diff options
Diffstat (limited to 'wqflask/base/webqtlFormData.py')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 90 |
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), |