Fixed issue with parent strains appearing twice and began replacing variable names (strain -> sample, for example)

2 files changed, 62 insertions, 62 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),
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 8240eafc..4d642ffe 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -160,20 +160,20 @@ class webqtlTrait:
     __str__ = getName
     __repr__ = __str__
 
-    def exportData(self, strainlist, type="val"):
+    def exportData(self, samplelist, type="val"):
         """
-                export data according to strainlist
+                export data according to samplelist
                 mostly used in calculating correlation
         """
         result = []
-        for strain in strainlist:
-            if self.data.has_key(strain):
+        for sample in samplelist:
+            if self.data.has_key(sample):
                 if type=='val':
-                    result.append(self.data[strain].val)
+                    result.append(self.data[sample].val)
                 elif type=='var':
-                    result.append(self.data[strain].var)
+                    result.append(self.data[sample].var)
                 elif type=='N':
-                    result.append(self.data[strain].N)
+                    result.append(self.data[sample].N)
                 else:
                     raise KeyError, `type`+' type is incorrect.'
             else:
@@ -182,19 +182,19 @@ class webqtlTrait:
 
     def exportInformative(self, incVar=0):
         """
-                export informative strain
+                export informative sample
                 mostly used in qtl regression
         """
-        strains = []
+        samples = []
         vals = []
         vars = []
-        for strain, value in self.data.items():
+        for sample, value in self.data.items():
             if value.val != None:
                 if not incVar or value.var != None:
-                    strains.append(strain)
+                    samples.append(sample)
                     vals.append(value.val)
                     vars.append(value.var)
-        return  strains, vals, vars
+        return  samples, vals, vars
 
 
     #
@@ -225,10 +225,10 @@ class webqtlTrait:
 
 
 
-    def retrieveData(self, strainlist=None):
+    def retrieveData(self, samplelist=None):
         
-        if strainlist == None:
-            strainlist = []
+        if samplelist == None:
+            samplelist = []
         assert self.db and self.cursor
 
         if self.db.type == 'Temp':
@@ -334,10 +334,10 @@ class webqtlTrait:
         
         if results:
             self.mysqlid = results[0][-1]
-            #if strainlist:
+            #if samplelist:
             for item in results:
                 #name, value, variance, num_cases = item
-                if not strainlist or (strainlist and name in strainlist):
+                if not samplelist or (samplelist and name in samplelist):
                     #if value != None:
                     #    num_cases = None
                     #    if self.db.type in ('Publish', 'Temp'):