diff options
Diffstat (limited to 'web/webqtl')
| -rwxr-xr-x | web/webqtl/basicStatistics/updatedBasicStatisticsPage.py | 54 | ||||
| -rwxr-xr-x | web/webqtl/correlation/CorrelationPage.py | 171 | ||||
| -rwxr-xr-x[-rw-r--r--] | web/webqtl/showTrait/DataEditingPage.py | 49 |
3 files changed, 145 insertions, 129 deletions
diff --git a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py index 156dafe7..ab7ed07d 100755 --- a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py +++ b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py @@ -63,9 +63,9 @@ class updatedBasicStatisticsPage(templatePage): thisValFull = [strain_names[i], this_strain_val, this_strain_var] vals.append(thisValFull) - stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), + stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"), HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), - HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")] + HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")] stats_tabs = HT.List(stats_tab_list) stats_container = HT.Div(id="stats_tabs", Class="ui-tabs") @@ -73,7 +73,7 @@ class updatedBasicStatisticsPage(templatePage): stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs - table_div = HT.Div(id="statstabs-1") + table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;") table_container = HT.Paragraph() statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") @@ -86,16 +86,21 @@ class updatedBasicStatisticsPage(templatePage): table_div.append(table_container) stats_container.append(table_div) - boxplot_div = HT.Div(id="statstabs-2") - boxplot_container = HT.Paragraph() - boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) - boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) - boxplot_container.append(boxplot) - boxplot_div.append(boxplot_container) - stats_container.append(boxplot_div) + normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;") + normalplot_container = HT.Paragraph() + normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + plotTitle = fd.formdata.getvalue("normalPlotTitle","") + normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + normalplot.append(HT.TR(HT.TD(normalplot_img))) + normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + normalplot_container.append(normalplot) + normalplot_div.append(normalplot_container) + stats_container.append(normalplot_div) - barName_div = HT.Div(id="statstabs-3") + barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;") barName_container = HT.Paragraph() barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") @@ -104,7 +109,7 @@ class updatedBasicStatisticsPage(templatePage): barName_div.append(barName_container) stats_container.append(barName_div) - barRank_div = HT.Div(id="statstabs-4") + barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;") barRank_container = HT.Paragraph() barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") @@ -112,20 +117,15 @@ class updatedBasicStatisticsPage(templatePage): barRank_container.append(barRank) barRank_div.append(barRank_container) stats_container.append(barRank_div) - - normalplot_div = HT.Div(id="statstabs-5") - normalplot_container = HT.Paragraph() - normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - plotTitle = fd.formdata.getvalue("normalPlotTitle","") - normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) - normalplot.append(HT.TR(HT.TD(normalplot_img))) - normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ - normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), - "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", - target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) - normalplot_container.append(normalplot) - normalplot_div.append(normalplot_container) - stats_container.append(normalplot_div) + + boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;") + boxplot_container = HT.Paragraph() + boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + boxplot_container.append(boxplot) + boxplot_div.append(boxplot_container) + stats_container.append(boxplot_div) stats_cell.append(stats_container) stats_script.append(stats_script_text) diff --git a/web/webqtl/correlation/CorrelationPage.py b/web/webqtl/correlation/CorrelationPage.py index ce8b8165..72e53f1d 100755 --- a/web/webqtl/correlation/CorrelationPage.py +++ b/web/webqtl/correlation/CorrelationPage.py @@ -91,7 +91,7 @@ class Trait(object): #ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for #There's probably a better way of dealing with this, but I'll have to ask Christian - updated_raw_values = [] + updated_raw_values = [] updated_values = [] for i in range(len(values)): if values[i] != "None": @@ -120,7 +120,7 @@ class Trait(object): ZValue = ZValue*sqrt(self.overlap-3) self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) - + #XZ, 01/14/2009: This method is for parallel computing only. #XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1) @@ -151,7 +151,7 @@ def get_correlation_method_key(form_data): #XZ, 09/28/2008: if user select "2", then