypeIndex,addConstant)
#Log-transforming
if logTransform:
print "Log transforming phenotype"
phed.logTransform(phenotypeIndex)
#Converting phenotypes to Ranks
elif phenotypeRanks:
phed.transformToRanks(phenotypeIndex)
if not chr:
snpsDataset = snpsdata.SNPsDataSet(newSnpsds,[1,2,3,4,5])
kinshipSnpsDataset = snpsdata.SNPsDataSet(kinshipSnpsds,[1,2,3,4,5])
else:
snpsDataset = snpsdata.SNPsDataSet(newSnpsds,[chr])
kinshipSnpsDataset = snpsdata.SNPsDataSet(kinshipSnpsds,[chr])
phenotypeName = phed.getPhenotypeName(phenotypeIndex)
sys.stdout.flush()
if testRobustness:
print "Starting a robustness test"
allSNPs = []
for snpsd in snpsDataset.snpsDataList:
allSNPs += snpsd.snps
phenVals = phed.getPhenVals(phenotypeIndex)
_robustness_test_(allSNPs,phenVals,rFile,filter=permutationFilter)
sys.exit(0)
if (not sr) or (sr and not srSkipFirstRun):
sys.stdout.write("Running Primary Emma.\n")
sys.stdout.flush()
pvalFile = _runEmmaScript_(snpsDataset, kinshipSnpsDataset, phed, phenotypeIndex, rFile, chr=chr, delim=delim, missingVal=missingVal, boundaries=boundaries, lrt=lrt)
res = gwaResults.Result(pvalFile,name="EMMA_"+phenotypeName, phenotypeID=phenotypeIndex)
res.filterMAF()
res.negLogTransform()
pngFile = pvalFile+".png"
plotResults.plotResult(res,pngFile=pngFile,percentile=90,type="pvals",ylab="$-$log$_{10}(p)$", plotBonferroni=True,usePylab=False)
srInput = pvalFile
if sr:
_secondRun_(srOutput,srInput,srTopQuantile,srWindowSize,newSnpsds,phed,phenotypeIndex,kinshipSnpsDataset)
print "Generating second run GW plot."
res = gwaResults.Result(srInput,name="KW_"+phenotypeName, phenotypeID=phenotypeIndex)
res.filterMAF()
res.negLogTransform()
srRes = gwaResults.Result(srOutput,name="EMMA_SR_"+phenotypeName, phenotypeID=phenotypeIndex)
srRes.filterMAF()
srRes.negLogTransform()
srPngFile = pvalFile+".sr.png"
plotResults.plotResultWithSecondRun(res,srRes,pngFile=srPngFile,ylab="$-$log$_{10}(p)$", plotBonferroni=True)
def _run_():
if len(sys.argv)==1:
print __doc__
sys.exit(2)
long_options_list=["outputFile=", "delim=", "missingval=", "phenotypeFileType=",
"help", "parallel=", "parallelAll", "addToDB",
"callMethodID=", "comment=", "onlyOriginal192","onlyOriginal96", "subSample=" ,
"subSampleLikePhenotype=", "subsampleTest=", "complement", "onlyBelowLatidue=",
"onlyAboveLatidue=", "srInput=", "sr","srOutput=", "srPar=","srSkipFirstRun",
"permTest=", "savePermutations", "permutationFilter=", "testRobustness",
"memReq=","walltimeReq=",]
try:
opts, args=getopt.getopt(sys.argv[1:], "o:c:d:m:h", long_options_list)
except:
traceback.print_exc()
print sys.exc_info()
print __doc__
sys.exit(2)
phenotypeFileType=1
outputFile=None
delim=","
missingVal="NA"
help=0
parallel=None
parallelAll=False
addToDB=False
callMethodID=None
comment=""
subSample=None
onlyOriginal96=False
onlyOriginal192 = False
subSampleLikePhenotype = None
subsampleTest = False
numSubSamples = None
complement = False
onlyBelowLatidue = None
onlyAboveLatidue = None
sr = False
srOutput = False
srInput = False
srSkipFirstRun = False
srTopQuantile = 0.95
srWindowSize = 30000
permTest = None
savePermutations = False
permutationFilter = 1.0
testRobustness = False
memReq = "5g"
walltimeReq = "100:00:00"
for opt, arg in opts:
if opt in ("-h", "--help"):
help=1
print __doc__
elif opt in ("-o", "--outputFile"):
outputFile=arg
elif opt in ("--phenotypeFileType"):
phenotypeFileType=int(arg)
elif opt in ("--parallel"):
parallel=arg
elif opt in ("--parallelAll"):
parallelAll=True
elif opt in ("--addToDB"):
addToDB=True
elif opt in ("--onlyOriginal96"):
onlyOriginal96=True
elif opt in ("--onlyOriginal192"):
onlyOriginal192=True
elif opt in ("--complement"):
complement=True
elif opt in ("--subSample"):
subSample=int(arg)
elif opt in ("--subsampleTest"):
subsampleTest = True
l = arg.split(",")
subSample=int(l[0])
numSubSamples=int(l[1])
elif opt in ("--onlyBelowLatidue"):
onlyBelowLatidue=float(arg)
