def readData(self, strainlst=[], incf1=[]):
"read user input data or from trait data and analysis form"
if not self.genotype:
self.readGenotype()
if not strainlst:
if incf1:
strainlst = self.f1list + self.strainlist
else:
strainlst = self.strainlist
traitfiledata = self.formdata.getfirst("traitfile")
traitpastedata = self.formdata.getfirst("traitpaste")
variancefiledata = self.formdata.getfirst("variancefile")
variancepastedata = self.formdata.getfirst("variancepaste")
Nfiledata = self.formdata.getfirst("Nfile")
if traitfiledata:
tt = string.split(traitfiledata)
vals = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
tt = string.split(traitpastedata)
vals = map(webqtlUtil.StringAsFloat, tt)
else:
vals = map(self.FormDataAsFloat, strainlst)
if len(vals) < len(strainlst):
vals += [None] * (len(strainlst) - len(vals))
elif len(vals) > len(strainlst):
vals = vals[: len(strainlst)]
else:
pass
if variancefiledata:
tt = string.split(variancefiledata)
vars = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
tt = string.split(variancepastedata)
vars = map(webqtlUtil.StringAsFloat, tt)
else:
vars = map(self.FormVarianceAsFloat, strainlst)
if len(vars) < len(strainlst):
vars += [None] * (len(strainlst) - len(vars))
elif len(vars) > len(strainlst):
vars = vars[: len(strainlst)]
else:
pass
if Nfiledata:
tt = string.split(Nfiledata)
nstrains = map(webqtlUtil.IntAsFloat, tt)
if len(nstrains) < len(strainlst):
nstrains += [None] * (len(strainlst) - len(nstrains))
else:
nstrains = map(self.FormNAsFloat, strainlst)
##vals, vars, nstrains is obsolete
self.allTraitData = {}
for i, _strain in enumerate(strainlst):
if vals[i] != None:
self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i])
def Sample(self):
"Create some dummy data for testing"
self.RISet = "BXD"
self.incparentsf1 = "on"
# self.display = 9.2
# self.significance = 16.1
self.readGenotype()
self.identification = "BXD : Coat color example by Lu Lu, et al"
# self.readGenotype()
# self.genotype.ReadMM('AXBXAforQTL')
# self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
# self.strainlist.sort()
self.allTraitData = {
"BXD29": webqtlCaseData(3),
"BXD28": webqtlCaseData(2),
"BXD25": webqtlCaseData(2),
"BXD24": webqtlCaseData(2),
"BXD27": webqtlCaseData(2),
"BXD21": webqtlCaseData(1),
"BXD20": webqtlCaseData(4),
"BXD23": webqtlCaseData(4),
"BXD22": webqtlCaseData(3),
"BXD14": webqtlCaseData(4),
"BXD15": webqtlCaseData(2),
"BXD16": webqtlCaseData(3),
"BXD11": webqtlCaseData(4),
"BXD12": webqtlCaseData(3),
"BXD13": webqtlCaseData(2),
"BXD18": webqtlCaseData(3),
"BXD19": webqtlCaseData(3),
"BXD38": webqtlCaseData(3),
"BXD39": webqtlCaseData(3),
"BXD36": webqtlCaseData(2),
"BXD34": webqtlCaseData(4),
"BXD35": webqtlCaseData(4),
"BXD32": webqtlCaseData(4),
"BXD33": webqtlCaseData(3),
"BXD30": webqtlCaseData(1),
"BXD31": webqtlCaseData(4),
"DBA/2J": webqtlCaseData(1),
"BXD8": webqtlCaseData(3),
"BXD9": webqtlCaseData(1),
"BXD6": webqtlCaseData(3),
"BXD5": webqtlCaseData(3),
"BXD2": webqtlCaseData(4),
"BXD1": webqtlCaseData(1),
"C57BL/6J": webqtlCaseData(4),
"B6D2F1": webqtlCaseData(4),
"BXD42": webqtlCaseData(4),
"BXD40": webqtlCaseData(3),
}
def Sample(self):
'Create some dummy data for testing'
self.group = 'BXD'
self.incparentsf1 = 'on'
#self.display = 9.2
#self.significance = 16.1
self.readGenotype()
self.identification = 'BXD : Coat color example by Lu Lu, et al'
#self.readGenotype()
#self.genotype.ReadMM('AXBXAforQTL')
#self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
#self.samplelist.sort()
self.allTraitData = {
'BXD29': webqtlCaseData(3),
'BXD28': webqtlCaseData(2),
'BXD25': webqtlCaseData(2),
'BXD24': webqtlCaseData(2),
'BXD27': webqtlCaseData(2),
'BXD21': webqtlCaseData(1),
'BXD20': webqtlCaseData(4),
'BXD23': webqtlCaseData(4),
'BXD22': webqtlCaseData(3),
'BXD14': webqtlCaseData(4),
'BXD15': webqtlCaseData(2),
'BXD16': webqtlCaseData(3),
'BXD11': webqtlCaseData(4),
'BXD12': webqtlCaseData(3),
'BXD13': webqtlCaseData(2),
'BXD18': webqtlCaseData(3),
'BXD19': webqtlCaseData(3),
'BXD38': webqtlCaseData(3),
'BXD39': webqtlCaseData(3),
'BXD36': webqtlCaseData(2),
'BXD34': webqtlCaseData(4),
'BXD35': webqtlCaseData(4),
'BXD32': webqtlCaseData(4),
'BXD33': webqtlCaseData(3),
'BXD30': webqtlCaseData(1),
'BXD31': webqtlCaseData(4),
