def readDB(self):
prefix, dbId = self.getDBId(self.database)
if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet = self.getRISet(prefix, dbId)
traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
if not traitdata:
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
dataset = reaper.Dataset()
dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
strainList = list(dataset.prgy)
strains = []
trait = []
_prgy = dataset.prgy
for item in traitdata:
if item[0] in _prgy:
strains.append(item[0])
trait.append(item[1])
qtlscan = dataset.regression(strains, trait)
LRS = dataset.permutation(strains, trait)
nperm = len(LRS)
if qtlscan:
self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value")
qtlresult = []
if self.returnnumber:
self.returnnumber = min(self.returnnumber,len(qtlscan))
if self.sort == 'lrs':
qtlscan.sort(self.cmpLRS)
for item in qtlscan[:self.returnnumber]:
p_value = reaper.pvalue(item.lrs,LRS)
qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
else:#sort by position
qtlscan2 = qtlscan[:]
qtlscan2.sort(self.cmpLRS)
LRSthresh = qtlscan2[self.returnnumber].lrs
for item in qtlscan:
if item.lrs >= LRSthresh:
p_value = reaper.pvalue(item.lrs,LRS)
qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
else:
for item in qtlscan:
p_value = reaper.pvalue(item.lrs,LRS)
qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
if self.sort == 'lrs':
qtlresult.sort(self.cmpLRS2)
for item in qtlresult:
self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item)
else:
self.contents.append("###Error: Error occurs while regression.")
return
def read(file_geno, file_pheno, file_result1, file_result2):
genotype = reaper.Dataset()
genotype.read(file_geno)
##open output file
outputFile = file_result1
fout = open(outputFile, "wb")
fout.write("ID\tLocus\tChr\tcM\tLRS\tAdditive\tpValue\n")
outputFile2 = file_result2
fout2 = open(outputFile2, "wb")
fout2.write("ID\tLocus\tChr\tcM\tLRS\tAdditive\tpValue\n")
##Open Trait File
DataStart = 1
fp = open(file_pheno, "rb")
header = fp.readline()
header = map(string.strip, header.strip().split("\t"))
_strains = header[DataStart:]
##Read input file line by line
line = fp.readline()
while line:
line = map(string.strip, line.strip().split("\t"))
traitName = line[0]
print "Calculate Trait %s" % traitName
_traitData = map(float, line[DataStart:])
qtlresults = genotype.regression(strains = _strains, trait = _traitData)
permu = genotype.permutation(strains = _strains, trait = _traitData)
##Save all the results
for qtl in qtlresults:
pvalue = reaper.pvalue(qtl.lrs, permu)
fout.write("%s\t%s\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\t\n" % (traitName,
qtl.locus.name, qtl.locus.chr, qtl.locus.cM, qtl.lrs, qtl.additive, pvalue))
##Save highest LRS only
maxqtl = max(qtlresults)
pvalue = reaper.pvalue(maxqtl.lrs, permu)
fout2.write("%s\t%s\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\t\n" % (traitName,
maxqtl.locus.name, maxqtl.locus.chr, maxqtl.locus.cM, maxqtl.lrs, maxqtl.additive, pvalue))
line = fp.readline()
fp.close()
fout.close()
fout2.close()
def readDB(self):
prefix, dbId = self.getDBId(self.database)
if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet = self.getRISet(prefix, dbId)
traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
if not traitdata:
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
dataset0 = reaper.Dataset()
dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
strainList = list(dataset0.prgy)
dataset = dataset0.addinterval()
if self.chr != None:
for _chr in dataset:
if string.lower(_chr.name) == string.lower(self.chr):
dataset.chromosome = [_chr]
break
strains = []
trait = []
_prgy = dataset.prgy
for item in traitdata:
if item[0] in _prgy:
strains.append(item[0])
trait.append(item[1])
qtlscan = dataset.regression(strains, trait)
LRS = dataset.permutation(strains, trait)
nperm = len(LRS)
#print inter1[0]
returnPeak = []
nqtl = len(qtlscan)
if self.peak:
for i in range(nqtl):
if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
if qtlscan[i].lrs < qtlscan[i+1].lrs:
continue
elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
if qtlscan[i].lrs < qtlscan[i-1].lrs:
continue
else:
if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
continue
returnPeak.append(qtlscan[i])
else:
returnPeak = qtlscan[:]
if returnPeak:
self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM")
qtlresult = []
for item in returnPeak:
p_value = reaper.pvalue(item.lrs,LRS)
qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
if self.sort == 'lrs':
qtlresult.sort(self.cmpLRS2)
for item in qtlresult:
self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
else:
self.contents.append("###Error: Error occurs while regression.")
return
header = map(string.strip, header.strip().split("\t"))
_strains = header[DataStart:]
##Read input file line by line
line = fp.readline()
while line:
line = map(string.strip, line.strip().split("\t"))
traitName = line[0]
print "Calculate Trait %s" % traitName
_traitData = map(float, line[DataStart:])
qtlresults = genotype.regression(strains = _strains, trait = _traitData)
permu = genotype.permutation(strains = _strains, trait = _traitData)
##Save all the results
for qtl in qtlresults:
pvalue = reaper.pvalue(qtl.lrs, permu)
fout.write("%s\t%s\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\t\n" % (traitName,
qtl.locus.name, qtl.locus.chr, qtl.locus.cM, qtl.lrs, qtl.additive, pvalue))
##Save highest LRS only
maxqtl = max(qtlresults)
pvalue = reaper.pvalue(maxqtl.lrs, permu)
fout2.write("%s\t%s\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\t\n" % (traitName,
maxqtl.locus.name, maxqtl.locus.chr, maxqtl.locus.cM, maxqtl.lrs, maxqtl.additive, pvalue))
line = fp.readline()
fp.close()
fout.close()
fout2.close()