elif opt in ("--onlyAboveLatidue"):
onlyAboveLatidue=float(arg)
elif opt in ("--subSampleLikePhenotype"):
subSampleLikePhenotype=int(arg)
elif opt in ("--callMethodID"):
callMethodID=int(arg)
elif opt in ("--comment"):
comment=arg
elif opt in ("-d", "--delim"):
delim=arg
elif opt in ("-m", "--missingval"):
missingVal=arg
elif opt in ("--sr"):
sr = True
elif opt in ("--testRobustness"):
testRobustness = True
elif opt in ("--permTest"):
permTest = int(arg)
elif opt in ("--savePermutations"):
savePermutations = True
elif opt in ("--permutationFilter"):
permutationFilter = float(arg)
elif opt in ("--srSkipFirstRun"):
srSkipFirstRun = True
elif opt in ("--srInput"):
srInput = arg
elif opt in ("--srOutput"):
srOutput = arg
elif opt in ("--srPar"):
vals = arg.split(",")
srTopQuantile = float(vals[0])
srWindowSize = int(vals[1])
elif opt in ("--memReq"):
memReq=arg
elif opt in ("--walltimeReq"):
walltimeReq=arg
else:
if help==0:
print "Unkown option!!\n"
print __doc__
sys.exit(2)
if len(args)<3 and not parallel:
if help==0:
print "Arguments are missing!!\n"
print __doc__
sys.exit(2)
snpsDataFile=args[0]
phenotypeDataFile=args[1]
print "Kruskal-Wallis is being set up with the following parameters:"
print "phenotypeDataFile:",phenotypeDataFile
print "snpsDataFile:",snpsDataFile
print "parallel:",parallel
print "parallelAll:",parallelAll
print "onlyOriginal96:",onlyOriginal96
print "onlyOriginal192:",onlyOriginal192
print "onlyBelowLatidue:",onlyBelowLatidue
print "onlyAboveLatidue:",onlyAboveLatidue
print "complement:",complement
print "subSampleLikePhenotype:",subSampleLikePhenotype
print "subsampleTest:",subsampleTest
print "numSubSamples:",numSubSamples
print "subSample:",subSample
print "sr:",sr
print "srSkipFirstRun:",srSkipFirstRun
print "srInput:",srInput
print "srOutput:",srOutput
print "srTopQuantile:",srTopQuantile
print "srWindowSize:",srWindowSize
print "permTest:",permTest
print "savePermutations:",savePermutations
print "permutationFilter:",permutationFilter
print "testRobustness:",testRobustness
print "walltimeReq:",walltimeReq
print "memReq:",memReq
def runParallel(phenotypeIndex,id=""):
#Cluster specific parameters
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
phenName=phed.getPhenotypeName(phenotypeIndex)
print phenName
outputFile=resultDir+"KW_"+parallel+"_"+phenName+id
shstr = "#!/bin/csh\n"
shstr += "#PBS -l walltime="+walltimeReq+"\n"
shstr += "#PBS -l mem="+memReq+"\n"
shstr +="#PBS -q cmb\n"
shstr+="#PBS -N K"+phenName+"_"+parallel+"\n"
shstr+="set phenotypeName="+parallel+"\n"
shstr+="set phenotype="+str(phenotypeIndex)+"\n"
shstr+="(python "+scriptDir+"KW.py -o "+outputFile+" "
if subSample:
shstr+=" --subSample="+str(subSample)+" "
elif onlyOriginal96:
shstr+=" --onlyOriginal96 "
elif onlyOriginal192:
shstr+=" --onlyOriginal192 "
if onlyBelowLatidue:
shstr+=" --onlyBelowLatidue="+str(onlyBelowLatidue)+" "
elif onlyAboveLatidue:
shstr+=" --onlyAboveLatidue="+str(onlyAboveLatidue)+" "
if complement:
shstr+=" --complement "
if permTest:
shstr+=" --permTest="+str(permTest)+" "
if savePermutations:
shstr+=" --savePermutations "
shstr+=" --permutationFilter="+str(permutationFilter)+" "
if testRobustness:
shstr+=" --testRobustness "
if sr:
shstr += " --sr "
if not srOutput:
output = resultDir+"KW_"+parallel+"_"+phenName+".sr.pvals"
shstr += " --srOutput="+str(output)+" "
if srSkipFirstRun:
if not srInput:
output = resultDir+"KW_"+parallel+"_"+phenName+".pvals"
shstr += " --srInput="+str(output)+" "
shstr += " --srSkipFirstRun "
shstr += " --srPar="+str(srTopQuantile)+","+str(srWindowSize)+" "
shstr+=snpsDataFile+" "+phenotypeDataFile+" "+str(phenotypeIndex)+" "
shstr+="> "+outputFile+"_job"+".out) >& "+outputFile+"_job"+".err\n"
f=open(parallel+".sh", 'w')
f.write(shstr)
f.close()
#Execute qsub script
os.system("qsub "+parallel+".sh ")
if parallel: #Running on the cluster..
