#AddToSelectionPage.py import string from htmlgen import HTMLgen2 as HT import os import cPickle import reaper from base import webqtlConfig from base.templatePage import templatePage from utility.THCell import THCell from utility.TDCell import TDCell from utility import webqtlUtil from showTrait import ShowProbeInfoPage # NL, 07/27/2010: add 'import webqtlDatabaseFunction' for retrieveSpecies function from dbFunction import webqtlDatabaseFunction from base.webqtlTrait import webqtlTrait ######################################### # Add to Selection Page ######################################### class AddToSelectionPage(templatePage): def __init__(self,fd): templatePage.__init__(self, fd) if not self.openMysql(): return if not fd.genotype: fd.readGenotype() self.searchResult = fd.formdata.getvalue('searchResult', []) if type("1") == type(self.searchResult): self.searchResult = [self.searchResult] if fd.formdata.getvalue('fromDataEditingPage'): searchResult2 = fd.formdata.getvalue('fullname') if searchResult2: self.searchResult.append(searchResult2) if self.searchResult: pass else: templatePage.__init__(self, fd) heading = 'Add Collections' detail = ['You need to select at least one trait to add to your selection.'] self.error(heading=heading,detail=detail) return if self.genSelection(fd=fd): self.writeHTML(fd) def genSelection(self, fd=None, checkPreSelection = 1): collectionName = '%s_Select' % fd.RISet if checkPreSelection: try: preSelection = fd.input_session_data[collectionName] preSelection = list(string.split(preSelection,',')) except: preSelection = [] else: preSelection = [] if preSelection: for item in preSelection: if item not in self.searchResult: self.searchResult.append(item) self.searchResult = map(self.transfer2NewName, self.searchResult) for item in self.searchResult: if not item: self.searchResult.remove(item) if len(self.searchResult) > 3000: heading = 'Add Collections' detail = ['You are adding over 3000 traits to selections, please reduce your number of traits.'] self.error(heading=heading,detail=detail) return 0 searchResult2 = [] self.theseTraits = [] for item in self.searchResult: try: thisTrait = webqtlTrait(fullname=item, cursor=self.cursor) thisTrait.retrieveInfo(QTL=1) self.theseTraits.append(thisTrait) searchResult2.append(item) except: pass allTraitStr = string.join(searchResult2,',') self.session_data_changed[collectionName] = allTraitStr return 1 def writeHTML(self,fd): TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top") pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left") seq = 1 SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title") mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}") mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;") mintmap.append(mintmap_img) mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}") mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;") mcorr.append(mcorr_img) cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}") cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;") cormatrix.append(cormatrix_img) networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}") networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;") networkGraph.append(networkGraph_img) heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}") heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;") heatmap.append(heatmap_img) partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}") partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;") partialCorr.append(partialCorr_img) BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}") networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;") BN.append(networkGraph_img) removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet) removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;") removeselect.append(removeselect_img) selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);") selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;") selectall.append(selectall_img) reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);") reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;") reset.append(reset_img) exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');") exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;") exportSelect.append(exportSelect_img) selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);") selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;") selectinvert.append(selectinvert_img) chrMenu = HT.Input(type='hidden',name='chromosomes',value='all') importFile = HT.Input(type='file', name='importfile', size=15) importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button") exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button") importMenu = HT.Select(name='importmethod') importMenu.append(('append','append')) importMenu.append(('replace','replace')) ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');") ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none") ODE.append(ODE_img) GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');") GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none") GCATButton.append(GCATButton_img) GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');") GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none") GeneSet.append(GeneSet_img) #need to be refined if fd.genotype.Mbmap: scale = HT.Input(name="scale", value="physic", type="hidden") else: scale = "" formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden')) #XZ, July 22, 2011: I add parameters for interval mapping hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None} for key in hddn.keys(): formMain.append(HT.Input(name=key, value=hddn[key], type='hidden')) if not self.searchResult: SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title") formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton) TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain)) self.dict['body'] = str(TD_LR) self.dict['title'] = "%s Trait Collection" % fd.RISet return ######################################### # Creating table object for AJAX table # ######################################### tblobj = {} mainfmName = 'showDatabase' # NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py; species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) if species == 'human': chrMenu = scale = mintmap = heatmap = "" tblobj['header'] = self.getCollectionTableHeader() sortby = self.getSortByValue() thisRISet = fd.RISet tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species) filename= webqtlUtil.genRandStr("Search_") objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') cPickle.dump(tblobj, objfile) objfile.close() div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable") containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left") postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left") optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="400", border=0, align="Left") optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(removeselect), HT.TD(exportSelect))) optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*1,"Remove"), HT.TD(" "*1,"Export"))) postContainerTable.append(HT.TR(HT.TD(optionsTable))) containerTable.append(HT.TR(HT.TD(optionsTable))) functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left") functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap)) if species == "human": labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare"))) else: labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map"))) functionTable.append(functionRow, labelRow) postContainerTable.append(HT.TR(HT.TD(functionTable))) containerTable.append(HT.TR(HT.TD(functionTable))) moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle") fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle") if (fd.formdata.getvalue('showHideOptions') == 'less'): postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide")))) containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide")))) else: postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide")))) LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",border=0, align="Left") LinkOutRow = HT.TR(HT.TD(GeneSet, width="33%"), HT.TD(GCATButton, width="33%"), HT.TD(ODE, width="33%"), style="display:none;", Class="extra_options") LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options") LinkOutTable.append(LinkOutRow,LinkOutLabels) postContainerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable))) containerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable))) pageTable.append(HT.TR(HT.TD(containerTable))) chrMenu = scale = "" pageTable.append(HT.TR(HT.TD(div))) pageTable.append(HT.TR(HT.TD(" "))) if len(self.theseTraits) > 20: pageTable.append(HT.TR(HT.TD(postContainerTable))) pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton))) #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010 formMain.append(chrMenu,scale,pageTable) #Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js self.dict['js1'] = '' TD_LR.append(SelectionHeading,formMain) self.dict['body'] = str(TD_LR) self.dict['js2'] = 'onLoad="pageOffset()"' self.dict['layer'] = self.generateWarningLayer() self.dict['title'] = "%s Trait Collection" % thisRISet def transfer2NewName(self, str): "this is temporary" if str.find("::") < 0: return str.replace(":", "::") else: return str def generateWarningLayer(self): layerString = """ <!-- BEGIN FLOATING LAYER CODE //--> <div id="warningLayer" style="padding:3px; border: 1px solid #222; background-color: #fff; position:absolute;width:250px;left:100;top:100;visibility:hidden"> <table border="0" width="250" class="cbrb" cellspacing="0" cellpadding="5"> <tr> <td width="100%"> <table border="0" width="100%" cellspacing="0" cellpadding="0" height="36"> <tr> <td class="cbrb cw ff15 fwb" align="Center" width="100%" style="padding:4px"> Sort Table </td> </tr> <tr> <td width="100%" bgcolor="#eeeeee" align="Center" style="padding:4px"> <!-- PLACE YOUR CONTENT HERE //--> Resorting this table <br> <!-- END OF CONTENT AREA //--> </td> </tr> </table> </td> </tr> </table> </div> <!-- END FLOATING LAYER CODE //--> """ return layerString def getCollectionTableHeader(self): tblobj_header = [] className = "fs13 fwb ffl b1 cw cbrb" tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1), THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2), THCell(HT.TD('Symbol', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="symbol", idx=3), THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=4), THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=5), THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=6), THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=7), THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=8), THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=9)]] return tblobj_header def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''): tblobj_body = [] className = "fs12 fwn b1 c222" for thisTrait in traitList: tr = [] if not thisTrait.haveinfo: thisTrait.retrieveInfo(QTL=1) if thisTrait.riset != RISet: continue trId = str(thisTrait) #XZ: check box column tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className))) #XZ: Dataset column tr.append(TDCell(HT.TD(thisTrait.db.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.upper())) #XZ: Trait ID column if thisTrait.cellid: tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid)) else: tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name)) #XZ: Symbol column and Description column if (thisTrait.db.type == "Publish"): AbbreviationString = "--" if (thisTrait.post_publication_abbreviation != None): AbbreviationString = thisTrait.post_publication_abbreviation PhenotypeString = thisTrait.post_publication_description if thisTrait.confidential: if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): if thisTrait.pre_publication_abbreviation: AbbreviationString = thisTrait.pre_publication_abbreviation else: AbbreviationString = "--" PhenotypeString = thisTrait.pre_publication_description if AbbreviationString == "--": tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) else: tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper())) tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper())) elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"): description_string = str(thisTrait.description).strip() if (thisTrait.db.type == "ProbeSet"): if (thisTrait.symbol != None): if thisTrait.geneid: symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn") else: symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn") tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol)) else: tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) target_string = str(thisTrait.probe_target_description).strip() description_display = '' if len(description_string) > 1 and description_string != 'None': description_display = description_string else: description_display = thisTrait.symbol if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None': description_display = description_display + '; ' + target_string.strip() description_string = description_display else: tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string)) else: if (thisTrait.name != None): tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name)) else: tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) #XZ: Location column if (thisTrait.db.type == "Publish"): tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) else: if thisTrait.db.type == "ProbeSet" and thisTrait.cellid: EnsemblProbeSetID = thisTrait.name if '_at' in thisTrait.name: EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3] #These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10. self.cursor.execute(''' SELECT EnsemblProbeLocation.* FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End''' ,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id)) LocationFields = self.cursor.fetchall() Chr='' Mb='' Start='' End='' if (len(LocationFields)>=1): Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0]) Start /= 1000000.0 End /= 1000000.0 Mb = Start if (len(LocationFields)>1): self.cursor.execute(''' SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id''' ,(thisTrait.name, thisTrait.db.id)) ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0]) self.cursor.execute(''' SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and EnsemblProbeLocation.Chr=%s and ProbeSetFreezeId=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1''' ,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id)) NewLocationFields = self.cursor.fetchall() if (len(NewLocationFields)>0): Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0]) Start /= 1000000.0 End /= 1000000.0 Mb = Start #ZS: trait_location_value is used for sorting trait_location_repr = "--" trait_location_value = 1000000 if Chr and Mb: try: trait_location_value = int(Chr)*1000 + Mb except: if Chr.upper() == "X": trait_location_value = 20*1000 + Mb else: trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) ) tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value)) else: #ZS: trait_location_value is used for sorting trait_location_repr = "--" trait_location_value = 1000000 if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb: try: trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb except: if thisTrait.chr.upper() == "X": trait_location_value = 20*1000 + thisTrait.mb else: trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) ) tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value)) #XZ: Mean column if (thisTrait.db.type == "ProbeSet"): if thisTrait.cellid: mean = -10000.0 try: thisTrait.retrieveData() mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1]) except: pass repr = '%2.3f' % mean mean = '%2.2f' % mean tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) else: self.cursor.execute(""" select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet where ProbeSetXRef.ProbeSetFreezeId = %d and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSet.Name = '%s' """ % (thisTrait.db.id, thisTrait.name)) result = self.cursor.fetchone() if result: if result[0]: mean = result[0] else: mean=0 else: mean = 0 #XZ, 06/05/2009: It is neccessary to turn on nowrap repr = "%2.3f" % mean tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) elif (thisTrait.db.type == "Publish"): self.cursor.execute(""" select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze where PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d """ % (thisTrait.name, thisTrait.db.id)) result = self.cursor.fetchone() if result: if result[0] and result[1]: mean = result[1]/result[0] else: mean = 0 else: mean = 0 repr = "%2.3f" % mean tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) else: tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0)) #Number of cases n_cases_value = 0 n_cases_repr = "--" if (thisTrait.db.type == "Publish"): self.cursor.execute(""" select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze where PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d """ % (thisTrait.name, thisTrait.db.id)) result = self.cursor.fetchone() if result: if result[0]: n_cases_value = result[0] n_cases_repr = result[0] if (n_cases_value == "--"): tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) else: tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) elif (thisTrait.db.type == "ProbeSet"): self.cursor.execute(""" select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze where ProbeSet.Name='%s' and ProbeSetXRef.ProbeSetId = ProbeSet.Id and ProbeSetXRef.DataId = ProbeSetData.Id and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = '%s' """ % (thisTrait.name, thisTrait.db.name)) result = self.cursor.fetchone() if result: if result[0]: n_cases_value = result[0] n_cases_repr = result[0] if (n_cases_value == "--"): tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) else: tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) elif (thisTrait.db.type == "Geno"): self.cursor.execute(""" select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain where Geno.SpeciesId = %s and Geno.Name='%s' and GenoXRef.GenoId = Geno.Id and GenoXRef.DataId = GenoData.Id and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoData.StrainId = Strain.Id and GenoFreeze.Name = '%s' """ % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name)) result = self.cursor.fetchone() if result: if result[0]: n_cases_value = result[0] n_cases_repr = result[0] if (n_cases_value == "--"): tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) else: tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value)) else: tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value)) #XZ: Max LRS column and Max LRS Location column if (thisTrait.db.type != "Geno"): #LRS and its location LRS_score_repr = '--' LRS_score_value = 0 LRS_location_repr = '--' LRS_location_value = 1000000 LRS_flag = 1 #Max LRS and its Locus location if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus: self.cursor.execute(""" select Geno.Chr, Geno.Mb from Geno, Species where Species.Name = '%s' and Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, thisTrait.locus)) result = self.cursor.fetchone() if result: if result[0] and result[1]: LRS_Chr = result[0] LRS_Mb = result[1] #XZ: LRS_location_value is used for sorting try: LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb) except: if LRS_Chr.upper() == 'X': LRS_location_value = 20*1000 + float(LRS_Mb) else: LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb) LRS_score_repr = '%3.1f' % thisTrait.lrs LRS_score_value = thisTrait.lrs LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) ) LRS_flag = 0 tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value)) tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)) if LRS_flag: tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value)) tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)) else: tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0)) tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000)) tblobj_body.append(tr) return tblobj_body def getSortByValue(self): sortby = ("pv", "up") return sortby def nullRecord(self,x): if x or x == 0: return x else: return ""