display 2, 3 and 5. #XZ, 09/28/2008: if user select "3", then display 1, 3 and 4. #XZ, 09/28/2008: if user select "4", then display 1, 3 and 4. - #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5. + #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5. method = form_data.formdata.getvalue("method") if method not in ["1", "2", "3" ,"4", "5"]: @@ -172,7 +172,7 @@ def get_custom_trait(form_data, cursor): return None -#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form. +#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form. def get_sample_data(form_data): if form_data.allstrainlist: mdpchoice = form_data.formdata.getvalue('MDPChoice') @@ -194,8 +194,8 @@ def get_sample_data(form_data): strainlist = form_data.allstrainlist #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData form_data.readData(form_data.allstrainlist) - else: - mdpchoice = None + else: + mdpchoice = None strainlist = form_data.strainlist #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData form_data.readData() @@ -267,7 +267,7 @@ class CorrelationPage(templatePage): CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)", "2" : "Genetic Correlation (Spearman's rho)", "3" : "SGO Literature Correlation", - "4" : "Tissue Correlation (Pearson's r)", + "4" : "Tissue Correlation (Pearson's r)", "5" : "Tissue Correlation (Spearman's rho)"} RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1} @@ -338,7 +338,7 @@ class CorrelationPage(templatePage): # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against self.trait_symbol = myTrait.symbol - + #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.species, self.gene_id) @@ -347,7 +347,7 @@ class CorrelationPage(templatePage): self.tissue_probeset_freeze_id = 1 traitList = self.correlate(vals) - + _log.info("Done doing correlation calculation") ############################################################################################################################################ @@ -356,12 +356,12 @@ class CorrelationPage(templatePage): mainfmName = webqtlUtil.genRandStr("fm_") form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden')) - hddn = {'FormID': 'showDatabase', + hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', - 'database': self.target_db_name, - 'databaseFull': self.db.fullname, - 'CellID': '_', - 'RISet': fd.RISet, + 'database': self.target_db_name, + 'databaseFull': self.db.fullname, + 'CellID': '_', + 'RISet': fd.RISet, 'identification': fd.identification} if myTrait: @@ -400,7 +400,7 @@ class CorrelationPage(templatePage): ############## # Excel file # - ############## + ############## filename= webqtlUtil.genRandStr("Corr_") xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button') # Create a new Excel workbook @@ -432,7 +432,7 @@ class CorrelationPage(templatePage): heatmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'heatmap');" % mainfmName) heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='mintmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;") heatmap.append(heatmap_img) - partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName) + partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName) partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;") partialCorr.append(partialCorr_img) addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, mainfmName)) @@ -454,7 +454,7 @@ class CorrelationPage(templatePage): selectandor.append(('AND','and')) selectandor.append(('OR','or')) selectandor.selected.append('AND') - + #External analysis tools GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GCAT');" % mainfmName) @@ -473,8 +473,8 @@ setTimeout('openWebGestalt()', 2000); function openWebGestalt(){ var thisForm = document['WebGestalt']; makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); -} - """ % (mainfmName, len(traitList))) +} + """ % (mainfmName, len(traitList))) ''' self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % self.db.name) @@ -484,15 +484,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); GO_tree_value = result[0] if GO_tree_value: - + WebGestalt = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GOTree');" % mainfmName) - WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none") - WebGestalt.append(WebGestalt_img) - + WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none") + WebGestalt.append(WebGestalt_img) + hddnWebGestalt = { 'id_list':'', 'correlation':'', - 'id_value':'', + 'id_value':'', 'llid_list':'', 'id_type':GO_tree_value, 'idtype':'', @@ -512,7 +512,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); hddnWebGestalt['org'] = 'Mus musculus' else: hddnWebGestalt['org'] = '' - + for key in hddnWebGestalt.keys(): form.