if parallelAll:
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
for phenotypeIndex in phed.phenIds:
runParallel(phenotypeIndex)
elif subsampleTest:
phenotypeIndex=int(args[2])
for i in range(0,numSubSamples):
runParallel(phenotypeIndex,id="_r"+str(subSample)+"_"+str(i))
else:
phenotypeIndex=int(args[2])
runParallel(phenotypeIndex)
return
else:
phenotypeIndex=int(args[2])
print "phenotypeIndex:",phenotypeIndex
print "output:",outputFile
print "\nStarting program now!\n"
#Load phenotype file
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
#If onlyOriginal96, then remove all other phenotypes..
if onlyOriginal96:
print "Filtering for the first 96 accessions"
original_96_ecotypes = phenotypeData._getFirst96Ecotypes_()
original_96_ecotypes = map(str,original_96_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_96_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_96_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyOriginal192:
print "Filtering for the first 192 accessions"
original_192_ecotypes = phenotypeData._getFirst192Ecotypes_()
original_192_ecotypes = map(str,original_192_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_192_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_192_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyBelowLatidue:
print "Filtering for the accessions which orginate below latitude",onlyBelowLatidue
eiDict = phenotypeData._getEcotypeIdInfoDict_()
print eiDict
keepEcotypes = []
for acc in phed.accessions:
acc = int(acc)
if eiDict.has_key(acc) and eiDict[acc][2] and eiDict[acc][2]<onlyBelowLatidue:
keepEcotypes.append(str(acc))
elif eiDict.has_key(acc) and eiDict[acc][2]==None:
keepEcotypes.append(str(acc))
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
elif onlyAboveLatidue:
print "Filtering for the accessions which orginate above latitude",onlyAboveLatidue
eiDict = phenotypeData._getEcotypeIdInfoDict_()
print eiDict
keepEcotypes = []
for acc in phed.accessions:
acc = int(acc)
if eiDict.has_key(acc) and eiDict[acc][2] and eiDict[acc][2]>onlyAboveLatidue:
keepEcotypes.append(str(acc))
elif eiDict.has_key(acc) and eiDict[acc][2]==None:
keepEcotypes.append(str(acc))
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if subSampleLikePhenotype:
p_name = phed.getPhenotypeName(subSampleLikePhenotype)
print "Picking sample as in",p_name
ecotypes = phed.getNonNAEcotypes(subSampleLikePhenotype)
print ecotypes
phed.filterAccessions(ecotypes)
print "len(phed.accessions)", len(phed.accessions)
if subSample:
sample_ecotypes = []
ecotypes = phed.getNonNAEcotypes(phenotypeIndex)
sample_ecotypes = random.sample(ecotypes,subSample)
phed.filterAccessions(sample_ecotypes)
print "len(phed.accessions)", len(phed.accessions)
sys.stdout.write("Finished prefiltering phenotype accessions.\n")
sys.stdout.flush()
#Load genotype file
snpsds=dataParsers.parseCSVData(snpsDataFile, format = 1, deliminator = delim, missingVal = missingVal)
#Checking overlap between phenotype and genotype accessions.
