diff options
Diffstat (limited to 'web/webqtl/collection/AddToSelectionPage.py')
| -rw-r--r-- | web/webqtl/collection/AddToSelectionPage.py | 695 |
1 files changed, 0 insertions, 695 deletions
diff --git a/web/webqtl/collection/AddToSelectionPage.py b/web/webqtl/collection/AddToSelectionPage.py deleted file mode 100644 index 2a99e8c1..00000000 --- a/web/webqtl/collection/AddToSelectionPage.py +++ /dev/null @@ -1,695 +0,0 @@ -#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 "" - |