diff options
Diffstat (limited to 'web/webqtl/showTrait/ShowProbeInfoPage.py')
| -rwxr-xr-x | web/webqtl/showTrait/ShowProbeInfoPage.py | 486 |
1 files changed, 486 insertions, 0 deletions
diff --git a/web/webqtl/showTrait/ShowProbeInfoPage.py b/web/webqtl/showTrait/ShowProbeInfoPage.py new file mode 100755 index 00000000..989238b4 --- /dev/null +++ b/web/webqtl/showTrait/ShowProbeInfoPage.py @@ -0,0 +1,486 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by GeneNetwork Core Team 2010/10/20 + +import string +import sys,os + +import cPickle + +import reaper +from htmlgen import HTMLgen2 as HT + +from base import webqtlConfig +from utility import webqtlUtil +from dbFunction import webqtlDatabaseFunction +from base.templatePage import templatePage +from base.webqtlDataset import webqtlDataset +from base.webqtlTrait import webqtlTrait +from utility.THCell import THCell +from utility.TDCell import TDCell + +######################################### +# Probe Infomation Page +######################################### + +class ShowProbeInfoPage(templatePage): + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not self.openMysql(): + return + + fd.readGenotype() + TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') + self.database = fd.formdata.getfirst('database') + self.ProbeSetID = fd.formdata.getfirst('ProbeSetID') + self.CellID = fd.formdata.getfirst('CellID') + + self.db = webqtlDataset(self.database, self.cursor) + thisTrait = webqtlTrait(db= self.db, cursor=self.cursor, name=self.ProbeSetID) #, cellid=CellID) + thisTrait.retrieveInfo() + + try: + self.cursor.execute('SELECT ProbeFreeze.Name FROM ProbeFreeze,ProbeSetFreeze WHERE ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Name = "%s"' % self.db.name) + self.probeDatabase = self.cursor.fetchall()[0][0] + self.probeInfoDatabase = 'Probe' + except: + heading = 'Probe Information' + intro = ['Trying to retrieve the probe information for ProbeSet ',HT.Span('%s' % self.ProbeSetID, Class="fwb cdg"),' in Database ',HT.Href(text='%s' % self.db.fullname,url=webqtlConfig.infopagehref % self.database)] + detail = ['The information you just requested is not available at this time.'] + self.error(heading=heading,intro=intro,detail=detail) + return + + + form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden')) + hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'} + if fd.RISet == 'BXD': + hddn['parentsf1']='ON' + + for key in hddn.keys(): + form.append(HT.Input(name=key, value=hddn[key], type='hidden')) + + + #Buttons on search page + linkinfo ="%s/probeInfo.html" % webqtlConfig.PORTADDR + mintmap = "" + probeinfo = HT.Input(type='button' ,name='mintmap',value='Info', onClick="openNewWin('%s');" % linkinfo, Class="button") + cormatrix = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');") + cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;") + cormatrix.append(cormatrix_img) + heatmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');") + 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) + if self.ProbeSetID[-2:] in ('_A', '_B'): + thisProbeSetID = self.ProbeSetID[:-2] + else: + thisProbeSetID = self.ProbeSetID + thisurl = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' % thisProbeSetID + verifyButton = HT.Input(type="button",value="Verify Ensembl",onClick= "openNewWin('%s')" % thisurl, Class="button") + + addselect = HT.Input(type='button' ,name='addselect',value='Add to Collection', onClick="addRmvSelection('%s', this.form, 'addToSelection');" % fd.RISet,Class="button") + selectall = HT.Input(type='button' ,name='selectall',value='Select All', onClick="checkAll(this.form);",Class="button") + selectpm = HT.Input(type='button' ,name='selectall',value='Select PM', onClick="checkPM(this.form);",Class="button") + selectmm = HT.Input(type='button' ,name='selectall',value='Select MM', onClick="checkMM(this.form);",Class="button") + selectinvert = HT.Input(type='button' ,name='selectinvert',value='Select Invert', onClick="checkInvert(this.form);",Class="button") + reset = HT.Input(type='reset',name='',value='Select None',Class="button") + chrMenu = HT.Input(type='hidden',name='chromosomes',value='all') + probedata = HT.Input(type='hidden',name='probedata',value='all') + + url_rudi_track = self.getProbeTrackURL(self.probeDatabase, self.ProbeSetID) + if url_rudi_track: + rudi_track = HT.Input(type='button', name='ruditrack', value='Probe Track', onClick="openNewWin('%s')"%url_rudi_track, Class="button") + else: rudi_track = None + + pinfopage = "/probeInfo.html" + + #updated by NL: 07-22-2011 get chosenStrains + _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[fd.RISet] + chosenStrains="%s,%s"%(_mat,_pat) + tblobj = {} + tblobj['header']=[] + + tblobj['header'].append([ + THCell(HT.TD("", Class="cbrb cw fwb fs13 b1", rowspan=2,nowrap='ON'), sort=0), + THCell(HT.TD(HT.Href(target="_PROBEINFO", url=pinfopage+"#probe", text=HT.Span('Probe', Class="cw fwb fs13")), HT.Sup(HT.Italic('1')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="probe", idx=1), + THCell(HT.TD(HT.Href(text=HT.Span('Sequence', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Sequence"),HT.Sup(HT.Italic('2')), Class="cbrb cw fwb fs13 b1", align='center',rowspan=2,nowrap='ON'), text="seq", idx=2), + THCell(HT.TD(HT.Href(text=HT.Span('bl2seq', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#bl2seq"),HT.Sup(HT.Italic('3')), Class="cbrb cw fwb fs13 b1", align='center',rowspan=2,nowrap='ON'), sort=0), + THCell(HT.TD(HT.Href(text=HT.Span('Exons', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Exon"),HT.Sup(HT.Italic('4')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), sort=0), + THCell(HT.TD(HT.Href(text=HT.Span('Tm °C', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Tm"),HT.Sup(HT.Italic('5')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="tm", idx=5), + THCell(HT.TD(HT.Href(text=HT.Span('Stacking Energy K', HT.Sub('B'),'T', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#KBT"),HT.Sup(HT.Italic('6')), Class="cbrb cw fwb fs13 b1",align='center',colspan=2,NOWRAP="yes",nowrap='ON'), sort=0), + THCell(HT.TD(HT.Href(text=HT.Span('Mean', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Mean"),HT.Sup(HT.Italic('7')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="mean", idx=8), + THCell(HT.TD(HT.Href(text=HT.Span('Stdev', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Stdev"),HT.Sup(HT.Italic('8')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="std", idx=9), + THCell(HT.TD(HT.Href(text=HT.Span('Probe h2', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#h2"),HT.Sup(HT.Italic('9')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes"), text="h2", idx=10), + THCell(HT.TD(HT.Href(text=HT.Span('Probe Location', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#location"), HT.Sup(HT.Italic('10')),Class="cbrb cw fwb fs13 b1",align='center',colspan=3)), + THCell(HT.TD(HT.Href(text=HT.Span('SNPs', HT.BR(), '(Across all strains)', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#snps"), HT.Sup(HT.Italic('11')),Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes")), + THCell(HT.TD(HT.Href(text=HT.Span('SNPs', HT.BR(),'(Different alleles only between %s and %s)'%(_mat,_pat), Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#snps"), HT.Sup(HT.Italic('11')),Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes")) + + ]) + + tblobj['header'].append([ + THCell(HT.TD(HT.Span('GSB', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",), text="gsb", idx=6), + THCell(HT.TD(HT.Span('NSB', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",), text="nsb", idx=7), + THCell(HT.TD(HT.Span('Chr', Class="cw fwb fs13"), align='center', Class="cbrb ffl2 fwb fs13 