diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 90 | ||||
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 34 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 373 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 30 |
6 files changed, 232 insertions, 303 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'): diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 13de0b40..01541e9e 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -108,9 +108,9 @@ class DataEditingPage(templatePage): bootCheck = None, permCheck = None, applyVarianceSE = None, - strainNames = '_', - strainVals = '_', - strainVars = '_', + sampleNames = '_', + sampleVals = '_', + sampleVars = '_', otherStrainNames = '_', otherStrainVals = '_', otherStrainVars = '_', @@ -196,8 +196,8 @@ class DataEditingPage(templatePage): # self.dispTraitValues(fd, varianceDataPage, nCols, thisTrait) # - if fd.allstrainlist: - hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') + if fd.allsamplelist: + hddn['allsamplelist'] = string.join(fd.allsamplelist, ' ') # We put isSE into hddn if nCols == 6 and fd.varianceDispName != 'Variance': @@ -892,87 +892,87 @@ class DataEditingPage(templatePage): ########################################## def dispBasicStatistics(self, fd, thisTrait): - #XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later. + #XZ, June 22, 2011: The definition and usage of primary_samples, other_samples, specialStrains, all_samples are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.samplelist later. #stats_row = HT.TR() #stats_cell = HT.TD() if fd.genotype.type == "riset": - strainlist = fd.f1list + fd.strainlist + samplelist = fd.f1list + fd.samplelist else: - strainlist = fd.f1list + fd.parlist + fd.strainlist + samplelist = fd.f1list + fd.parlist + fd.samplelist - other_strains = [] #XZ: strain that is not of primary group - specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains. - all_strains = [] - primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS + other_samples = [] #XZ: sample that is not of primary group + specialStrains = [] #XZ: This might be replaced by other_samples / ZS: It is just other samples without parent/f1 samples. + all_samples = [] + primary_samples = [] #XZ: sample of primary group, e.g., BXD, LXS #self.MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp') self.MDP_menu = [] # We're going to use the same named data structure as in the old version # but repurpose it for Jinja2 as an array - for strain in thisTrait.data.keys(): - strainName = strain.replace("_2nd_", "") - if strain not in strainlist: - if thisTrait.data[strainName].value != None: - if strain.find('F1') < 0: - specialStrains.append(strain) - if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)): - other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group + for sample in thisTrait.data.keys(): + sampleName = sample.replace("_2nd_", "") + if sample not in samplelist: + if thisTrait.data[sampleName].value != None: + if sample.find('F1') < 0: + specialStrains.append(sample) + if (thisTrait.data[sampleName].value != None) and (sample not in (fd.f1list + fd.parlist)): + other_samples.append(sample) #XZ: at current stage, other_samples doesn't include parent samples and F1 samples of primary group else: - if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)): - primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) - - if len(other_strains) > 3: - other_strains.sort(key=webqtlUtil.natsort_key) - primary_strains.sort(key=webqtlUtil.natsort_key) - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added. - all_strains = primary_strains + other_strains - other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #XZ: note that fd.f1list and fd.parlist are added. + if (thisTrait.data[sampleName].value != None) and (sample not in (fd.f1list + fd.parlist)): + primary_samples.append(sample) #XZ: at current stage, the primary_samples is the same as fd.samplelist / ZS: I tried defining primary_samples as fd.samplelist instead, but in some cases it ended up including the parent samples (1436869_at BXD) + + if len(other_samples) > 3: + other_samples.sort(key=webqtlUtil.natsort_key) + primary_samples.sort(key=webqtlUtil.natsort_key) + primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples #XZ: note that fd.f1list and fd.parlist are added. + all_samples = primary_samples + other_samples + other_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_samples #XZ: note that fd.f1list and fd.parlist are added. print("ac1") # This is the one used for first sall3 self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.RISet, '1')) self.MDP_menu.append(('Non-%s Only' % fd.RISet, '2')) else: - if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3): + if (len(other_samples) > 0) and (len(primary_samples) + len(other_samples) > 