phenotype=phed.getPhenIndex(phenotypeIndex)
accIndicesToKeep=[]
phenAccIndicesToKeep=[]
numAcc=len(snpsds[0].accessions)
sys.stdout.write("Removing accessions which do not have a phenotype value for "+phed.phenotypeNames[phenotype]+".")
sys.stdout.flush()
for i in range(0, len(snpsds[0].accessions)):
acc1=snpsds[0].accessions[i]
for j in range(0, len(phed.accessions)):
acc2=phed.accessions[j]
if acc1==acc2 and phed.phenotypeValues[j][phenotype]!='NA':
accIndicesToKeep.append(i)
phenAccIndicesToKeep.append(j)
break
#Filter accessions which do not have the phenotype value.
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.removeAccessionIndices(accIndicesToKeep)
print ""
print numAcc-len(accIndicesToKeep), "accessions removed, leaving", len(accIndicesToKeep), "accessions in all."
print "Filtering phenotype data."
phed.removeAccessions(phenAccIndicesToKeep) #Removing accessions that don't have genotypes or phenotype values
#Ordering accessions according to the order of accessions in the genotype file
accessionMapping=[]
i=0
for acc in snpsds[0].accessions:
if acc in phed.accessions:
accessionMapping.append((phed.accessions.index(acc), i))
i+=1
phed.orderAccessions(accessionMapping)
#Filtering monomorphic
print "Filtering monomorphic SNPs"
for snpsd in snpsds:
print "Removed", str(snpsd.filterMonoMorphicSnps()), "Snps"
#Converting format to 01
newSnpsds=[]
sys.stdout.write("Converting data format")
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
newSnpsds.append(snpsd.getSnpsData())
print ""
#Double check genotype file:
problems = 0
for i in range(0,len(newSnpsds)):
snpsd = newSnpsds[i]
for j in range(0,len(snpsd.snps)):
snp = snpsd.snps[j]
sc = snp.count(0)
if sc==0 or sc==len(snp):
print "Problem in file found at chr,pos",(i+1),",",snpsd.positions[i]
problems += 1
if problems >0:
print "Genotype file appears to have potential problems"
else:
print "Genotype file appears to be good"
if permTest:
print "Starting a permutation test"
allSNPs = []
for snpsd in newSnpsds:
allSNPs += snpsd.snps
phenVals = phed.getPhenVals(phenotypeIndex)
test_type = "KW"
if phed.isBinary(phenotypeIndex):
test_type = "Fisher"
permTest = 100
_perm_test_(allSNPs,phenVals,permTest,outputFile, test_type=test_type,savePermutations=savePermutations, filter=permutationFilter)
sys.exit(0)
if testRobustness:
print "Starting a robustness test"
allSNPs = []
for snpsd in newSnpsds:
allSNPs += snpsd.snps
phenVals = phed.getPhenVals(phenotypeIndex)
test_type = "KW"
if phed.isBinary(phenotypeIndex):
test_type = "Fisher"
_robustness_test_(allSNPs,phenVals,outputFile, test_type=test_type, filter=permutationFilter)
sys.exit(0)
sys.stdout.flush()
print "sr:",sr, ", srSkipFirstRun:",srSkipFirstRun
if (not sr) or (sr and not srSkipFirstRun):
#Writing files
#phed and phenotype
sd=snpsdata.SNPsDataSet(newSnpsds, [1, 2, 3, 4, 5])
phenotypeName=phed.getPhenotypeName(phenotypeIndex)
if phed.isBinary(phenotypeIndex):
pvals = run_fet(sd.getSnps(),phed.getPhenVals(phenotypeIndex))
else:
snps = sd.getSnps()
phen_vals = phed.getPhenVals(phenotypeIndex)
try:
kw_res = util.kruskal_wallis(snps,phen_vals)
pvals = kw_res['ps']
except:
print snps
print phen_vals
print len(snps),len(snps[0]),len(phen_vals)
raise Exception
res = gwaResults.Result(scores = pvals,name="KW_"+phenotypeName, snpsds=newSnpsds, load_snps=False)
pvalFile=outputFile+".pvals"
res.writeToFile(pvalFile)
print "Generating a GW plot."
res.negLogTransform()
pngFile = pvalFile+".png"
plotResults.plotResult(res,pngFile=pngFile,percentile=90,type="pvals",ylab="$-$log$_{10}(p)$", plotBonferroni=True,usePylab=False)
srInput = pvalFile
else:
print "Skipping first stage analysis."
