diff options
Diffstat (limited to 'web/webqtl')
| -rwxr-xr-x | web/webqtl/markerRegression/MarkerRegressionPage.py | 97 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/DataEditingPage.py | 20 |
2 files changed, 111 insertions, 6 deletions
diff --git a/web/webqtl/markerRegression/MarkerRegressionPage.py b/web/webqtl/markerRegression/MarkerRegressionPage.py index 7f830b4b..43988d29 100755 --- a/web/webqtl/markerRegression/MarkerRegressionPage.py +++ b/web/webqtl/markerRegression/MarkerRegressionPage.py @@ -151,6 +151,100 @@ class MarkerRegressionPage(templatePage): detail = ['There is no association with marker that meets this criteria. Please provide a less stringend threshold. The minimun p-value is %s.'%minPvalue] self.error(heading=heading,detail=detail) return + + if self.mappingMethodId == '5': # For GEMMA + + traitInfoList = string.split(string.strip(fd.identification),':') + probesetName = string.strip(traitInfoList[-1]) + plinkOutputFileName= webqtlUtil.genRandStr("%s_%s_"%(fd.RISet,probesetName)) + + # get related values from fd.allTraitData; the format of 'allTraitValueDict'is {strainName1: value=-0.2...} + fd.readData() + allTraitValueDict = fd.allTraitData + + #automatically generate pheno txt file for PLINK + self.genPhenoTxtFileForPlink(phenoFileName=plinkOutputFileName,RISetName=fd.RISet,probesetName=probesetName, valueDict=allTraitValueDict) + # os.system full path is required for input and output files; specify missing value is -9999 + gemma_command = './%sgemma/gemma -bfile %s -k %s.kin -lmm 1 -o %s_output' % (webqtlConfig.HTMLPATH, fd.RISet, fd.RISet, fd.RISet) + #plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.HTMLPATH, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName) + + os.system(gemma_command) + + if fd.identification: + heading2 = HT.Paragraph('Trait ID: %s' % fd.identification) + heading2.__setattr__("class","subtitle") + self.dict['title'] = '%s: Genome Association' % fd.identification + else: + heading2 = "" + self.dict['title'] = 'Genome Association' + + if fd.traitInfo: + symbol,chromosome,MB = string.split(fd.traitInfo,'\t') + heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB)) + else: + heading3 = "" + + heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet) + heading.__setattr__("class","title") + + # header info part:Trait Data Entered for HLC Set & Trait ID: + headerdiv = HT.TR(HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee')) + + self.ChrList=ChrList # get chr name from '1' to 'X' + self.ChrLengthMbList = ChrLengthMbList + + # build plink result dict based on chr, key is chr name, value is in list type including Snpname, bp and pvalue info + plinkResultDict={} + count,minPvalue,plinkResultDict =self.getPlinkResultDict(outputFileName=plinkOutputFileName,thresholdPvalue=self.pValue,ChrOrderIdNameDict=ChrOrderIdNameDict) + + # if can not find results which are matched with assigned p-value, system info will show up + if count >0: + + #for genome association report table + reportTable="" + # sortable table object + resultstable,tblobj,bottomInfo = self.GenReportForPLINK(ChrNameOrderIdDict=ChrNameOrderIdDict, RISet=fd.RISet,plinkResultDict=plinkResultDict,thresholdPvalue=self.pValue,chrList=self.ChrList) + + # creat object for result table for sort function + objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') + cPickle.dump(tblobj, objfile) + objfile.close() + + sortby = ("Index", "up") + reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable") + + descriptionTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0) + descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3))) + descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR()))) + descriptionTable.append(bottomInfo) + + # get each chr's length + self.ChrLengthMbList = map(lambda x: x/1000000.0, self.ChrLengthMbList) # change unit from bp to mb + self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)# get total length of all chrs + if self.ChrLengthMbList: + self.GraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval + else: + self.GraphInterval = 1 + + # for human data, there's no CM value + self.ChrLengthCMList = [] + self.ChrLengthCMSum = 0 + + # begin: common part with human data + intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight)) + gifmap = self.plotIntMappingForPLINK(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, plinkResultDict=plinkResultDict) + + intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') + intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap') + + TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200)) + self.dict['body'] = str(headerdiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable))) + + else: + heading = "Genome Association" + detail = ['There is no association with marker that meets this criteria. Please provide a less stringend threshold. The minimun p-value is %s.'%minPvalue] + self.error(heading=heading,detail=detail) + return elif self.mappingMethodId == '1': # QTLreaper result if not fd.genotype: @@ -1459,6 +1553,9 @@ class MarkerRegressionPage(templatePage): canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR) + + + # build dict based on plink result, key is chr, value is list of [snp,BP,pValue] def getPlinkResultDict(self,outputFileName='',thresholdPvalue=-1,ChrOrderIdNameDict={}): diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py index c240d8a0..20231429 100755 --- a/web/webqtl/showTrait/DataEditingPage.py +++ b/web/webqtl/showTrait/DataEditingPage.py @@ -1552,13 +1552,21 @@ class DataEditingPage(templatePage): attribute_ids = [] attribute_names = [] try: + + if thisTrait.db.type=='ProbeSet': #ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create - self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND - CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId - group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) - + self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) + elif thisTrait.db.type=='Publish': + self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.PublishFreezeId = '%s' AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) + exclude_menu = HT.Select(name="exclude_menu") dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) |