b1",)), + THCell(HT.TD(HT.Span('Start', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",)), + THCell(HT.TD(HT.Span('End', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",)), + ]) + + tblobj['body'] = [] + + blatbutton = '' + + fetchField = ['Probe.Name','Probe.Sequence','Probe.ExonNo','Probe.Tm', 'Probe.E_GSB','Probe.E_NSB', 'ProbeH2.h2', 'ProbeH2.weight'] + + query = "SELECT %s FROM (Probe, ProbeSet, ProbeFreeze) left join ProbeH2 on ProbeH2.ProbeId = Probe.Id and ProbeH2.ProbeFreezeId = ProbeFreeze.Id WHERE ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeFreeze.Name = '%s' order by Probe.SerialOrder" % (string.join(fetchField,','), self.ProbeSetID, self.probeDatabase) + self.cursor.execute(query) + results = self.cursor.fetchall() + + blatsequence = "" + + # add by NL: get strains' name in SnpPattern database table + strainsInSnpPatternDBtable=self.getStrainNameIndexPair() # after snpBrowserPage.py change to MVC, this function can be removed in this class and called from other class; + allStrainNameList=[v[0] for v in strainsInSnpPatternDBtable] + + speciesid = webqtlDatabaseFunction.retrieveSpeciesId(cursor=self.cursor,RISet=fd.RISet) + for result in results: + """ + ProbeId, CellID,Sequence,ExonNo,Tm, E_GSB,E_NSB = map(self.nullRecord,result) + h2 = '' + query = "SELECT h2 FROM ProbeH2 WHERE ProbeFreezeId = '%s' and ProbeId=%s" % (self.probeDatabase, ProbeId) + self.cursor.execute(query) + results = self.cursor.fetchall() + """ + + CellID,Sequence,ExonNo,Tm, E_GSB,E_NSB,h2, weight = map(self.nullRecord,result) + + + Average = '' + STDEV = '' + mean = -10000.0 + stdev = -10000.0 + try: + thisTrait.cellid = CellID + thisTrait.retrieveData() + + mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1]) + + if mean: + Average = '%2.2f' % mean + if stdev: + STDEV = '%2.2f' % stdev + except: + pass + + if CellID == self.CellID: + bkColor = "cbrdull fs11 b1" + else: + bkColor = "fs11 b1" + seqcolor= '' + + if thisTrait.blatseq: + blatsequence = thisTrait.blatseq + if int(CellID[-1]) % 2 == 1: + seqcolor= 'cdg' + else: + if int(CellID[-1]) % 2 == 1: + seqcolor= 'cdg' + blatsequence += string.strip(Sequence) + + if thisTrait.genbankid and (int(CellID[-1]) % 2 == 1): + probeurl = 'http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi?one=%s&sseq=%s' % (thisTrait.genbankid, Sequence) + probefy1 = HT.Input(type="button",value="Blast",onClick= "openNewWin('%s')" % probeurl, Class="buttonsmaller") + else: + probefy1 = '' + + traitName = str(thisTrait) + + #XZ, Aug 08, 2011: Note that probesets on some affy chips are not name as "xxx_at" (i.e., Affy Mouse Gene 1.0 ST (GPL6246)). + #EnsemblProbeSetID = self.ProbeSetID[0:self.ProbeSetID.index('_at')+3] + EnsemblProbeSetID = self.ProbeSetID + if '_at' in self.ProbeSetID: + EnsemblProbeSetID = self.ProbeSetID[0:self.ProbeSetID.index('_at')+3] + + self.cursor.execute(''' + SELECT EnsemblProbeLocation.* + 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 + ProbeFreeze.Name=%s group by Chr, Start, End''' + ,(CellID, EnsemblProbeSetID, self.probeDatabase)) + LocationFields = self.cursor.fetchall() + + Chr='' + Start='' + End='' + if (len(LocationFields)>=1): + Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0]) + Start /= 1000000.0 + End /= 1000000.0 + if (len(LocationFields)>1): + self.cursor.execute(''' + SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze + WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeFreeze.Name=%s''' + ,(self.ProbeSetID, self.probeDatabase)) + 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 ProbeFreeze.Name=%s order by Mb limit 1''' + ,(ProbeSetMb, CellID, EnsemblProbeSetID, ProbeSetChr, self.probeDatabase)) + 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 + + snp_collection = [] + snpDiff_collection=[] + + startIndex=3 + if Chr != '' and Start != '' and End != '' and speciesid != None: + + self.cursor.execute(''' + SELECT a.SnpName, a.Id, b.