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden')) @@ -523,11 +523,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); containerTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="90%",border=0, align="Left") - + if not GO_tree_value: optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="480", height="80", border=0, align="Left") optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), align="left")) - optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*3,"Add"), HT.TD("Gene Set"), HT.TD(" "*2,"GCAT"))) + optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*3,"Add"), HT.TD("Gene Set"), HT.TD(" "*2,"GCAT"))) else: optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="560", height="80", border=0, align="Left") optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), HT.TD(WebGestalt), align="left")) @@ -548,11 +548,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle") """ - if (fd.formdata.getvalue('showHideOptions') == 'less'): + if (fd.formdata.getvalue('showHideOptions') == 'less'): containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide")))) containerTable.append(HT.TR(HT.TD(" "))) - else: - containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) + else: + containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) containerTable.append(HT.TR(HT.TD(" "))) """ @@ -566,8 +566,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); tblobj = {} if self.db.type=="Geno": - - containerTable.append(HT.TR(HT.TD(xlsUrl, height=40))) + containerTable.append(HT.TR(HT.TD(xlsUrl, height=60))) pageTable.append(HT.TR(HT.TD(containerTable))) @@ -579,7 +578,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); corrScript = HT.Script(language="Javascript") corrScript.append("var corrArray = new Array();") - tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript) + tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript) workbook.close() objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') @@ -604,15 +603,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); containerTable.append(HT.TR(HT.TD(xlsUrl, height=40))) pageTable.append(HT.TR(HT.TD(containerTable))) - + tblobj['header'], worksheet = self.getTableHeaderForPublish(method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle) newrow += 1 sortby = self.getSortByValue( calculationMethod = self.method ) - + corrScript = HT.Script(language="Javascript") corrScript.append("var corrArray = new Array();") - + tblobj['body'], worksheet, corrScript = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=self.species) workbook.close() @@ -650,7 +649,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); workbook.close() objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') cPickle.dump(tblobj, objfile) - objfile.close() + objfile.close() #XZ: here is the table of traits div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1", hiddenColumns=["Gene ID","Homologene ID"]), corrScript, Id="sortable") @@ -708,11 +707,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); if self.species == 'human': heatmap = "" - + form.append(HT.Input(name='ShowStrains',type='hidden', value =1), HT.Input(name='ShowLine',type='hidden', value =1), info, HT.BR(), pageTable, HT.BR()) - + TD_LR.append(corrHeading, form, HT.P()) @@ -745,7 +744,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php'); sortby = ("Tissue r", "down") elif calculationMethod == "5": sortby = ("Tissue rho", "down") - + return sortby @@ -808,7 +807,7 @@ Resorting this table <br> def getStrainIds(self, species=None, strains=[]): StrainIds = [] for item in strains: - self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE + self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE Strain.Name="%s" and Strain.SpeciesId=Species.Id and Species.name = "%s" ''' % (item, species)) Id = self.cursor.fetchone()[0] StrainIds.append(Id) @@ -855,16 +854,16 @@ Resorting this table <br> #XZ, 12/16/2008: the input geneid is of mouse type def checkSymbolForTissueCorr(self, tissueProbeSetFreezeId=0, symbol=""): - q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol) + q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol) self.cursor.execute(q) try: x = self.cursor.fetchone() if x: return True else: raise except: return False - - + + def fetchAllDatabaseData(self, species, GeneId, GeneSymbol, strains, db, method, returnNumber, tissueProbeSetFreezeId): StrainIds = [] @@ -879,9 +878,9 @@ Resorting this table <br> nnn += 1 oridata = [] - #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId + #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId tempTable = None - if GeneId and db.type == "ProbeSet": + if GeneId and db.type == "ProbeSet": if method == "3": tempTable = self.getTempLiteratureTable(species=species, input_species_geneid=GeneId, returnNumber=returnNumber) @@ -892,7 +891,7 @@ Resorting this table <br> temp = [] StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)] for item in StrainIdstep: temp.append('T%s.value' % item) - + if db.type == "Publish": query = "SELECT PublishXRef.Id, " dataStartPos = 1 @@ -910,12 +909,12 @@ Resorting this table <br> # as we would not have litCorr data. if method == "3": - query = "SELECT %s.Name, %s.value," % (db.type,tempTable) - dataStartPos = 2 + query = "SELECT %s.Name, %s.value," % (db.type,tempTable) + dataStartPos = 2 if method == "4" or method == "5": - query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable) - dataStartPos = 3 - + query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable) + dataStartPos = 3 + query += string.join(temp,', ') query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type) if method == "3": @@ -925,8 +924,8 @@ Resorting this table <br> #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item) for item in StrainIdstep: query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item) - - if method == "3": + + if method == "3": query += "WHERE ProbeSet.GeneId IS NOT NULL AND %s.value IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type) if method == "4" or method == "5": query += "WHERE ProbeSet.Symbol IS NOT NULL AND %s.Correlation IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type) @@ -939,7 +938,7 @@ Resorting this table <br> for item in StrainIdstep: query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item) query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type) - + self.cursor.execute(query) results = self.cursor.fetchall() oridata.append(results) @@ -971,17 +970,17 @@ Resorting this table <br> - # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name. + # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name. # XZ, 09/20/2008: It stores top literature correlation values associated with the input geneId. # XZ, 09/20/2008: Attention: In each row, the input geneId is always in column GeneId1. #XZ, 12/16/2008: the input geneid can be of mouse, rat or human type def getTempLiteratureTable(self, species, input_species_geneid, returnNumber): # according to mysql the TEMPORARY TABLE name should not have to be unique because - # it is only available to the current connection. This program will be invoked via command line, but if it + # it is only available to the current connection. This program will be invoked via command line, but if it # were to be invoked over mod_python this could cuase problems. mod_python will keep the connection alive # in its executing threads ( i think) so there is a potential for the table not being dropped between users. #XZ, 01/29/2009: To prevent the potential risk, I generate random table names and drop the tables after use them. - + # the 'input_species_geneid' could be rat or human geneid, need to translate it to mouse geneid translated_mouse_geneid = self.translateToMouseGeneID (species, input_species_geneid) @@ -1022,7 +1021,7 @@ Resorting this table <br> translated_species_geneid = record[0] if translated_species_geneid: - self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) ) + self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) ) counter = counter + 1 #pay attention to the number @@ -1054,9 +1053,9 @@ Resorting this table <br> symbolCorrList.sort(cmpTissCorrAbsoluteValue) symbolCorrList = symbolCorrList[0 : 2*returnNumber] - + tmpTableName = webqtlUtil.genRandStr(prefix="TOPTISSUE") - + q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmpTableName self.cursor.execute(q1) @@ -1166,7 +1165,7 @@ Resorting this table <br> return traitList def get_trait(self, cached, vals): - + if cached: _log.info("Using the fast method because the file exists") lit_corrs = {} @@ -1194,7 +1193,7 @@ Resorting this table <br> #XZ: The new method uses all strains stored in variable dataset_strains to create a new variable #XZ: _newvals. _newvals has the same length as dataset_strains. The items in _newvals is in #XZ: the same order of items in dataset_strains. The value of each item in _newvals is either - #XZ: the value of correspinding strain in _vals or 'None'. + #XZ: the value of correspinding strain in _vals or 'None'. new_vals = [] for name in cached_sample_names: if name in self.sample_names: @@ -1211,13 +1210,13 @@ Resorting this table <br> data_start = 1 for line in datasetFile: raw_trait = webqtlUtil.readLineCSV(line) - trait = Trait.from_csv(raw_trait, data_start) + trait = Trait.from_csv(raw_trait, data_start) trait.lit_corr = lit_corrs.get(trait.name) trait.tissue_corr, trait.p_tissue = tissue_corrs.get(trait.name, (None, None)) traits.append(trait) return traits, new_vals - + else: _log.info("Using the slow method for correlation") @@ -1318,7 +1317,7 @@ Resorting this table <br> #the top ones always have p value 0. So comparing p values actually does nothing. #In addition, for the tissue data in our database, the N is always the same. #So it's safe to compare with tissue corr statistic value. - #That's the same as literature corr. + #That's the same as literature corr. #if self.method in [METHOD_LIT, METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] and self.gene_id: # traits.sort(webqtlUtil.cmpLitCorr) #else: @@ -1348,13 +1347,13 @@ Resorting this table <br> # NL, 07/19/2010 # js function changed, add a new parameter rankOrder for js function 'showTissueCorrPlot' db_trait.RANK_ORDER = self.RANK_ORDERS[self.method] - + #XZ, 26/09/2008: Method is 4 or 5. Have fetched tissue corr, but no literature correlation yet. if self.method in TISSUE_METHODS: db_trait.tissueCorr = trait.tissue_corr db_trait.tissuePValue = trait.p_tissue addTissueCorr = True - + #XZ, 26/09/2008: Method is 3, Have fetched literature corr, but no tissue corr yet. elif self.method == METHOD_LIT: @@ -1374,13 +1373,13 @@ Resorting this table <br> trait_list.append(db_trait) if addLiteratureCorr: - trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id, + trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id, self.species, trait_list) if addTissueCorr: trait_list = self.getTissueCorrelationByList( - primaryTraitSymbol = self.trait_symbol, + primaryTraitSymbol = self.trait_symbol, traitList = trait_list, - TissueProbeSetFreezeId = TISSUE_MOUSE_DB, + TissueProbeSetFreezeId = TISSUE_MOUSE_DB, method=self.method) return trait_list @@ -1446,7 +1445,7 @@ Resorting this table <br> if myTrait: if method in ["1","2"]: #genetic correlation - info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"), + info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"), " database were compared to all %d records in the " % self.record_count, HT.Href(text=db.fullname,url=webqtlConfig.INFOPAGEHREF % target_db_name,target="_blank", Class="fwn"), ' database. The top %d correlations ranked by the %s are displayed.' % (returnNumber,methodDict[method]), ' You can resort this list using the small arrowheads in the top row.') @@ -1498,7 +1497,7 @@ Resorting this table <br> titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray") ##Write title Info - # Modified by Hongqiang Li + # Modified by Hongqiang Li worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle) worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle) worksheet.write([2, 0], "Trait : %s" % identification, titleStyle) @@ -1568,7 +1567,7 @@ Resorting this table <br> tr = [] trId = str(thisTrait) - + corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr)) tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId)) @@ -1616,7 +1615,7 @@ Resorting this table <br> tblobj_header = [] if method in ["1","3","4"]: - tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0), + tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0), THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1), THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2), THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3), @@ -1626,7 +1625,7 @@ Resorting this table <br> THCell(HT.TD(HT.Href( text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"), target = '_blank', - url = "/correlationAnnotation.html#genetic_r"), + url = "/correlationAnnotation.html#genetic_r"), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=7), THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8), THCell(HT.TD(HT.Href( @@ -1639,7 +1638,7 @@ Resorting this table <br> worksheet.write([newrow, ncol], item, headingStyle) worksheet.set_column([ncol, ncol], 2*len(item)) else: - tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0), + tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0), THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1), THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2), THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3), @@ -1649,7 +1648,7 @@ Resorting this table <br> THCell(HT.TD(HT.Href( text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"), target = '_blank', - url = "/correlationAnnotation.html#genetic_rho"), + url = "/correlationAnnotation.html#genetic_rho"), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=7), THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8), THCell(HT.TD(HT.Href( @@ -1674,7 +1673,7 @@ Resorting this table <br> tr = [] trId = str(thisTrait) - + corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr)) tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId)) @@ -1757,7 +1756,7 @@ Resorting this table <br> tr.append(TDCell(HT.TD(repr,nowrap='ON', Class="fs12 fwn ffl b1 c222", align='right'),repr,thisTrait.corrPValue)) tblobj_body.append(tr) - + for ncol, item in enumerate([thisTrait.name, PhenotypeString, thisTrait.authors, thisTrait.year, thisTrait.pubmed_id, LRS_score_repr, LRS_location_repr, thisTrait.corr, thisTrait.nOverlap, thisTrait.corrPValue]): worksheet.write([newrow, ncol], item) newrow += 1 @@ -1783,7 +1782,7 @@ Resorting this table <br> THCell(HT.TD(HT.Href( text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"), target = '_blank', - url = "/correlationAnnotation.html#genetic_r"), + url = "/correlationAnnotation.html#genetic_r"), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=10), THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11), THCell(HT.TD(HT.Href( @@ -1825,7 +1824,7 @@ Resorting this table <br> THCell(HT.TD(HT.Href( text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"), target = '_blank', - url = "/correlationAnnotation.html#genetic_rho"), + url = "/correlationAnnotation.html#genetic_rho"), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=10), THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11), THCell(HT.TD(HT.Href( @@ -1885,17 +1884,17 @@ Resorting