3): print("ac2") self.MDP_menu.append(('All Cases','0')) self.MDP_menu.append(('%s Only' % fd.RISet,'1')) self.MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) - all_strains = primary_strains - all_strains.sort(key=webqtlUtil.natsort_key) - all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains + all_samples = primary_samples + all_samples.sort(key=webqtlUtil.natsort_key) + all_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_samples + primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples else: print("ac3") - all_strains = strainlist + all_samples = samplelist - other_strains.sort(key=webqtlUtil.natsort_key) - all_strains = all_strains + other_strains + other_samples.sort(key=webqtlUtil.natsort_key) + all_samples = all_samples + other_samples - if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4): - #One set of vals for all, selected strain only, and non-selected only + if (len(other_samples)) > 0 and (len(primary_samples) + len(other_samples) > 4): + #One set of vals for all, selected sample only, and non-selected only vals1 = [] vals2 = [] vals3 = [] - #Using all strains/cases for values - #for strain_type in (all_strains, primary_strains, other_strains): - for strainNameOrig in all_strains: - strainName = strainNameOrig.replace("_2nd_", "") + #Using all samples/cases for values + #for sample_type in (all_samples, primary_samples, other_samples): + for sampleNameOrig in all_samples: + sampleName = sampleNameOrig.replace("_2nd_", "") #try: print("* type of thisTrait:", type(thisTrait)) print(" name:", thisTrait.__class__.__name__) print(" thisTrait:", thisTrait) - print(" type of thisTrait.data[strainName]:", type(thisTrait.data[strainName])) - print(" name:", thisTrait.data[strainName].__class__.__name__) - print(" thisTrait.data[strainName]:", thisTrait.data[strainName]) - thisval = thisTrait.data[strainName].value + print(" type of thisTrait.data[sampleName]:", type(thisTrait.data[sampleName])) + print(" name:", thisTrait.data[sampleName].__class__.__name__) + print(" thisTrait.data[sampleName]:", thisTrait.data[sampleName]) + thisval = thisTrait.data[sampleName].value print(" thisval:", thisval) - thisvar = thisTrait.data[strainName].variance + thisvar = thisTrait.data[sampleName].variance print(" thisvar:", thisvar) - thisValFull = [strainName, thisval, thisvar] + thisValFull = [sampleName, thisval, thisvar] print(" thisValFull:", thisValFull) #except: # continue @@ -980,33 +980,33 @@ class DataEditingPage(templatePage): vals1.append(thisValFull) - #vals1 = [[strainNameOrig.replace("_2nd_", ""), - # thisTrait.data[strainName].val, - # thisTrait.data[strainName].var] - # for strainNameOrig in all_strains]] + #vals1 = [[sampleNameOrig.replace("_2nd_", ""), + # thisTrait.data[sampleName].val, + # thisTrait.data[sampleName].var] + # for sampleNameOrig in all_samples]] # - #Using just the RISet strain - for strainNameOrig in primary_strains: - strainName = strainNameOrig.replace("_2nd_", "") + #Using just the RISet sample + for sampleNameOrig in primary_samples: + sampleName = sampleNameOrig.replace("_2nd_", "") #try: - thisval = thisTrait.data[strainName].value - thisvar = thisTrait.data[strainName].variance - thisValFull = [strainName,thisval,thisvar] + thisval = thisTrait.data[sampleName].value + thisvar = thisTrait.data[sampleName].variance + thisValFull = [sampleName,thisval,thisvar] #except: # continue vals2.append(thisValFull) - #Using all non-RISet strains only - for strainNameOrig in other_strains: - strainName = strainNameOrig.replace("_2nd_", "") + #Using all non-RISet samples only + for sampleNameOrig in other_samples: + sampleName = sampleNameOrig.replace("_2nd_", "") #try: - thisval = thisTrait.data[strainName].value - thisvar = thisTrait.data[strainName].variance - thisValFull = [strainName,thisval,thisvar] + thisval = thisTrait.data[sampleName].value + thisvar = thisTrait.data[sampleName].variance + thisValFull = [sampleName,thisval,thisvar] #except: # continue @@ -1017,14 +1017,14 @@ class DataEditingPage(templatePage): else: vals = [] - #Using all strains/cases for values - for strainNameOrig in all_strains: - strainName = strainNameOrig.replace("_2nd_", "") + #Using all samples/cases for values + for sampleNameOrig in all_samples: + sampleName = sampleNameOrig.replace("_2nd_", "") #try: - thisval = thisTrait.data[strainName].value - thisvar = thisTrait.data[strainName].variance - thisValFull = [strainName,thisval,thisvar] + thisval = thisTrait.data[sampleName].value + thisvar = thisTrait.data[sampleName].variance + thisValFull = [sampleName,thisval,thisvar] #except: # continue @@ -1041,10 +1041,10 @@ class DataEditingPage(templatePage): stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #stats_cell.append(stats_container) break - elif (i == 1 and