* FROM SnpAll a, SnpPattern b + WHERE a.Chromosome=%s and a.Position>=%s and a.Position<=%s + and a.SpeciesId=%s and a.Id=b.SnpId''' + ,(Chr, Start, End, speciesid)) #chr,Start, End, 1)) + snpresults = self.cursor.fetchall() + + index1=allStrainNameList.index(_mat) #_mat index in results + index2=allStrainNameList.index(_pat) #_pat index in results + + for v in snpresults: + #updated by NL: 07-22-2011 check 'limit to' to get snpBrowser snpresults + snp_collection.append(HT.Href(text=v[0], url=os.path.join(webqtlConfig.CGIDIR, + "main.py?FormID=SnpBrowserResultPage&submitStatus=1&customStrain=1")+ "&geneName=%s" % v[0], Class="fs12 fwn", target="_blank")) + snp_collection.append(HT.BR()) + #updated by NL: 07-27-2011 link snp info for different allele only + strain1_allele=v[startIndex+index1] + strain2_allele=v[startIndex+index2] + + if strain1_allele!=strain2_allele: + snpDiff_collection.append(HT.Href(text=v[0], url=os.path.join(webqtlConfig.CGIDIR, + "main.py?FormID=SnpBrowserResultPage&submitStatus=1&customStrain=1&diffAlleles=1&chosenStrains=%s"%chosenStrains)+ "&geneName=%s" % v[0], Class="fs12 fwn", target="_blank")) + snpDiff_collection.append(HT.BR()) + + + tr = [] + tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class='checkbox', name="searchResult",value=traitName, onClick="highlight(this)"), align="right", Class=bkColor, nowrap="on"), text=traitName)) + + tr.append(TDCell(HT.TD(HT.Href(text=CellID, url = "javascript:showDatabase2('%s','%s','%s');" % (self.database,self.ProbeSetID,CellID),Class="fs12 fwn"),Class=bkColor), traitName, traitName.upper())) + + tr.append(TDCell(HT.TD(Sequence, Class=bkColor + " %s ffmono fs14" % seqcolor),Sequence,Sequence.upper())) + tr.append(TDCell(HT.TD(probefy1,align='center',Class=bkColor))) + tr.append(TDCell(HT.TD(ExonNo,align='center',Class=bkColor))) + + try: + TmValue = float(Tm) + except: + TmValue = 0.0 + tr.append(TDCell(HT.TD(Tm,align='center',Class=bkColor), Tm, TmValue)) + + try: + E_GSBValue = float(E_GSB) + except: + E_GSBValue = -10000.0 + tr.append(TDCell(HT.TD(E_GSB,align='center',Class=bkColor), E_GSB, E_GSBValue)) + + try: + E_NSBValue = float(E_NSB) + except: + E_NSBValue = -10000.0 + tr.append(TDCell(HT.TD(E_NSB,align='center',Class=bkColor), E_NSB, E_NSBValue)) + + tr.append(TDCell(HT.TD(Average,align='center',Class=bkColor), Average, mean)) + tr.append(TDCell(HT.TD(STDEV,align='center',Class=bkColor), STDEV, stdev)) + + try: + h2Value = float(h2) + except: + h2Value = -10000.0 + tr.append(TDCell(HT.TD(h2,align='center',Class=bkColor), h2, h2Value)) + + tr.append(TDCell(HT.TD(Chr,align='left',Class=bkColor))) + tr.append(TDCell(HT.TD(Start,align='left',Class=bkColor))) + tr.append(TDCell(HT.TD(End,align='left',Class=bkColor))) + + snp_td = HT.TD(align='left',Class=bkColor) + for one_snp_href in snp_collection: + snp_td.append(one_snp_href) + + tr.append(TDCell(snp_td)) + + #07-27-2011:add by NL: show SNP results for different allele only + snpDiff_td= HT.TD(align='left', valign='top', Class=bkColor) + for one_snpDiff_href in snpDiff_collection: + snpDiff_td.append(one_snpDiff_href) + tr.append(TDCell(snpDiff_td)) + + tblobj['body'].append(tr) + + # import cPickle + filename = webqtlUtil.genRandStr("Probe_") + objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') + cPickle.dump(tblobj, objfile) + objfile.close() + # NL, 07/27/2010. genTableObj function has been moved from templatePage.py to webqtlUtil.py; + div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=("", ""), tableID = "sortable", addIndex = "1"), Id="sortable") + + #UCSC + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + if _Species == "rat": + thisurl = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + elif _Species == "mouse": + thisurl = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) + else: + thisurl = "" + if thisurl: + blatbutton = HT.Input(type='button' ,name='blatPM',value='Verify