sys.stdout.flush()
if sr:
_secondRun_(srOutput,srInput,srTopQuantile,srWindowSize,newSnpsds,phed,phenotypeIndex,binary=binary)
print "Generating second run GW plot."
res = gwaResults.Result(srInput,name="KW_"+phenotypeName, phenotypeID=phenotypeIndex)
res.negLogTransform()
srRes = gwaResults.Result(srOutput,name="KW_SR_"+phenotypeName, phenotypeID=phenotypeIndex)
srRes.negLogTransform()
srPngFile = pvalFile+".sr.png"
plotResults.plotResultWithSecondRun(res,srRes,pngFile=srPngFile,ylab="$-$log$_{10}(p)$", plotBonferroni=True)
def _run_():
if len(sys.argv)==1:
print __doc__
sys.exit(2)
long_options_list=["outputFile=", "delim=", "missingval=", "withArrayId=", "phenotypeFileType=",
"help", "parallel=", "parallelAll", "addToDB",
"callMethodID=", "comment=", "onlyOriginal192","onlyOriginal96", "subSample=" ,
"subSampleLikePhenotype=", "subsampleTest=", "complement", "onlyBelowLatidue=",
"onlyAboveLatidue=", "srInput=", "sr","srOutput=", "srPar=","srSkipFirstRun",
"permTest=", "savePermutations", "permutationFilter=", "testRobustness"]
try:
opts, args=getopt.getopt(sys.argv[1:], "o:c:d:m:a:h", long_options_list)
except:
traceback.print_exc()
print sys.exc_info()
print __doc__
sys.exit(2)
phenotypeFileType=1
outputFile=None
delim=","
missingVal="NA"
help=0
withArrayIds=1
parallel=None
parallelAll=False
addToDB=False
callMethodID=None
comment=""
subSample=None
onlyOriginal96=False
onlyOriginal192 = False
subSampleLikePhenotype = None
subsampleTest = False
numSubSamples = None
complement = False
onlyBelowLatidue = None
onlyAboveLatidue = None
sr = False
srOutput = False
srInput = False
srSkipFirstRun = False
srTopQuantile = 0.95
srWindowSize = 30000
permTest = None
savePermutations = False
permutationFilter = 1.0
testRobustness = False
for opt, arg in opts:
if opt in ("-h", "--help"):
help=1
print __doc__
elif opt in ("-a", "--withArrayId"):
withArrayIds=int(arg)
elif opt in ("-o", "--outputFile"):
outputFile=arg
elif opt in ("--phenotypeFileType"):
phenotypeFileType=int(arg)
elif opt in ("--parallel"):
parallel=arg
elif opt in ("--parallelAll"):
parallelAll=True
elif opt in ("--addToDB"):
addToDB=True
elif opt in ("--onlyOriginal96"):
onlyOriginal96=True
elif opt in ("--onlyOriginal192"):
onlyOriginal192=True
elif opt in ("--complement"):
complement=True
elif opt in ("--subSample"):
subSample=int(arg)
elif opt in ("--subsampleTest"):
subsampleTest = True
l = arg.split(",")
subSample=int(l[0])
numSubSamples=int(l[1])
elif opt in ("--onlyBelowLatidue"):
onlyBelowLatidue=float(arg)
elif opt in ("--onlyAboveLatidue"):
onlyAboveLatidue=float(arg)
elif opt in ("--subSampleLikePhenotype"):
subSampleLikePhenotype=int(arg)
elif opt in ("--callMethodID"):
callMethodID=int(arg)
elif opt in ("--comment"):
comment=arg
elif opt in ("-d", "--delim"):
delim=arg
elif opt in ("-m", "--missingval"):
missingVal=arg
elif opt in ("--sr"):
sr = True
elif opt in ("--testRobustness"):
testRobustness = True
elif opt in ("--permTest"):
permTest = int(arg)
elif opt in ("--savePermutations"):
savePermutations = True
elif opt in ("--permutationFilter"):
permutationFilter = float(arg)
elif opt in ("--srSkipFirstRun"):
srSkipFirstRun = True
elif opt in ("--srInput"):
srInput = arg
elif opt in ("--srOutput"):
srOutput = arg
elif opt in ("--srPar"):
vals = arg.split(",")
srTopQuantile = float(vals[0])
srWindowSize = int(vals[1])
else:
if help==0:
print "Unkown option!!\n"
print __doc__
sys.exit(2)
if len(args)<3 and not parallel:
if help==0:
print "Arguments are missing!!\n"
print __doc__
sys.exit(2)
snpsDataFile=args[0]
phenotypeDataFile=args[1]
print "Kruskal-Wallis is being set up with the following parameters:"
print "phenotypeDataFile:",phenotypeDataFile
print "snpsDataFile:",snpsDataFile
print "parallel:",parallel
print "parallelAll:",parallelAll
print "onlyOriginal96:",onlyOriginal96
print "onlyOriginal192:",onlyOriginal192
print "onlyBelowLatidue:",onlyBelowLatidue
print "onlyAboveLatidue:",onlyAboveLatidue
print "subSampleLikePhenotype:",subSampleLikePhenotype
print "subsampleTest:",subsampleTest
print "numSubSamples:",numSubSamples
print "subSample:",subSample
print "sr:",sr
print "srSkipFirstRun:",srSkipFirstRun
print "srInput:",srInput
print "srOutput:",srOutput
print "srTopQuantile:",srTopQuantile
print "srWindowSize:",srWindowSize
print "permTest:",permTest
print "savePermutations:",savePermutations
print "permutationFilter:",permutationFilter
print "testRobustness:",testRobustness
def runParallel(phenotypeIndex,id=""):
#Cluster specific parameters
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
phenName=phed.getPhenotypeName(phenotypeIndex)
phenName=phenName.replace("/", "_div_")
phenName=phenName.replace("*", "_star_")
outputFile=resultDir+"KW_"+parallel+"_"+phenName+id
shstr="""#!/bin/csh
#PBS -l walltime=100:00:00
#PBS -l mem=4g
#PBS -q cmb
"""
shstr+="#PBS -N K"+phenName+"_"+parallel+"\n"
shstr+="set phenotypeName="+parallel+"\n"
shstr+="set phenotype="+str(phenotypeIndex)+"\n"
shstr+="(python "+scriptDir+"KW.py -o "+outputFile+" "
shstr+=" -a "+str(withArrayIds)+" "
if subSample:
shstr+=" --subSample="+str(subSample)+" "
elif onlyOriginal96:
shstr+=" --onlyOriginal96 "
elif onlyOriginal192:
shstr+=" --onlyOriginal192 "
if onlyBelowLatidue:
shstr+=" --onlyBelowLatidue="+str(onlyBelowLatidue)+" "
elif onlyAboveLatidue:
shstr+=" --onlyAboveLatidue="+str(onlyAboveLatidue)+" "
if complement:
shstr+=" --complement "
if permTest:
shstr+=" --permTest="+str(permTest)+" "
if savePermutations:
shstr+=" --savePermutations "
shstr+=" --permutationFilter="+str(permutationFilter)+" "
if testRobustness:
shstr+=" --testRobustness "
if sr:
shstr += " --sr "
if not srOutput:
output = resultDir+"KW_"+parallel+"_"+phenName+".sr.pvals"
shstr += " --srOutput="+str(output)+" "
if srSkipFirstRun:
if not srInput:
output = resultDir+"KW_"+parallel+"_"+phenName+".pvals"
shstr += " --srInput="+str(output)+" "
shstr += " --srSkipFirstRun "
shstr += " --srPar="+str(srTopQuantile)+","+str(srWindowSize)+" "
shstr+=snpsDataFile+" "+phenotypeDataFile+" "+str(phenotypeIndex)+" "
shstr+="> "+outputFile+"_job"+".out) >& "+outputFile+"_job"+".err\n"
f=open(parallel+".sh", 'w')
f.write(shstr)
f.close()
#Execute qsub script
os.system("qsub "+parallel+".sh ")
if parallel: #Running on the cluster..
if parallelAll:
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
for phenotypeIndex in phed.phenIds:
runParallel(phenotypeIndex)
elif subsampleTest:
phenotypeIndex=int(args[2])
for i in range(0,numSubSamples):
runParallel(phenotypeIndex,id="_r"+str(subSample)+"_"+str(i))
else:
phenotypeIndex=int(args[2])
runParallel(phenotypeIndex)
return
else:
phenotypeIndex=int(args[2])
print "phenotypeIndex:",phenotypeIndex
print "output:",outputFile
print "\nStarting program now!\n"
#Load phenotype file
phed=phenotypeData.readPhenotypeFile(phenotypeDataFile, delimiter = '\t') #Get Phenotype data
#If onlyOriginal96, then remove all other phenotypes..