len(primary_strains) < 4): + elif (i == 1 and len(primary_samples) < 4): stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) - elif (i == 2 and len(other_strains) < 4): + elif (i == 2 and len(other_samples) < 4): stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" @@ -1609,14 +1609,15 @@ class DataEditingPage(templatePage): print("in dispTraitValues") if fd.genotype.type == "riset": - allstrainlist_neworder = fd.f1list + fd.strainlist + allsamplelist_neworder = fd.f1list + fd.samplelist else: - allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist + allsamplelist_neworder = fd.f1list + fd.parlist + fd.samplelist attribute_ids = [] attribute_names = [] #try: - #ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create + #ZS: Id values for this trait's extra attributes; + #used to create "Exclude" dropdown and query for attribute values and create self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name FROM CaseAttribute, CaseAttributeXRef WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND @@ -1624,150 +1625,78 @@ class DataEditingPage(templatePage): group by CaseAttributeXRef.CaseAttributeId""", (str(thisTrait.db.id),)) - #exclude_menu = HT.Select(name="exclude_menu") - #dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) - - #for attribute in self.cursor.fetchall(): - # #attribute_ids.append(attribute[0]) - # #attribute_names.append(attribute[1]) - # pass for this_attr_name in attribute_names: - #exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) # Todo: Needs testing still! self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value FROM CaseAttribute, CaseAttributeXRef WHERE CaseAttribute.Name = %s AND CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""", (this_attr_name,)) - #try: + distinct_values = self.cursor.fetchall() - #attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - #attr_value_menu = HT.Select(name=this_attr_name) - #attr_value_menu.append(("None", "show_all")) - #for value in distinct_values: - # #attr_value_menu.append((str(value[0]), value[0])) - # pass - #attr_value_menu_div.append(attr_value_menu) - #dropdown_menus.append(attr_value_menu_div) - #except: - # pass - #except: - # pass - - #for strain in thisTrait.data.keys(): - # if strain not in allstrainlist_neworder: - # pass - # #other_strains.append(strain) - # - #if other_strains: - # #blockMenu.append(('%s Only' % fd.RISet,'1')) - # #blockMenu.append(('Non-%s Only' % fd.RISet,'0')) - # #blockMenuSpan.append(blockMenu) - # pass - #else: - # pass - - #showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') - #showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") - #if other_strains: - # pass - #showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockMenuSpan, " ", blockSamplesButton, HT.BR()) - #else: - # pass - #showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockSamplesButton, HT.BR()) - #exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') - #if len(attribute_names) > 0: - # excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') - #showHideMenuOptions.append(HT.Bold(" Block samples by group:"), " "*5, exclude_menu, " "*5) - #for menu in dropdown_menus: - # pass - #showHideMenuOptions.append(menu) - #showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) - #showHideMenuOptions.append(HT.Bold(" Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) - - #traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) - #traitTableOptions.append(HT.Span(" Outliers highlighted in ", HT.Bold(" red ", style="background-color:red;"), " can be hidden using the ", - # HT.Strong(" Hide Outliers "), " button,",HT.BR()," and samples with no value (x) can be hidden by clicking ", - # HT.Strong(" Hide No Value "), "."), HT.BR()) - - - #dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;") - # - #table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work - #container = HT.Div() #This will contain everything and be put into a cell of the table defined above - # - #container.append(dispintro, traitTableOptions, HT.BR()) - - #primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter") - #primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object - - #other_strainsExist = False - this_trait_strains = set(thisTrait.data.keys()) - #ZS - Checks if there are any strains in this_trait_strains that aren't in allstrainlist_neworder - other_strainsExist = this_trait_strains - set(allstrainlist_neworder) - - #for strain in thisTrait.data.keys(): - # print("hjl - strain is:", strain) - # if strain not in allstrainlist_neworder: - # other_strainsExist = True - # break + this_trait_samples = set(thisTrait.data.keys()) + #ZS - Checks if there are any samples in this_trait_samples that aren't in allsamplelist_neworder + other_samplesExist = this_trait_samples - set(allsamplelist_neworder) mainForm = None # Just trying to get things working - primary_strainlist = fd.parlist + allstrainlist_neworder + primary_samplelist = allsamplelist_neworder + + print("primary_samplelist is:", pf(primary_samplelist)) - primary_strains = self.create_strain_objects(fd=fd, + primary_samples = self.create_sample_objects(fd=fd, varianceDataPage=varianceDataPage, - strainlist=primary_strainlist, + samplelist=primary_samplelist, mainForm=mainForm, thisTrait=thisTrait, - other_strainsExist=other_strainsExist, + other_samplesExist=other_samplesExist, attribute_ids=attribute_ids, attribute_names=attribute_names, - strains='primary') - + samples='primary') + - other_strains = [] - for strain in thisTrait.data.keys(): - print("hjk - strain is:", strain) - if strain not in allstrainlist_neworder + fd.f1list + fd.parlist: - allstrainlist_neworder.append(strain) - other_strains.append(strain) + other_samples = [] + for sample in thisTrait.data.keys(): + print("hjk - sample is:", sample) + if sample not in allsamplelist_neworder: + allsamplelist_neworder.append(sample) + other_samples.append(sample) - if other_strains: + if other_samples: unappended_par_f1 = fd.f1list + fd.parlist - par_f1_strains = ["_2nd_" + strain for strain in unappended_par_f1] + par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1] - other_strains.sort() #Sort other strains - other_strains = par_f1_strains + other_strains + other_samples.sort() #Sort other samples + other_samples = par_f1_samples + other_samples - other_strains = self.create_strain_objects(fd=fd, + other_samples = self.create_sample_objects(fd=fd, varianceDataPage=varianceDataPage, - strainlist=other_strains, + samplelist=other_samples, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, - strains='other') + samples='other') #TODO: Figure out why this if statement is written this way - Zach - if (other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) + if (other_samples or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) or (fd.f1list and thisTrait.data.has_key(fd.f1list[1]))): print("hjs") - fd.allstrainlist = allstrainlist_neworder + fd.allsamplelist = allsamplelist_neworder - self.primary_strains = dict(header = "%s Only" % (fd.RISet), - strains = primary_strains,) + self.primary_samples = dict(header = "%s Only" % (fd.RISet), + samples = primary_samples,) - self.other_strains = dict(header = "Non-%s" % (fd.RISet), - strains = other_strains,) + self.other_samples = dict(header = "Non-%s" % (fd.RISet), + samples = other_samples,) + - def create_strain_objects(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, - other_strainsExist=None, attribute_ids=None, - attribute_names=None, strains='primary'): + def create_sample_objects(self, fd, varianceDataPage, samplelist, mainForm, thisTrait, + other_samplesExist=None, attribute_ids=None, + attribute_names=None, samples='primary'): if attribute_ids == None: attribute_ids = [] @@ -1776,47 +1705,47 @@ class DataEditingPage(templatePage): attribute_names = [] #XZ, Aug 23, 2010: I commented the code related to the display of animal case - #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo - print("in create_strain_objects") + #sampleInfo = thisTrait.has_key('sampleInfo') and thisTrait.sampleInfo + print("in create_sample_objects") #table_body = [] ################### Only used to find upperBound and lowerBound #vals = [] - #for strainNameOrig in strainlist: - # strainName = strainNameOrig.replace("_2nd_", "") - # print("pen: %s - %s" % (strainNameOrig, strainName)) + #for sampleNameOrig in samplelist: + # sampleName = sampleNameOrig.replace("_2nd_", "") + # print("pen: %s - %s" % (sampleNameOrig, sampleName)) # try: - # thisval = thisTrait.data[strainName].value - # thisvar = thisTrait.data[strainName].variance - # thisValFull = [strainName, thisval, thisvar] + # thisval = thisTrait.data[sampleName].value + # thisvar = thisTrait.data[sampleName].variance + # thisValFull = [sampleName, thisval, thisvar] # # vals.append(thisValFull) # except KeyError: - # print("**x** Skipping:", strainName) + # print("**x** Skipping:", sampleName) # #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - the_strains = [] + the_samples = [] - for counter, strainNameOrig in enumerate(strainlist, 1): - strainName = strainNameOrig.replace("_2nd_", "") - strainNameAdd = '' - if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): - strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") + for counter, sampleNameOrig in enumerate(samplelist, 1): + sampleName = sampleNameOrig.replace("_2nd_", "") + sampleNameAdd = '' + if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): + sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") try: - strain = thisTrait.data[strainName] + sample = thisTrait.data[sampleName] except KeyError: - print("No