this table <br> #XZ, 12/08/2008: probeset name tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name,url="javascript:showTrait('%s', '%s')" % (formName,thisTrait.name), Class="fs12 fwn"), Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name.upper())) - #XZ, 12/08/2008: gene id + #XZ, 12/08/2008: gene id if thisTrait.geneid: tr.append(TDCell(None, thisTrait.geneid, val=999)) else: - tr.append(TDCell(None, thisTrait.geneid, val=999)) - + tr.append(TDCell(None, thisTrait.geneid, val=999)) + #XZ, 12/08/2008: homologene id if thisTrait.homologeneid: tr.append(TDCell("", thisTrait.homologeneid, val=999)) else: - tr.append(TDCell("", thisTrait.homologeneid, val=999)) + tr.append(TDCell("", thisTrait.homologeneid, val=999)) #XZ, 12/08/2008: gene symbol tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),thisTrait.symbol, thisTrait.symbol.upper())) diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py index f38b9880..c240d8a0 100644..100755 --- a/web/webqtl/showTrait/DataEditingPage.py +++ b/web/webqtl/showTrait/DataEditingPage.py @@ -280,13 +280,13 @@ class DataEditingPage(templatePage): if snpurl: snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) - snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="addselect", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") + snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") snpBrowserButton.append(snpBrowserButton_img) snpBrowserText = "SNPs" #XZ: Show GeneWiki for all species geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol)) - geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="addselect", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") + geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") geneWikiButton.append(geneWikiButton_img) geneWikiText = 'GeneWiki' @@ -295,7 +295,7 @@ class DataEditingPage(templatePage): if _Species in ("mouse", "rat", "human"): similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species) similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) - similarButton_img = HT.Image("/images/find_icon.jpg", name="addselect", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") + similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") similarButton.append(similarButton_img) similarText = "Find" else: @@ -416,13 +416,15 @@ class DataEditingPage(templatePage): UTHSC_BLAT_URL = "" if UCSC_BLAT_URL: - verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") + verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", + title=" Check probe locations at UCSC ", style="border:none;") verifyButton.append(verifyButtonImg) verifyText = 'Verify' if UTHSC_BLAT_URL: - rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", + title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") rnaseqButton.append(rnaseqButtonImg) rnaseqText = 'RNA-seq' tSpan.append(HT.BR()) @@ -442,8 +444,8 @@ class DataEditingPage(templatePage): if probeResult[0] > 0: probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \ % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet) - probeButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % probeurl) - probeButton_img = HT.Image("/images/probe_icon.jpg", name="addselect", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") + probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) + probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") probeButton.append(probeButton_img) probeText = "Probes" @@ -590,10 +592,24 @@ class DataEditingPage(templatePage): url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ % thisTrait.symbol,Class="fs14 fwn", \ title="Protein interactions: known and inferred"), style=linkStyle), " "*2) - if thisTrait.geneid: + if thisTrait.symbol: + #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input + #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users + if _Species == "mouse": + species_scientific = "Mus%20musculus" + elif _Species == "rat": + species_scientific = "Rattus%20norvegicus" + elif _Species == "human": + species_scientific = "Homo%20sapiens" + elif _Species == "drosophila": + species_scientific = "Drosophila%20melanogaster" + else: + species_scientific = "all" + + species_scientific tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ - url="http://www.pantherdb.org/genes/gene.do?acc=%s" \ - % thisTrait.geneid,Class="fs14 fwn", \ + url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ + % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \ title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) else: pass @@ -755,12 +771,13 @@ class DataEditingPage(templatePage): UCSC_BLAT_URL = "" UTHSC_BLAT_URL = "" if UCSC_BLAT_URL: - verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") + #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) + verifyButton = HT.Href(url="#") + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") verifyButton.append(verifyButtonImg) verifyText = "Verify" - rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") rnaseqButton.append(rnaseqButtonImg) rnaseqText = "RNA-seq" |