if onlyOriginal96:
print "Filtering for the first 96 accessions"
original_96_ecotypes = phenotypeData._getFirst96Ecotypes_()
original_96_ecotypes = map(str,original_96_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_96_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_96_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyOriginal192:
print "Filtering for the first 192 accessions"
original_192_ecotypes = phenotypeData._getFirst192Ecotypes_()
original_192_ecotypes = map(str,original_192_ecotypes)
keepEcotypes = []
if complement:
for acc in phed.accessions:
if not acc in original_192_ecotypes:
keepEcotypes.append(acc)
else:
keepEcotypes = original_192_ecotypes
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if onlyBelowLatidue:
print "Filtering for the accessions which orginate below latitude",onlyBelowLatidue
eiDict = phenotypeData._getEcotypeIdInfoDict_()
print eiDict
keepEcotypes = []
for acc in phed.accessions:
acc = int(acc)
if eiDict.has_key(acc) and eiDict[acc][2] and eiDict[acc][2]<onlyBelowLatidue:
keepEcotypes.append(str(acc))
elif eiDict.has_key(acc) and eiDict[acc][2]==None:
keepEcotypes.append(str(acc))
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
elif onlyAboveLatidue:
print "Filtering for the accessions which orginate above latitude",onlyAboveLatidue
eiDict = phenotypeData._getEcotypeIdInfoDict_()
print eiDict
keepEcotypes = []
for acc in phed.accessions:
acc = int(acc)
if eiDict.has_key(acc) and eiDict[acc][2] and eiDict[acc][2]>onlyAboveLatidue:
keepEcotypes.append(str(acc))
elif eiDict.has_key(acc) and eiDict[acc][2]==None:
keepEcotypes.append(str(acc))
phed.filterAccessions(keepEcotypes)
print "len(phed.accessions)", len(phed.accessions)
if subSampleLikePhenotype:
p_name = phed.getPhenotypeName(subSampleLikePhenotype)
print "Picking sample as in",p_name
ecotypes = phed.getNonNAEcotypes(subSampleLikePhenotype)
print ecotypes
phed.filterAccessions(ecotypes)
print "len(phed.accessions)", len(phed.accessions)
if subSample:
sample_ecotypes = []
ecotypes = phed.getNonNAEcotypes(phenotypeIndex)
sample_ecotypes = random.sample(ecotypes,subSample)
phed.filterAccessions(sample_ecotypes)
print "len(phed.accessions)", len(phed.accessions)
sys.stdout.write("Finished prefiltering phenotype accessions.\n")
sys.stdout.flush()
#Load genotype file
snpsds=dataParsers.parseCSVData(snpsDataFile, format = 1, deliminator = delim, missingVal = missingVal, withArrayIds = withArrayIds)
#Checking overlap between phenotype and genotype accessions.
phenotype=phed.getPhenIndex(phenotypeIndex)
accIndicesToKeep=[]
phenAccIndicesToKeep=[]
numAcc=len(snpsds[0].accessions)
sys.stdout.write("Removing accessions which do not have a phenotype value for "+phed.phenotypeNames[phenotype]+".")
sys.stdout.flush()
for i in range(0, len(snpsds[0].accessions)):
acc1=snpsds[0].accessions[i]
for j in range(0, len(phed.accessions)):
acc2=phed.accessions[j]
if acc1==acc2 and phed.phenotypeValues[j][phenotype]!='NA':
accIndicesToKeep.append(i)
phenAccIndicesToKeep.append(j)
break
#Filter accessions which do not have the phenotype value.
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
snpsd.removeAccessionIndices(accIndicesToKeep)
print ""
print numAcc-len(accIndicesToKeep), "accessions removed, leaving", len(accIndicesToKeep), "accessions in all."
print "Filtering phenotype data."
phed.removeAccessions(phenAccIndicesToKeep) #Removing accessions that don't have genotypes or phenotype values
#Ordering accessions according to the order of accessions in the genotype file
accessionMapping=[]
i=0
for acc in snpsds[0].accessions:
if acc in phed.accessions:
accessionMapping.append((phed.accessions.index(acc), i))
i+=1
phed.orderAccessions(accessionMapping)
#Filtering monomorphic
print "Filtering monomorphic SNPs"
for snpsd in snpsds:
print "Removed", str(snpsd.filterMonoMorphicSnps()), "Snps"
#Converting format to 01
newSnpsds=[]
sys.stdout.write("Converting data format")
for snpsd in snpsds:
sys.stdout.write(".")