strain %s, let's create it now" % strainName) - strain = webqtlCaseData.webqtlCaseData(strainName) - print("zyt - strainNameOrig:", strainNameOrig) + print("No sample %s, let's create it now" % sampleName) + sample = webqtlCaseData.webqtlCaseData(sampleName) + print("zyt - sampleNameOrig:", sampleNameOrig) - if strains == 'primary': - strain.this_id = "Primary_" + str(counter) + if samples == 'primary': + sample.this_id = "Primary_" + str(counter) else: - strain.this_id = "Other_" + str(counter) + sample.this_id = "Other_" + str(counter) #### For extra attribute columns; currently only used by two human datasets - Zach if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': @@ -1828,9 +1757,9 @@ class DataEditingPage(templatePage): WHERE Strain.Name = '%s' and StrainXRef.StrainId = Strain.Id and InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (strainName, fd.RISet)) + InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) - strain_id = self.cursor.fetchone()[0] + sample_id = self.cursor.fetchone()[0] attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). for attribute_id in attribute_ids: @@ -1841,7 +1770,7 @@ class DataEditingPage(templatePage): WHERE ProbeSetFreezeId = '%s' AND StrainId = '%s' AND CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id))) + group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, sample_id, str(attribute_id))) attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any @@ -1851,17 +1780,17 @@ class DataEditingPage(templatePage): except: pass - span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1) + span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) attr_container = HT.Span(attributeValue, Id=span_Id) attr_className = str(attributeValue) + " " + className table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) attr_counter += 1 - the_strains.append(strain) + the_samples.append(sample) #table_body.append(table_row) - do_outliers(the_strains) - print("*the_strains are [%i]: %s" % (len(the_strains), pf(the_strains))) - return the_strains + do_outliers(the_samples) + print("*the_samples are [%i]: %s" % (len(the_samples), pf(the_samples))) + return the_samples def getTableHeader(self, fd, thisTrait, nCols, attribute_names): @@ -1909,15 +1838,15 @@ class DataEditingPage(templatePage): -def do_outliers(strain_objects): - values = [strain.value for strain in strain_objects if strain.value != None] +def do_outliers(sample_objects): + values = [sample.value for sample in sample_objects if sample.value != None] upper_bound, lower_bound = Plot.find_outliers(values) - for strain in strain_objects: - if strain.value: - if upper_bound and strain.value > upper_bound: - strain.outlier = True - elif lower_bound and strain.value < lower_bound: - strain.outlier = True + for sample in sample_objects: + if sample.value: + if upper_bound and sample.value > upper_bound: + sample.outlier = True + elif lower_bound and sample.value < lower_bound: + sample.outlier = True else: - strain.outlier = False + sample.outlier = False diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee index 94ae0203..803045d5 100644 --- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee +++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee @@ -46,13 +46,13 @@ $ -> all_cases: new Stats([]) console.log("at beginning:", sample_sets) - values = $('#value_table').find(".edit_strain_value") + values = $('#value_table').find(".edit_sample_value") for value in values real_value = $(value).val() row = $(value).closest("tr") category = row[0].id - checkbox = $(row).find(".edit_strain_checkbox") + checkbox = $(row).find(".edit_sample_checkbox") checked = $(checkbox).attr('checked') if checked and is_number(real_value) and real_value != "" diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js index 9d7918a1..55bc1302 100644 --- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js +++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js @@ -69,13 +69,13 @@ all_cases: new Stats([]) }; console.log("at beginning:", sample_sets); - values = $('#value_table').find(".edit_strain_value"); + values = $('#value_table').find(".edit_sample_value"); for (_i = 0, _len = values.length; _i < _len; _i++) { value = values[_i]; real_value = $(value).val(); row = $(value).closest("tr"); category = row[0].id; - checkbox = $(row).find(".edit_strain_checkbox"); + checkbox = $(row).find(".edit_sample_checkbox"); checked = $(checkbox).attr('checked'); if (checked && is_number(real_value) && real_value !