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Diffstat (limited to 'wqflask/base/webqtlFormData.py')
-rwxr-xr-xwqflask/base/webqtlFormData.py90
1 files changed, 45 insertions, 45 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index a8aef2a5..eb1ebd5e 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -46,7 +46,7 @@ from utility import webqtlUtil
class webqtlFormData:
'Represents data from a WebQTL form page, needed to generate the next page'
- attrs = ('formID','RISet','genotype','strainlist','allstrainlist',
+ attrs = ('formID','RISet','genotype','samplelist','allsamplelist',
'suggestive','significance','submitID','identification', 'enablevariance',
'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
@@ -116,12 +116,12 @@ class webqtlFormData:
self.nboot = set_number(self.nboot)
- #if self.allstrainlist:
- # self.allstrainlist = map(string.strip, string.split(self.allstrainlist))
- print("self.allstrainlist is:", self.allstrainlist)
- if self.allstrainlist:
- self.allstrainlist = self.allstrainlist.split()
- print("now self.allstrainlist is:", self.allstrainlist)
+ #if self.allsamplelist:
+ # self.allsamplelist = map(string.strip, string.split(self.allsamplelist))
+ print("self.allsamplelist is:", self.allsamplelist)
+ if self.allsamplelist:
+ self.allsamplelist = self.allsamplelist.split()
+ print("now self.allsamplelist is:", self.allsamplelist)
#self.readGenotype()
#self.readData()
@@ -183,7 +183,7 @@ class webqtlFormData:
self.incparentsf1 = 0
self.genotype = self.genotype_1
- self.strainlist = list(self.genotype.prgy)
+ self.samplelist = list(self.genotype.prgy)
self.f1list = []
self.parlist = []
@@ -193,7 +193,7 @@ class webqtlFormData:
self.parlist = [_mat, _pat]
- def readData(self, strainlist, incf1=None):
+ def readData(self, samplelist, incf1=None):
'''read user input data or from trait data and analysis form'''
if incf1 == None:
@@ -201,11 +201,11 @@ class webqtlFormData:
if not self.genotype:
self.readGenotype()
- if not strainlist:
+ if not samplelist:
if incf1:
- strainlist = self.f1list + self.strainlist
+ samplelist = self.f1list + self.samplelist
else:
- strainlist = self.strainlist
+ samplelist = self.samplelist
#print("before traitfiledata self.traitfile is:", pf(self.traitfile))
@@ -223,7 +223,7 @@ class webqtlFormData:
except ValueError:
return None
- print("bottle strainlist is:", strainlist)
+ print("bottle samplelist is:", samplelist)
if traitfiledata:
tt = traitfiledata.split()
values = map(webqtlUtil.StringAsFloat, tt)
@@ -232,15 +232,15 @@ class webqtlFormData:
values = map(webqtlUtil.StringAsFloat, tt)
else:
print("mapping formdataasfloat")
- #values = map(self.FormDataAsFloat, strainlist)
- values = [to_float(getattr(self, key)) for key in strainlist]
+ #values = map(self.FormDataAsFloat, samplelist)
+ values = [to_float(getattr(self, key)) for key in samplelist]
print("rocket values is:", values)
- if len(values) < len(strainlist):
- values += [None] * (len(strainlist) - len(values))
- elif len(values) > len(strainlist):
- values = values[:len(strainlist)]
+ 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)
@@ -251,58 +251,58 @@ class webqtlFormData:
tt = variancepastedata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
else:
- variances = map(self.FormVarianceAsFloat, strainlist)
+ variances = map(self.FormVarianceAsFloat, samplelist)
- if len(variances) < len(strainlist):
- variances += [None]*(len(strainlist) - len(variances))
- elif len(variances) > len(strainlist):
- variances = variances[:len(strainlist)]
+ 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)
- nstrains = map(webqtlUtil.IntAsFloat, tt)
- if len(nstrains) < len(strainlist):
- nstrains += [None]*(len(strainlist) - len(nstrains))
+ nsamples = map(webqtlUtil.IntAsFloat, tt)
+ if len(nsamples) < len(samplelist):
+ nsamples += [None]*(len(samplelist) - len(nsamples))
else:
- nstrains = map(self.FormNAsFloat, strainlist)
+ nsamples = map(self.FormNAsFloat, samplelist)
- ##values, variances, nstrains is obsolete
+ ##values, variances, nsamples is obsolete
self.allTraitData = {}
- for i, _strain in enumerate(strainlist):
+ for i, _sample in enumerate(samplelist):
if values[i] != None:
- self.allTraitData[_strain] = webqtlCaseData(
- _strain, values[i], variances[i], nstrains[i])
+ self.allTraitData[_sample] = webqtlCaseData(
+ _sample, values[i], variances[i], nsamples[i])
print("allTraitData is:", pf(self.allTraitData))
- def informativeStrains(self, strainlist=None, include_variances = None):
- '''if readData was called, use this to output informative strains (strain with values)'''
+ def informativeStrains(self, samplelist=None, include_variances = None):
+ '''if readData was called, use this to output informative samples (sample with values)'''
- if not strainlist:
- strainlist = self.strainlist
+ if not samplelist:
+ samplelist = self.samplelist
- strains = []
+ samples = []
values = []
variances = []
#print("self.allTraitData is:", pf(self.allTraitData))
- for strain in strainlist:
- if strain in self.allTraitData:
- _val, _var = self.allTraitData[strain].value, self.allTraitData[strain].variance
+ for sample in samplelist:
+ if sample in self.allTraitData:
+ _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
if _val != None:
if include_variances:
if _var != None:
- strains.append(strain)
+ samples.append(sample)
values.append(_val)
variances.append(_var)
else:
- strains.append(strain)
+ samples.append(sample)
values.append(_val)
variances.append(None)
- return strains, values, variances, len(strains)
+ return samples, values, variances, len(samples)
@@ -336,8 +336,8 @@ class webqtlFormData:
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.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),