diff options
Diffstat (limited to 'web/webqtl/showTrait')
| -rwxr-xr-x | web/webqtl/showTrait/DataEditingPage.py | 1908 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/ShowBestTrait.py | 195 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/ShowProbeInfoPage.py | 486 | ||||
| -rw-r--r-- | web/webqtl/showTrait/ShowTraitPage.py | 170 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/exportPage.py | 141 | ||||
| -rwxr-xr-x | web/webqtl/showTrait/testTraitPage.py | 36 |
7 files changed, 0 insertions, 2936 deletions
diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py deleted file mode 100755 index 20231429..00000000 --- a/web/webqtl/showTrait/DataEditingPage.py +++ /dev/null @@ -1,1908 +0,0 @@ -import string -import os -import cPickle -import pyXLWriter as xl - -from htmlgen import HTMLgen2 as HT - -from base import webqtlConfig -from utility import webqtlUtil, Plot -from base.webqtlTrait import webqtlTrait -from dbFunction import webqtlDatabaseFunction -from base.templatePage import templatePage -from basicStatistics import BasicStatisticsFunctions - - -######################################### -# DataEditingPage -######################################### -class DataEditingPage(templatePage): - - def __init__(self, fd, thisTrait=None): - - templatePage.__init__(self, fd) - - self.dict['title'] = 'Data Editing' - TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") - - if not self.openMysql(): - return - if not fd.genotype: - fd.readData(incf1=1) - - ############################# - # determine data editing page format - ############################# - varianceDataPage = 0 - if fd.formID == 'varianceChoice': - varianceDataPage = 1 - - if varianceDataPage: - fmID='dataEditing' - nCols = 6 - else: - if fd.enablevariance: - fmID='pre_dataEditing' - nCols = 4 - else: - fmID='dataEditing' - nCols = 4 - - ############################# - ## titles, etc. - ############################# - - titleTop = HT.Div() - - title1 = HT.Paragraph(" Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader") - title1Body = HT.Paragraph(Id="sectionbody1") - - if fd.enablevariance and not varianceDataPage: - title2 = HT.Paragraph(" Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader") - else: - title2 = HT.Paragraph(" Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader") - title2Body = HT.Paragraph(Id="sectionbody2") - - title3 = HT.Paragraph(" Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader") - title3Body = HT.Paragraph(Id="sectionbody3") - - title4 = HT.Paragraph(" Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader") - title4Body = HT.Paragraph(Id="sectionbody4") - - title5 = HT.Paragraph(" Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader") - title5Body = HT.Paragraph(Id="sectionbody5") - - ############################# - ## Hidden field - ############################# - - # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery - hddn = {'FormID':fmID, 'RISet':fd.RISet, 'submitID':'', 'scale':'physic', 'additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'method':None,\ - 'parentsf14regression':'OFF', 'stats_method':'1', 'chromosomes':'-1', 'topten':'', 'viewLegend':'ON', 'intervalAnalystCheck':'ON', 'valsHidden':'OFF',\ - 'database':'', 'criteria':None, 'MDPChoice':None, 'bootCheck':None, 'permCheck':None, 'applyVarianceSE':None, 'strainNames':'_', 'strainVals':'_',\ - 'strainVars':'_', 'otherStrainNames':'_', 'otherStrainVals':'_', 'otherStrainVars':'_', 'extra_attributes':'_', 'other_extra_attributes':'_'} - - if fd.enablevariance: - hddn['enablevariance']='ON' - if fd.incparentsf1: - hddn['incparentsf1']='ON' - - if thisTrait: - hddn['fullname'] = str(thisTrait) - try: - hddn['normalPlotTitle'] = thisTrait.symbol - hddn['normalPlotTitle'] += ": " - hddn['normalPlotTitle'] += thisTrait.name - except: - hddn['normalPlotTitle'] = str(thisTrait.name) - hddn['fromDataEditingPage'] = 1 - if thisTrait.db and thisTrait.db.type and thisTrait.db.type == 'ProbeSet': - hddn['trait_type'] = thisTrait.db.type - if thisTrait.cellid: - hddn['cellid'] = thisTrait.cellid - else: - self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % thisTrait.mysqlid) - heritability = self.cursor.fetchone() - hddn['heritability'] = heritability - - hddn['attribute_names'] = "" - - hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet) - - ############################# - ## Display Trait Information - ############################# - - headSpan = self.dispHeader(fd,thisTrait) #Draw header - - titleTop.append(headSpan) - - if fd.identification: - hddn['identification'] = fd.identification - - else: - hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named - - self.dispTraitInformation(fd, title1Body, hddn, thisTrait) #Display trait information + function buttons - - ############################# - ## Generate form and buttons - ############################# - - mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), - name='dataInput', submit=HT.Input(type='hidden')) - - next=HT.Input(type='submit', name='submit',value='Next',Class="button") - reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - correlationMenus = [] - - if thisTrait == None: - thisTrait = webqtlTrait(data=fd.allTraitData, db=None) - - # Variance submit page only - if fd.enablevariance and not varianceDataPage: - title2Body.append("Click the next button to go to the variance submission form.", - HT.Center(next,reset)) - else: - self.dispBasicStatistics(fd, title2Body, thisTrait) - self.dispCorrelationTools(fd, title3Body, thisTrait) - self.dispMappingTools(fd, title4Body, thisTrait) - - ############################# - ## Trait