'DBA/2J': webqtlCaseData(1),
'BXD8': webqtlCaseData(3),
'BXD9': webqtlCaseData(1),
'BXD6': webqtlCaseData(3),
'BXD5': webqtlCaseData(3),
'BXD2': webqtlCaseData(4),
'BXD1': webqtlCaseData(1),
'C57BL/6J': webqtlCaseData(4),
'B6D2F1': webqtlCaseData(4),
'BXD42': webqtlCaseData(4),
'BXD40': webqtlCaseData(3)
}
def readData(self, samplelist, incf1=None):
'''read user input data or from trait data and analysis form'''
if incf1 == None:
incf1 = []
if not self.genotype:
self.readGenotype()
if not samplelist:
if incf1:
samplelist = self.f1list + self.samplelist
else:
samplelist = self.samplelist
#print("before traitfiledata self.traitfile is:", pf(self.traitfile))
traitfiledata = getattr(self, "traitfile", None)
traitpastedata = getattr(self, "traitpaste", None)
variancefiledata = getattr(self, "variancefile", None)
variancepastedata = getattr(self, "variancepaste", None)
Nfiledata = getattr(self, "Nfile", None)
#### Todo: Rewrite below when we get to someone submitting their own trait #####
def to_float(item):
try:
return float(item)
except ValueError:
return None
print("bottle samplelist is:", samplelist)
if traitfiledata:
tt = traitfiledata.split()
values = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
tt = traitpastedata.split()
values = map(webqtlUtil.StringAsFloat, tt)
else:
print("mapping formdataasfloat")
#values = map(self.FormDataAsFloat, samplelist)
values = [to_float(getattr(self, key)) for key in samplelist]
print("rocket values is:", values)
if len(values) < len(samplelist):
values += [None] * (len(samplelist) - len(values))
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
print("now values is:", values)
if variancefiledata:
tt = variancefiledata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
tt = variancepastedata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
else:
variances = map(self.FormVarianceAsFloat, samplelist)
if len(variances) < len(samplelist):
variances += [None] * (len(samplelist) - len(variances))
elif len(variances) > len(samplelist):
variances = variances[:len(samplelist)]
if Nfiledata:
tt = string.split(Nfiledata)
nsamples = map(webqtlUtil.IntAsFloat, tt)
if len(nsamples) < len(samplelist):
nsamples += [None] * (len(samplelist) - len(nsamples))
else:
nsamples = map(self.FormNAsFloat, samplelist)
##values, variances, nsamples is obsolete
self.allTraitData = {}
for i, _sample in enumerate(samplelist):
if values[i] != None:
self.allTraitData[_sample] = webqtlCaseData(
_sample, values[i], variances[i], nsamples[i])
print("allTraitData is:", pf(self.allTraitData))
def retrieveData(self, strainlist=[]):
assert self.db and self.cursor
if self.db.type == 'Temp':
query = '''
SELECT
Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
FROM
TempData, Temp, Strain
WHERE
TempData.StrainId = Strain.Id AND
TempData.Id = Temp.DataId AND
Temp.name = '%s'
Order BY
Strain.Name
''' % self.name
#XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
elif self.db.type == 'Publish':
query = '''
SELECT
Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
FROM
(PublishData, Strain, PublishXRef, PublishFreeze)
left join PublishSE on
(PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
left join NStrain on
(NStrain.DataId = PublishData.Id AND
NStrain.StrainId = PublishData.StrainId)
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.name, self.db.id)
#XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
elif self.cellid:
#Probe Data
query = '''
SELECT
Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id
FROM
(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef,
Strain, Probe, ProbeSet)
left join ProbeSE on
(ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
WHERE
Probe.Name = '%s' AND ProbeSet.Name = '%s' AND
Probe.ProbeSetId = ProbeSet.Id AND
ProbeXRef.ProbeId = Probe.Id AND
ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeXRef.DataId = ProbeData.Id AND
ProbeData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.cellid, self.name, self.db.name)
#XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
elif self.db.type == 'ProbeSet':
#ProbeSet Data
query = '''
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
FROM
(ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
WHERE
ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.name, self.db.name)
#XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
else:
#Geno Data
#XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
query = '''
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoFreeze.Name = '%s' AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name)
self.cursor.execute(query)
results = self.cursor.fetchall()
self.data.clear()
if results:
self.mysqlid = results[0][-1]
if strainlist:
for item in results:
if item[0] in strainlist:
val = item[1]
if val != None:
var = item[2]
ndata = None
if self.db.type in ('Publish', 'Temp'):
ndata = item[3]
self.data[item[0]] = webqtlCaseData(val, var, ndata)
#end for
else:
for item in results:
val = item[1]
if val != None:
var = item[2]
ndata = None
if self.db.type in ('Publish', 'Temp'):
ndata = item[3]
self.data[item[0]] = webqtlCaseData(val, var, ndata)
#end for
#end if
else:
pass
def Sample(self):
'Create some dummy data for testing'
self.group = 'BXD'
self.incparentsf1 = 'on'
#self.display = 9.2
#self.significance = 16.1
self.readGenotype()
self.identification = 'BXD : Coat color example by Lu Lu, et al'
#self.readGenotype()
#self.genotype.ReadMM('AXBXAforQTL')
#self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
#self.samplelist.sort()
self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2),
'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2),
'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4),
'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2),
'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3),
'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3),
'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2),
'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4),
'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4),
'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1),
'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4),
'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4),
'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
def readData(self, samplelist, incf1=None):
'''read user input data or from trait data and analysis form'''
if incf1 == None:
incf1 = []
if not self.genotype:
self.readGenotype()
if not samplelist:
if incf1:
samplelist = self.f1list + self.samplelist
else:
samplelist = self.samplelist
#print("before traitfiledata self.traitfile is:", pf(self.traitfile))
traitfiledata = getattr(self, "traitfile", None)
traitpastedata = getattr(self, "traitpaste", None)
variancefiledata = getattr(self, "variancefile", None)
variancepastedata = getattr(self, "variancepaste", None)
Nfiledata = getattr(self, "Nfile", None)
#### Todo: Rewrite below when we get to someone submitting their own trait #####
def to_float(item):
try:
return float(item)
except ValueError:
return None
print("bottle samplelist is:", samplelist)
if traitfiledata:
tt = traitfiledata.split()
values = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
tt = traitpastedata.split()
values = map(webqtlUtil.StringAsFloat, tt)
else:
print("mapping formdataasfloat")
#values = map(self.FormDataAsFloat, samplelist)
values = [to_float(getattr(self, key)) for key in samplelist]
print("rocket values is:", values)
if len(values) < len(samplelist):
values += [None] * (len(samplelist) - len(values))
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
print("now values is:", values)
if variancefiledata:
tt = variancefiledata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
tt = variancepastedata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
else:
variances = map(self.FormVarianceAsFloat, samplelist)
if len(variances) < len(samplelist):
variances += [None]*(len(samplelist) - len(variances))
elif len(variances) > len(samplelist):
variances = variances[:len(samplelist)]
if Nfiledata:
tt = string.split(Nfiledata)
nsamples = map(webqtlUtil.IntAsFloat, tt)
if len(nsamples) < len(samplelist):
nsamples += [None]*(len(samplelist) - len(nsamples))
else:
nsamples = map(self.FormNAsFloat, samplelist)
##values, variances, nsamples is obsolete
self.allTraitData = {}
for i, _sample in enumerate(samplelist):
if values[i] != None:
self.allTraitData[_sample] = webqtlCaseData(
_sample, values[i], variances[i], nsamples[i])
print("allTraitData is:", pf(self.allTraitData))