sys.stdout.flush()
newSnpsds.append(snpsd.getSnpsData())
print ""
#Double check genotype file:
problems = 0
for i in range(0,len(newSnpsds)):
snpsd = newSnpsds[i]
for j in range(0,len(snpsd.snps)):
snp = snpsd.snps[j]
sc = snp.count(0)
if sc==0 or sc==len(snp):
print "Problem in file found at chr,pos",(i+1),",",snpsd.positions[i]
problems += 1
if problems >0:
print "Genotype file appears to have potential problems"
else:
print "Genotype file appears to be good"
if permTest:
print "Starting a permutation test"
allSNPs = []
for snpsd in newSnpsds:
allSNPs += snpsd.snps
phenVals = phed.getPhenVals(phenotypeIndex)
test_type = "KW"
if phed.isBinary(phenotypeIndex):
test_type = "Fisher"
permTest = 100
_perm_test_(allSNPs,phenVals,permTest,outputFile, test_type=test_type,savePermutations=savePermutations, filter=permutationFilter)
sys.exit(0)
if testRobustness:
print "Starting a robustness test"
allSNPs = []
for snpsd in newSnpsds:
allSNPs += snpsd.snps
phenVals = phed.getPhenVals(phenotypeIndex)
test_type = "KW"
if phed.isBinary(phenotypeIndex):
test_type = "Fisher"
_robustness_test_(allSNPs,phenVals,outputFile, test_type=test_type, filter=permutationFilter)
sys.exit(0)
sys.stdout.flush()
print "sr:",sr, ", srSkipFirstRun:",srSkipFirstRun
if (not sr) or (sr and not srSkipFirstRun):
#Writing files
if env.user=="bjarni":
tempfile.tempdir='/tmp'
(fId, phenotypeTempFile)=tempfile.mkstemp()
os.close(fId)
(fId, genotypeTempFile)=tempfile.mkstemp()
os.close(fId)
phed.writeToFile(phenotypeTempFile, [phenotype])
sys.stdout.write("Phenotype file written\n")
sys.stdout.flush()
snpsDataset=snpsdata.SNPsDataSet(newSnpsds, [1, 2, 3, 4, 5])
decoder={1:1, 0:0,-1:'NA'}
snpsDataset.writeToFile(genotypeTempFile, deliminator = delim, missingVal = missingVal, withArrayIds = 0, decoder = decoder)
sys.stdout.write("Genotype file written\n")
sys.stdout.flush()
phenotypeName=phed.getPhenotypeName(phenotypeIndex)
rDataFile=outputFile+".rData"
pvalFile=outputFile+".pvals"
#Is the phenotype binary?
binary=phed.isBinary(phenotypeIndex)
rstr=_generateRScript_(genotypeTempFile, phenotypeTempFile, rDataFile, pvalFile, name = phenotypeName, binary = binary)
rFileName=outputFile+".r"
f=open(rFileName, 'w')
f.write(rstr)
f.close()
outRfile=rFileName+".out"
errRfile=rFileName+".err"
print "Running R file:"
cmdStr="(R --vanilla < "+rFileName+" > "+outRfile+") >& "+errRfile
sys.stdout.write(cmdStr+"\n")
sys.stdout.flush()
gc.collect()
os.system(cmdStr)
#print "Emma output saved in R format in", rDataFile
print "Generating a GW plot."
res = gwaResults.Result(pvalFile,name="KW_"+phenotypeName, phenotypeID=phenotypeIndex)
res.negLogTransform()
pngFile = pvalFile+".png"
plotResults.plotResult(res,pngFile=pngFile,percentile=90,type="pvals",ylab="$-$log$_{10}(p)$", plotBonferroni=True,usePylab=False)
srInput = pvalFile
else:
print "Skipping first stage analysis."
sys.stdout.flush()
if sr:
_secondRun_(srOutput,srInput,srTopQuantile,srWindowSize,newSnpsds,phed,phenotypeIndex,binary=binary)
print "Generating second run GW plot."
res = gwaResults.Result(srInput,name="KW_"+phenotypeName, phenotypeID=phenotypeIndex)
res.negLogTransform()
srRes = gwaResults.Result(srOutput,name="KW_SR_"+phenotypeName, phenotypeID=phenotypeIndex)
srRes.negLogTransform()
srPngFile = pvalFile+".sr.png"
plotResults.plotResultWithSecondRun(res,srRes,pngFile=srPngFile,ylab="$-$log$_{10}(p)$", plotBonferroni=True)