Value Table - ############################# - - self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait) - - if fd.allstrainlist: - hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') - for key in hddn.keys(): - mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) - - if fd.enablevariance and not varianceDataPage: - #pre dataediting page, need to submit variance - mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - else: - mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - TD_LR.append(HT.Paragraph(mainForm)) - self.dict['body'] = str(TD_LR) - - ########################################## - ## Function to display header - ########################################## - def dispHeader(self, fd, thisTrait): - headSpan = HT.Div(style="font-size:14px;") - - #If trait, use trait name; otherwise, use identification value - if thisTrait: - if thisTrait.cellid: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', thisTrait.cellid) - else: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', thisTrait.name) - else: - if fd.identification: - headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification) - else: - headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;')) - - return headSpan - - ########################################## - ## Function to display trait infos - ########################################## - def dispTraitInformation(self, fd, title1Body, hddn, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") - - reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - - #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object. - addSelectionButton = "" - verifyButton = "" - rnaseqButton = "" - geneWikiButton = "" - probeButton = "" - similarButton = "" - snpBrowserButton = "" - updateButton = "" - - addSelectionText = "" - verifyText = "" - rnaseqText = "" - geneWikiText = "" - probeText = "" - similarText = "" - snpBrowserText = "" - updateText = "" - - if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: - - if thisTrait==None or thisTrait.db.type=='Temp': - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - elif thisTrait.db.type != 'Temp': - if thisTrait.db.type == 'Publish' and thisTrait.confidential: #XZ: confidential phenotype trait - if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - updateButton.append(updateButton_img) - updateText = "Edit" - else: - pass - - self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.RISet) - if thisTrait: - addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, 'dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") - addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - elif self.cursor.fetchall(): - addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") - addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - else: - pass - - - # Microarray database information to display - if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': #before, this line was only reached if thisTrait != 0, but now we need to check - try: - hddn['GeneId'] = int(string.strip(thisTrait.geneid)) - except: - pass - - Info2Disp = HT.Paragraph() - - #XZ: Gene Symbol - if thisTrait.symbol: - #XZ: Show SNP Browser only for mouse - if _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=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] - else: - if thisTrait.chr and thisTrait.mb: - snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \ - "&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002) - else: - snpurl = "" - - if snpurl: - snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) - snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") - snpBrowserButton.append(snpBrowserButton_img) - snpBrowserText = "SNPs" - - #XZ: Show GeneWiki for all species - geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol)) - geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") - geneWikiButton.append(geneWikiButton_img) - geneWikiText = 'GeneWiki' - - #XZ: display similar traits in other selected datasets - if thisTrait and thisTrait.db and thisTrait.db.type=="ProbeSet" and thisTrait.symbol: - if _Species in ("mouse", "rat", "human"): - similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species) - similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) - similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") - similarButton.append(similarButton_img) - similarText = "Find" - else: - pass - tbl.append(HT.TR( - HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740) - )) - else: - tbl.append(HT.TR( - HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top") - )) - - #XZ: Gene Alias - if thisTrait.alias: - alias = string.replace(thisTrait.alias, ";", " ") - alias = string.join(string.split(alias), ", ") - tbl.append(HT.TR( - HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top") - )) - - #XZ: Description - if thisTrait.description: - tSpan = HT.Span(thisTrait.description, Class="fs13") - if thisTrait.probe_target_description: - tSpan.append('; ', thisTrait.probe_target_description) - else: - tSpan = HT.Span('Not available', Class="fs13") - tbl.append(HT.TR( - HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - #XZ: Location - - #XZ: deal with Chr and Mb - if thisTrait.chr and thisTrait.mb: - tSpan = HT.Span('Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb),Class="fs13") - elif (thisTrait.chr): - tSpan = HT.Span('Chr %s @ Unknown position' % (thisTrait.chr), Class="fs13") - else: - tSpan = HT.Span('Not available', Class="fs13") - - #XZ: deal with direction - if thisTrait.strand_probe == '+': - tSpan.append(' on the plus strand ') - elif thisTrait.strand_probe == '-': - tSpan.append(' on the minus strand ') - else: - pass - - tbl.append(HT.TR( - HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - ##display Verify Location button - try: - blatsequence = thisTrait.blatseq - if not blatsequence: - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) - seqs = self.cursor.fetchall() - if not seqs: - raise ValueError - else: - blatsequence = '' - for seqt in seqs: - if int(seqt[1][-1]) % 2 == 1: - blatsequence += string.strip(seqt[0]) - - #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe - blatsequence = '%3E'+thisTrait.name+'%0A'+blatsequence+'%0A' - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) - - seqs = self.cursor.fetchall() - for seqt in seqs: - if int(seqt[1][-1]) %2 == 1: - blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' - #-------- - #XZ, 07/16/2009: targetsequence is not used, so I comment out this block - #targetsequence = thisTrait.targetseq - #if targetsequence==None: - # targetsequence = "" - - #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. - if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) - UTHSC_BLAT_URL = "" - elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) - elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - UTHSC_BLAT_URL = "" - else: - UCSC_BLAT_URL = "" - UTHSC_BLAT_URL = "" - - if UCSC_BLAT_URL: - verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", - title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = 'Verify' - if UTHSC_BLAT_URL: - rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", - title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = 'RNA-seq' - tSpan.append(HT.BR()) - except: - pass - - #Display probe information (if any) - if thisTrait.db.name.find('Liver') >= 0 and thisTrait.db.name.find('F2') < 0: - pass - else: - #query database for number of probes associated with trait; if count > 0, set probe tool button and text - self.cursor.execute("""SELECT count(*) - FROM Probe, ProbeSet - WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (thisTrait.name)) - - probeResult = self.cursor.fetchone() - if probeResult[0] > 0: - probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \ - % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet) - probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) - probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") - probeButton.append(probeButton_img) - probeText = "Probes" - - tSpan = HT.Span(Class="fs13") - - #XZ: deal with blat score and blat specificity. - if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score: - if thisTrait.probe_set_specificity: - tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3) - if thisTrait.probe_set_blat_score: - tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2) - - onClick="openNewWin('/blatInfo.html')" - - tbl.append(HT.TR( - HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - tSpan = HT.Span(Class="fs13") - tSpan.append(str(_Species).capitalize(), ", ", fd.RISet) - - tbl.append(HT.TR( - HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - if thisTrait.cellid: - self.cursor.execute(""" - select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze - where - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Id = %d""" % thisTrait.db.id) - probeDBName = self.cursor.fetchone()[0] - tbl.append(HT.TR( - HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top") - )) - else: - tbl.append(HT.TR( - HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name, - target='_blank', Class="fs13 fwn non_bold"), valign="top") - )) - - #XZ: ID links - if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid: - idStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(Class="fs13") - if thisTrait.geneid: - gurl = HT.Href(text= 'Gene', target='_blank',\ - url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.omim: - gurl = HT.Href(text= 'OMIM', target='_blank', \ - url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.unigeneid: - try: - gurl = HT.Href(text= 'UniGene',target='_blank',\ - url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - except: - pass - if thisTrait.genbankid: - thisTrait.genbankid = '|'.join(thisTrait.genbankid.split('|')[0:10]) - if thisTrait.genbankid[-1]=='|': - thisTrait.genbankid=thisTrait.genbankid[0:-1] - gurl = HT.Href(text= 'GenBank', target='_blank', \ - url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes") - tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if thisTrait.homologeneid: - hurl = HT.Href(text= 'HomoloGene', target='_blank',\ - url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species") - tSpan.append(HT.Span(hurl, style=idStyle), " "*2) - - tbl.append( - HT.TR(HT.TD(colspan=3,height=6)), - HT.TR( - HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top") - )) - - #XZ: Resource Links: - if thisTrait.symbol: - linkStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px") - - #XZ,12/26/2008: Gene symbol may contain single quotation mark. - #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) - #I debug this by using double quotation marks. - if _Species == "rat": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Rattus norvegicus" - - #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % thisTrait.symbol) - self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % thisTrait.symbol) - try: - kgId, chr, txst, txen = self.cursor.fetchall()[0] - if chr and txst and txen and kgId: - txst = int(txst*1000000) - txen = int(txen*1000000) - tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle) - , " "*2) - except: - pass - if _Species == "mouse": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Mus