diff options
Diffstat (limited to 'web/webqtl/showTrait/ShowProbeInfoPage.py')
| -rwxr-xr-x | web/webqtl/showTrait/ShowProbeInfoPage.py | 486 |
1 files changed, 0 insertions, 486 deletions
diff --git a/web/webqtl/showTrait/ShowProbeInfoPage.py b/web/webqtl/showTrait/ShowProbeInfoPage.py deleted file mode 100755 index 989238b4..00000000 --- a/web/webqtl/showTrait/ShowProbeInfoPage.py +++ /dev/null @@ -1,486 +0,0 @@ -# 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 - - - |