UCSC', onClick="window.open('%s','_blank')" % thisurl,Class="button") + else: + blatbutton = "" + + #GenBank + genbankSeq = "" + if thisTrait.genbankid: + self.cursor.execute("SELECT Sequence FROM Genbank WHERE Id = '%s'" % thisTrait.genbankid ) + genbankSeq = self.cursor.fetchone() + if genbankSeq: + genbankSeq = genbankSeq[0] + + if genbankSeq: + if _Species == "rat": + thisurl2 = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', genbankSeq) + if _Species == "mouse": + thisurl2 = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', genbankSeq) + else: + thisurl2 = '' + if thisurl2: + blatbutton2 = HT.Input(type='button' ,name='blatPM',value='Verify GenBank', onClick="window.open('%s','_blank')" % thisurl2,Class="button") + else: + blatbutton2 = "" + + #Snp + snpBrowser = "" + if thisTrait.symbol and _Species == 'mouse': + self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", thisTrait.symbol) + geneName = self.cursor.fetchone() + if geneName: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=snpBrowser") + "&geneName=%s" % geneName[0] + else: + if thisTrait.chr and thisTrait.mb: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=snpBrowser") + \ + "&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002) + else: + snpurl = "" + + if snpurl: + snpBrowser = HT.Input(type="button",value="SNP Browser",onClick= \ + "openNewWin('%s')" % snpurl, Class="button") + + else: + snpBrowser = "" + #end if + + heading = HT.Paragraph('Probe Information', Class="title") + intro = HT.Paragraph('The table below lists information of all probes of probe set ',HT.Span(self.ProbeSetID, Class="fwb fs13"),' from database ', HT.Span(self.probeDatabase, Class="fwb fs13"), ".") + buttons = HT.Paragraph(probedata,probeinfo,heatmap,cormatrix,blatbutton,blatbutton2,verifyButton,snpBrowser, HT.P(),selectall,selectpm,selectmm,selectinvert,reset,addselect) + if rudi_track: + buttons.append(rudi_track) + form.append(buttons,div,HT.P()) + + TD_LR.append(heading,intro,form, HT.P()) + self.dict['basehref'] = '' + self.dict['body'] = str(TD_LR) + self.dict['title'] = self.db.shortname + ' : ' + self.ProbeSetID +' / Probe Information' + # updated by NL, javascript function xmlhttpPost(strURL, div, querystring) and function updatepage(Id, str) + # have been moved to dhtml.js + self.dict['js1'] = '' + + def nullRecord(self,x): + if x or x == 0: + return x + else: + return "" + +########################## +# UCSC Probe track by Ridi Albert +########################## + def convertChipName2Rudi(self, officialName): + rudiName = None + if officialName == 'Hu6800': + rudiName = "ANHuGeneFL" + else: + rudiName = officialName.replace('_','') + rudiName = rudiName.replace('-','') + rudiName = "AN%s"%rudiName + return rudiName + + def getProbeTrackURL(self, probesetfreeze_id, probeset_id): + try: + self.cursor.execute('SELECT GeneChip.Name, GeneChip.SpeciesId FROM ProbeFreeze,GeneChip WHERE ProbeFreeze.ChipId = GeneChip.Id and ProbeFreeze.Name = "%s"' % probesetfreeze_id) + chipname, species = self.cursor.fetchall()[0] + except: + return None + + if not species: + return None + + chipname_in_url = self.convertChipName2Rudi(chipname) + orgs = {1:"mouse", 2:"rat"} + dbs = {1:"mm8", 2:"mm6"} + + try: + url = webqtlConfig.UCSC_RUDI_TRACK_URL%(orgs[species], dbs[species],chipname_in_url, probeset_id) + except: + url = '' + + return url + + + #NL 05-13-2011: get field_names in query + def getStrainNameIndexPair(self): + + strainNameIndexPair=[] + query ='SELECT * FROM SnpPattern limit 1' + self.cursor.execute(query) + + num_fields = len(self.cursor.description) + field_names = [i[0] for i in self.cursor.description] + strainsNameList=field_names[1:] + + # index for strain name starts from 1 + for index, name in enumerate(strainsNameList): + index=index+1 + strainNameIndexPair.append((name,index)) + + return strainNameIndexPair + + + |