musculus" - - #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % thisTrait.symbol) - self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % thisTrait.symbol) - try: - chr, txst, txen = self.cursor.fetchall()[0] - if chr and txst and txen and thisTrait.refseq_transcriptid : - txst = int(txst*1000000) - txen = int(txen*1000000) - tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',thisTrait.refseq_transcriptid,chr,txst,txen), - Class="fs14 fwn"), style=linkStyle) - , " "*2) - except: - pass - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ - # url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \ - # % (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \ - # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): - tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\ - url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \ - % (_Species, thisTrait.geneid),Class="fs14 fwn", \ - title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\ - url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ - % thisTrait.symbol,Class="fs14 fwn", \ - title="Protein interactions: known and inferred"), style=linkStyle), " "*2) - if thisTrait.symbol: - #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input - #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users - if _Species == "mouse": - species_scientific = "Mus%20musculus" - elif _Species == "rat": - species_scientific = "Rattus%20norvegicus" - elif _Species == "human": - species_scientific = "Homo%20sapiens" - elif _Species == "drosophila": - species_scientific = "Drosophila%20melanogaster" - else: - species_scientific = "all" - - species_scientific - tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ - url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ - % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \ - title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) - else: - pass - #tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\ - # url="http://bind.ca/?textquery=%s" \ - # % thisTrait.symbol,Class="fs14 fwn", \ - # title="Protein interactions"), style=linkStyle), " "*2) - if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): - tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\ - url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \ - % thisTrait.geneid, Class="fs14 fwn", \ - title="Meta-analysis of gene expression data"), style=linkStyle), " "*2) - tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\ - url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \ - % thisTrait.symbol, Class="fs14 fwn", \ - title="Brain synapse database"), style=linkStyle), " "*2) - if _Species == "mouse": - tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - url="http://mouse.brain-map.org/brain/%s.html" \ - % thisTrait.symbol, Class="fs14 fwn", \ - title="Allen Brain Atlas"), style=linkStyle), " "*2) - - if thisTrait.geneid: - #if _Species == "mouse": - # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - # url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \ - # % thisTrait.geneid, Class="fs14 fwn", \ - # title="Allen Brain Atlas"), style=linkStyle), " "*2) - if _Species == "human": - tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \ - % thisTrait.geneid, Class="fs14 fwn", \ - title="Allen Brain Atlas"), style=linkStyle), " "*2) - tbl.append( - HT.TR(HT.TD(colspan=3,height=6)), - HT.TR( - HT.TD(' '), - HT.TD(width=10, valign="top"), - HT.TD(tSpan, valign="top"))) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - - #for zhou mi's cliques, need to be removed - #if self.database[:6] == 'BXDMic' and self.ProbeSetID in cliqueID: - # Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\ - # url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \ - # % self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR()) - - #linkTable.append(HT.TR(linkTD)) - #Info2Disp.append(linkTable) - title1Body.append(tbl, HT.BR(), menuTable) - - elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype - - if thisTrait.confidential: - tbl.append(HT.TR( - HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740) - )) - if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): - tbl.append(HT.TR( - HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740) - )) - else: - tbl.append(HT.TR( - HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Authors: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.authors, Class="fs13"), - valign="top", width=740) - )) - tbl.append(HT.TR( - HT.TD('Title: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(thisTrait.title, Class="fs13"), - valign="top", width=740) - )) - if thisTrait.journal: - journal = thisTrait.journal - if thisTrait.year: - journal = thisTrait.journal + " (%s)" % thisTrait.year - - tbl.append(HT.TR( - HT.TD('Journal: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(journal, Class="fs13"), - valign="top", width=740) - )) - PubMedLink = "" - if thisTrait.pubmed_id: - PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id - if PubMedLink: - tbl.append(HT.TR( - HT.TD('Link: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"), - style = "background:#cddcff;padding:2"), valign="top", width=740) - )) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype - - GenoInfo = HT.Paragraph() - if thisTrait.chr and thisTrait.mb: - location = ' Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb) - else: - location = "not available" - - if thisTrait.sequence and len(thisTrait.sequence) > 100: - if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', thisTrait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', thisTrait.sequence) - elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) - elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', thisTrait.sequence) - else: - UCSC_BLAT_URL = "" - UTHSC_BLAT_URL = "" - if UCSC_BLAT_URL: - #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - verifyButton = HT.Href(url="#") - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = "Verify" - rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = "RNA-seq" - - tbl.append(HT.TR( - HT.TD('Location: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740) - ), - HT.TR( - HT.TD('SNP Search: ', Class="fs13 fwb", - valign="top", nowrap="on", width=90), - HT.TD(width=10, valign="top"), - HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"), - valign="top", width=740) - )) - - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) - - TempInfo = HT.Paragraph() - if thisTrait != None: - if thisTrait.description: - tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15)) - else: - tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15)) - - if (updateText == "Edit"): - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") - else: - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1") - - menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") ) - menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) - - title1Body.append(tbl, HT.BR(), menuTable) - - else: - pass - - - ########################################## - ## Function to display analysis tools - ########################################## - def dispBasicStatistics(self, fd, title2Body, thisTrait): - - #XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later. - stats_row = HT.TR() - stats_cell = HT.TD() - - if fd.genotype.type == "riset": - strainlist = fd.f1list + fd.strainlist - else: - strainlist = fd.f1list + fd.parlist + fd.strainlist - - other_strains = [] #XZ: strain that is not of primary group - specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains. - all_strains = [] - primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS - - MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp') - - for strain in thisTrait.data.keys(): - strainName = strain.replace("_2nd_", "") - if strain not in strainlist: - if (thisTrait.data[strainName].val != None): - if strain.find('F1') < 0: - specialStrains.append(strain) - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): - other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group - else: - if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): - primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) - - if len(other_strains) > 3: - other_strains.sort(key=webqtlUtil.natsort_key) - primary_strains.sort(key=webqtlUtil.natsort_key) - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added. - all_strains = primary_strains + other_strains - other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #XZ: note that fd.f1list and fd.parlist are added. - MDP_menu.append(('All Cases','0')) - MDP_menu.append(('%s Only' % fd.RISet,'1')) - MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) - stats_row.append("Include: ", MDP_menu, HT.BR(), HT.BR()) - else: - if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3): - MDP_menu.append(('All Cases','0')) - MDP_menu.append(('%s Only' % fd.RISet,'1')) - MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) - stats_row.append("Include: ", MDP_menu, " "*3) - all_strains = primary_strains - all_strains.sort(key=webqtlUtil.natsort_key) - all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains - primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains - else: - all_strains = strainlist - - other_strains.sort(key=webqtlUtil.natsort_key) - all_strains = all_strains + other_strains - pass - - update_button = HT.Input(type='button',value=' Update Figures ', Class="button update") #This is used to reload the page and update the Basic Statistics figures with user-edited data - stats_row.append(update_button, HT.BR(), HT.BR()) - - if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4): - #One set of vals for all, selected strain only, and non-selected only - vals1 = [] - vals2 = [] - vals3 = [] - - #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals1.append(thisValFull) - - #Using just the RISet strain - for i, strainNameOrig in enumerate(primary_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals2.append(thisValFull) - - #Using all non-RISet strains only - for i, strainNameOrig in enumerate(other_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals3.append(thisValFull) - - vals_set = [vals1,vals2,vals3] - - else: - vals = [] - - #Using all strains/cases for values - for i, strainNameOrig in enumerate(all_strains): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals.append(thisValFull) - - vals_set = [vals] - - stats_script = HT.Script(language="Javascript") #script needed for tabs - - for i, vals in enumerate(vals_set): - if i == 0 and len(vals) < 4: - stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element - stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted."))) - stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" - stats_cell.append(stats_container) - break - elif (i == 1 and len(primary_strains) < 4): - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) - elif (i == 2 and len(other_strains) < 4): - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) - stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" - else: - stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") - stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" - if len(vals) > 4: - stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), - HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), - HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")] - stats_tabs = HT.List(stats_tab_list) - stats_container.append(stats_tabs) - - table_div = HT.Div(id="statstabs-1") - table_container = HT.Paragraph() - - statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - - if thisTrait.db: - if thisTrait.cellid: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type, cellid=thisTrait.cellid) - else: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type) - else: - statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals) - - statsTable.append(HT.TR(HT.TD(statsTableCell))) - - table_container.append(statsTable) - table_div.append(table_container) - stats_container.append(table_div) - - normalplot_div = HT.Div(id="statstabs-5") - normalplot_container = HT.Paragraph() - normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - - try: - plotTitle = thisTrait.symbol - plotTitle += ": " - plotTitle += thisTrait.name - except: - plotTitle = str(thisTrait.name) - - normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) - normalplot.append(HT.TR(HT.TD(normalplot_img))) - normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ - normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), - "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", - target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) - normalplot_container.append(normalplot) - normalplot_div.append(normalplot_container) - stats_container.append(normalplot_div) - - boxplot_div = HT.Div(id="statstabs-2") - boxplot_container = HT.Paragraph() - boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) - boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) - boxplot_container.append(boxplot) - boxplot_div.append(boxplot_container) - stats_container.append(boxplot_div) - - - barName_div = HT.Div(id="statstabs-3") - barName_container = HT.Paragraph() - barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") - barName.append(HT.TR(HT.TD(barName_img))) - barName_container.append(barName) - barName_div.append(barName_container) - stats_container.append(barName_div) - - barRank_div = HT.Div(id="statstabs-4") - barRank_container = HT.Paragraph() - barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") - barRank.append(HT.TR(HT.TD(barRank_img))) - barRank_container.append(barRank) - barRank_div.append(barRank_container) - stats_container.append(barRank_div) - - stats_cell.append(stats_container) - - stats_script.append(stats_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - stats_row.append(stats_cell) - - submitTable.append(stats_row) - submitTable.append(stats_script) - - title2Body.append(submitTable) - - - def dispCorrelationTools(self, fd, title3Body, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - RISetgp = fd.RISet - if RISetgp[:3] == 'BXD': - RISetgp = 'BXD' - - if RISetgp: - sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr") - lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr") - tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr") - methodText = HT.Span("Calculate:", Class="ffl fwb fs12") - - databaseText = HT.Span("Database:", Class="ffl fwb fs12") - databaseMenu1 = HT.Select(name='database1') - databaseMenu2 = HT.Select(name='database2') - databaseMenu3 = HT.Select(name='database3') - - nmenu = 0 - self.cursor.execute('SELECT PublishFreeze.FullName,PublishFreeze.Name FROM \ - PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id \ - and InbredSet.Name = "%s" and PublishFreeze.public > %d' % \ - (RISetgp,webqtlConfig.PUBLICTHRESH)) - for item in self.cursor.fetchall(): - databaseMenu1.append(item) - databaseMenu2.append(item) - databaseMenu3.append(item) - nmenu += 1 - self.cursor.execute('SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,\ - InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = \ - "%s" and GenoFreeze.public > %d' % (RISetgp,webqtlConfig.PUBLICTHRESH)) - for item in self.cursor.fetchall(): - databaseMenu1.append(item) - databaseMenu2.append(item) - databaseMenu3.append(item) - nmenu += 1 - #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob. - self.cursor.execute('SELECT Id, Name FROM Tissue order by Name') - for item in self.cursor.fetchall(): - TId, TName = item - databaseMenuSub = HT.Optgroup(label = '%s ------' % TName) - self.cursor.execute('SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, \ - InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and \ - ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like "%s%%" \ - order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ' % (TId,webqtlConfig.PUBLICTHRESH, RISetgp)) - for item2 in self.cursor.fetchall(): - databaseMenuSub.append(item2) - nmenu += 1 - databaseMenu1.append(databaseMenuSub) - databaseMenu2.append(databaseMenuSub) - databaseMenu3.append(databaseMenuSub) - if nmenu: - if thisTrait and thisTrait.db != None: - databaseMenu1.selected.append(thisTrait.db.fullname) - databaseMenu2.selected.append(thisTrait.db.fullname) - databaseMenu3.selected.append(thisTrait.db.fullname) - - criteriaText = HT.Span("Return:", Class="ffl fwb fs12") - - criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu1.append(('top 100','100')) - criteriaMenu1.append(('top 200','200')) - criteriaMenu1.append(('top 500','500')) - criteriaMenu1.append(('top 1000','1000')) - criteriaMenu1.append(('top 2000','2000')) - criteriaMenu1.append(('top 5000','5000')) - criteriaMenu1.append(('top 10000','10000')) - criteriaMenu1.append(('top 15000','15000')) - criteriaMenu1.append(('top 20000','20000')) - - criteriaMenu2 = HT.Select(name='criteria2', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu2.append(('top 100','100')) - criteriaMenu2.append(('top 200','200')) - criteriaMenu2.append(('top 500','500')) - criteriaMenu2.append(('top 1000','1000')) - criteriaMenu2.append(('top 2000','2000')) - criteriaMenu2.append(('top 5000','5000')) - criteriaMenu2.append(('top 10000','10000')) - criteriaMenu2.append(('top 15000','15000')) - criteriaMenu2.append(('top 20000','20000')) - - criteriaMenu3 = HT.Select(name='criteria3', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - criteriaMenu3.append(('top 100','100')) - criteriaMenu3.append(('top 200','200')) - criteriaMenu3.append(('top 500','500')) - criteriaMenu3.append(('top 1000','1000')) - criteriaMenu3.append(('top 2000','2000')) - criteriaMenu3.append(('top 5000','5000')) - criteriaMenu3.append(('top 10000','10000')) - criteriaMenu3.append(('top 15000','15000')) - criteriaMenu3.append(('top 20000','20000')) - - - self.MDPRow1 = HT.TR(Class='mdp1') - self.MDPRow2 = HT.TR(Class='mdp2') - self.MDPRow3 = HT.TR(Class='mdp3') - - correlationMenus1 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)), - self.MDPRow1, cellspacing=0, width="619px", cellpadding=2) - correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden')) # to replace the orderBy menu - correlationMenus2 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)), - self.MDPRow2, cellspacing=0, width="619px", cellpadding=2) - correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden')) - correlationMenus3 = HT.TableLite( - HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")), - HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)), - self.MDPRow3, cellspacing=0, width="619px", cellpadding=2) - correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden')) - - else: - correlationMenus = "" - - - corr_row = HT.TR() - corr_container = HT.Div(id="corr_tabs", Class="ui-tabs") - - if (thisTrait.db != None and thisTrait.db.type =='ProbeSet'): - corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), HT.Href(text='Literature r', url="#corrtabs-2"), HT.Href(text='Tissue r', url="#corrtabs-3")] - else: - corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")] - - corr_tabs = HT.List(corr_tab_list) - corr_container.append(corr_tabs) - - if correlationMenus1 or correlationMenus2 or correlationMenus3: - sample_div = HT.Div(id="corrtabs-1") - sample_container = HT.Span() - - sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked") - sample_type2 = HT.Input(type="radio", name="sample_method", value="2") - - sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - sampleTD = HT.TD(correlationMenus1, HT.BR(), - "Pearson", sample_type, " "*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(), - sample_correlation, HT.BR(), HT.BR()) - - sampleTD.append(HT.Span("The ",HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank", text="Sample Correlation")," is computed between trait data and", - " any ",HT.BR()," other traits in the sample database selected above. Use ", - HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"), - HT.BR(),"when the sample size is small (<20) or when there are influential \ - outliers.", HT.BR(),Class="fs12")) - - sampleTable.append(sampleTD) - - sample_container.append(sampleTable) - sample_div.append(sample_container) - corr_container.append(sample_div) - - literature_div = HT.Div(id="corrtabs-2") - literature_container = HT.Span() - - literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR()) - literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(), - "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"), - " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \ - but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(), - HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12")) - literatureTable.append(literatureTD) - - literature_container.append(literatureTable) - literature_div.append(literature_container) - - if thisTrait.db != None: - if (thisTrait.db.type =='ProbeSet'): - corr_container.append(literature_div) - - tissue_div = HT.Div(id="corrtabs-3") - tissue_container = HT.Span() - - tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked") - tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5") - - tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - tissueTD = HT.TD(correlationMenus3,HT.BR(), - "Pearson", tissue_type, " "*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(), - tissue_correlation, HT.BR(), HT.BR()) - tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"), - " (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \ - transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \ - Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \ - single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \ - of genes",HT.BR()," using data from mouse samples.", - HT.BR(), Class="fs12")) - tissueTable.append(tissueTD) - - tissue_container.append(tissueTable) - tissue_div.append(tissue_container) - if thisTrait.db != None: - if (thisTrait.db.type =='ProbeSet'): - corr_container.append(tissue_div) - - corr_row.append(HT.TD(corr_container)) - - corr_script = HT.Script(language="Javascript") - corr_script_text = """$(function() { $("#corr_tabs").tabs(); });""" - corr_script.append(corr_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4") - submitTable.append(corr_row) - submitTable.append(corr_script) - - title3Body.append(submitTable) - - - def dispMappingTools(self, fd, title4Body, thisTrait): - - _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - - RISetgp = fd.RISet - if RISetgp[:3] == 'BXD': - RISetgp = 'BXD' - - #check boxes - one