== "") { real_value = parseFloat(real_value); diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 3d2ec636..89ce7d46 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -14,10 +14,10 @@ <input type="hidden" name="otherStrainVals" value="_"> <input type="hidden" name="FormID" value="dataEditing"> <input type="hidden" name="normalPlotTitle" value="Sall3: 1441186_at"> - <input type="hidden" name="strainVars" value="_"> + <input type="hidden" name="sampleVars" value="_"> <input type="hidden" name="additiveCheck" value="ON"> <input type="hidden" name="incparentsf1" value="ON"> - <input type="hidden" name="strainNames" value="_"> + <input type="hidden" name="sampleNames" value="_"> <input type="hidden" name="submitID" value=""> <input type="hidden" name="scale" value="physic"> <input type="hidden" name="intervalAnalystCheck" value="ON"> @@ -32,11 +32,11 @@ <input type="hidden" name="showGenes" value="ON"> <input type="hidden" name="attribute_names" value=""> <input type="hidden" name="chromosomes" value="-1"> - <input type="hidden" name="allstrainlist" value="B6D2F1 D2B6F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD14 BXD15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a BXD24 BXD25 BXD27 BXD28 BXD29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD42 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BXD73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD87 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100 BXD101 BXD102 BXD103 BALB/cByJ PWK/PhJ A/J KK/HlJ LG/J 129S1/SvImJ NZO/HlLtJ CAST/EiJ PWD/PhJ AKR/J CXB13 CXB12 CXB11 CXB10 WSB/EiJ C3H/HeJ CXB7 CXB6 CXB5 CXB4 CXB3 CXB2 CXB1 CXB9 CXB8 NOD/ShiLtJ C57BL/6ByJ BALB/cJ"> + <input type="hidden" name="allsamplelist" value="B6D2F1 D2B6F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD14 BXD15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a BXD24 BXD25 BXD27 BXD28 BXD29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD42 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BXD73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD87 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100 BXD101 BXD102 BXD103 BALB/cByJ PWK/PhJ A/J KK/HlJ LG/J 129S1/SvImJ NZO/HlLtJ CAST/EiJ PWD/PhJ AKR/J CXB13 CXB12 CXB11 CXB10 WSB/EiJ C3H/HeJ CXB7 CXB6 CXB5 CXB4 CXB3 CXB2 CXB1 CXB9 CXB8 NOD/ShiLtJ C57BL/6ByJ BALB/cJ"> <input type="hidden" name="applyVarianceSE"> <input type="hidden" name="MDPChoice"> <input type="hidden" name="otherStrainVars" value="_"> - <input type="hidden" name="strainVals" value="_"> + <input type="hidden" name="sampleVals" value="_"> <input type="hidden" name="showSNP" value="ON"> <input type="hidden" name="bootCheck"> <input type="hidden" name="GeneId" value="20689"> @@ -1245,12 +1245,12 @@ </div><br> <div style="width:80%;margin:0;padding:0;border:none;"> - {% for strain_type in (primary_strains, other_strains) %} + {% for sample_type in (primary_samples, other_samples) %} <div style="float:left;width:50%;"> - <h2>{{ strain_type.header }}</h2> + <h2>{{ sample_type.header }}</h2> - <div id="{{ strain_type.strains[0]['this_id'].lower().partition('_')[0] }}"> {# Slightly tortuous, but best way to get the id we need #} + <div id="{{ sample_type.samples[0]['this_id'].lower().partition('_')[0] }}"> {# Slightly tortuous, but best way to get the id we need #} <table class="not_tablesorter" {# Todo: Turn tablesorter back on #} id="{{ 'sortable%i' % (loop.index) }}" cellpadding="0" cellspacing="0"> @@ -1266,21 +1266,21 @@ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th> </tr> - {% for strain in strain_type.strains %} - <tr class="{{ strain.class_outlier }} value_se" id="{{ strain.this_id }}"> + {% for sample in sample_type.samples %} + <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}"> <td class="fs13 b1 c222" align="right" width="45"> {{ loop.index }} - <input type="checkbox" name="selectCheck" class="checkbox edit_strain_checkbox" value="{{ strain.name }}" checked="checked"> + <input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked"> </td> <td class="fs13 b1 c222" align="right" width="100"> - <span class="fs14 fwn ffl edit_strain_strain_name">{{ strain.name }}</span> + <span class="fs14 fwn ffl edit_sample_sample_name">{{ sample.name }}</span> </td> {# Todo: Add IDs #} <td class="fs13 b1 c222" align="right" width="70"> - <input type="text" name="{{ strain.name }}" class="fs13 b1 c222 edit_strain_value valueField" - value="{{ strain.display_value }}" size="8" maxlength="8" + <input type="text" name="{{ sample.name }}" class="fs13 b1 c222 edit_sample_value valueField" + value="{{ sample.display_value }}" size="8" maxlength="8" style="text-align:right; background-color:#FFFFFF;"> </td> @@ -1290,8 +1290,8 @@ {# Todo: Add IDs #} <td class="fs13 b1 c222" align="right" width="80"> - <input type="text" name=""{{ 'V' + strain.name}}" class="fs13 b1 c222 valueField edit_strain_se" - value="{{ strain.display_variance }}" + <input type="text" name=""{{ 'V' + sample.name}}" class="fs13 b1 c222 valueField edit_sample_se" + value="{{ sample.display_variance }}" size="8" maxlength="8" style="text-align:right"></td> </tr> {% endfor %} |