for regular interval mapping, the other for composite - permCheck1= HT.Input(type='checkbox', Class='checkbox', name='permCheck1',checked="on") - bootCheck1= HT.Input(type='checkbox', Class='checkbox', name='bootCheck1',checked=0) - permCheck2= HT.Input(type='checkbox', Class='checkbox', name='permCheck2',checked="on") - bootCheck2= HT.Input(type='checkbox', Class='checkbox', name='bootCheck2',checked=0) - optionbox1 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression1',checked=0) - optionbox2 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression2',checked=0) - optionbox3 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression3',checked=0) - applyVariance1 = HT.Input(name='applyVarianceSE1',type='checkbox', Class='checkbox') - applyVariance2 = HT.Input(name='applyVarianceSE2',type='checkbox', Class='checkbox') - - IntervalMappingButton=HT.Input(type='button' ,name='interval',value=' Compute ', Class="button") - CompositeMappingButton=HT.Input(type='button' ,name='composite',value=' Compute ', Class="button") - MarkerRegressionButton=HT.Input(type='button',name='marker', value=' Compute ', Class="button") - - chrText = HT.Span("Chromosome:", Class="ffl fwb fs12") - - # updated by NL 5-28-2010 - # Interval Mapping - chrMenu = HT.Select(name='chromosomes1') - chrMenu.append(tuple(["All",-1])) - for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu.append(tuple([fd.genotype[i].name,i])) - - #Menu for Composite Interval Mapping - chrMenu2 = HT.Select(name='chromosomes2') - chrMenu2.append(tuple(["All",-1])) - for i in range(len(fd.genotype)): - if len(fd.genotype[i]) > 1: - chrMenu2.append(tuple([fd.genotype[i].name,i])) - - if fd.genotype.Mbmap: - scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") - scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") - scaleMenu1.append(("Megabase",'physic')) - scaleMenu1.append(("Centimorgan",'morgan')) - scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") - scaleMenu2.append(("Megabase",'physic')) - scaleMenu2.append(("Centimorgan",'morgan')) - - controlText = HT.Span("Control Locus:", Class="ffl fwb fs12") - controlMenu = HT.Input(type="text", name="controlLocus", Class="controlLocus") - - if fd.genotype.Mbmap: - intMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), - HT.TR(HT.TD(scaleText), HT.TD(scaleMenu1)), - cellspacing=0, width="263px", cellpadding=2) - compMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), - HT.TR(HT.TD(scaleText), HT.TD(scaleMenu2)), - HT.TR(HT.TD(controlText), HT.TD(controlMenu)), - cellspacing=0, width="325px", cellpadding=2) - else: - intMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), - cellspacing=0, width="263px", cellpadding=2) - compMappingMenu = HT.TableLite( - HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), - HT.TR(HT.TD(controlText), HT.TD(controlMenu)), - cellspacing=0, width="325px", cellpadding=2) - - directPlotButton = "" - directPlotButton = HT.Input(type='button',name='', value=' Compute ',\ - onClick="dataEditingFunc(this.form,'directPlot');",Class="button") - directPlotSortText = HT.Span(HT.Bold("Sort by: "), Class="ffl fwb fs12") - directPlotSortMenu = HT.Select(name='graphSort') - directPlotSortMenu.append(('LRS Full',0)) - directPlotSortMenu.append(('LRS Interact',1)) - directPlotPermuText = HT.Span("Permutation Test (n=500)", Class="ffl fs12") - directPlotPermu = HT.Input(type='checkbox', Class='checkbox',name='directPermuCheckbox', checked="on") - pairScanReturnText = HT.Span(HT.Bold("Return: "), Class="ffl fwb fs12") - pairScanReturnMenu = HT.Select(name='pairScanReturn') - pairScanReturnMenu.append(('top 50','50')) - pairScanReturnMenu.append(('top 100','100')) - pairScanReturnMenu.append(('top 200','200')) - pairScanReturnMenu.append(('top 500','500')) - - pairScanMenus = HT.TableLite( - HT.TR(HT.TD(directPlotSortText), HT.TD(directPlotSortMenu)), - HT.TR(HT.TD(pairScanReturnText), HT.TD(pairScanReturnMenu)), - cellspacing=0, width="232px", cellpadding=2) - - markerSuggestiveText = HT.Span(HT.Bold("Display LRS greater than:"), Class="ffl fwb fs12") - markerSuggestive = HT.Input(name='suggestive', size=5, maxlength=8) - displayAllText = HT.Span(" Display all LRS ", Class="ffl fs12") - displayAll = HT.Input(name='displayAllLRS', type="checkbox", Class='checkbox') - useParentsText = HT.Span(" Use Parents ", Class="ffl fs12") - useParents = optionbox2 - applyVarianceText = HT.Span(" Use Weighted ", Class="ffl fs12") - - markerMenu = HT.TableLite( - HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive)), - HT.TR(HT.TD(displayAll,displayAllText)), - HT.TR(HT.TD(useParents,useParentsText)), - HT.TR(HT.TD(applyVariance2,applyVarianceText)), - cellspacing=0, width="263px", cellpadding=2) - - - mapping_row = HT.TR() - mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") - - mapping_tab_list = [HT.Href(text="Interval", url="#mappingtabs-1"), HT.Href(text="Marker Regression", url="#mappingtabs-2"), HT.Href(text="Composite", url="#mappingtabs-3"), HT.Href(text="Pair-Scan", url="#mappingtabs-4")] - mapping_tabs = HT.List(mapping_tab_list) - mapping_container.append(mapping_tabs) - - interval_div = HT.Div(id="mappingtabs-1") - interval_container = HT.Span() - - intervalTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - intTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - intTD.append(intMappingMenu,HT.BR()) - - intTD.append(permCheck1,'Permutation Test (n=2000)',HT.BR(), - bootCheck1,'Bootstrap Test (n=2000)', HT.BR(), optionbox1, 'Use Parents', HT.BR(), - applyVariance1,'Use Weighted', HT.BR(), HT.BR(),IntervalMappingButton, HT.BR(), HT.BR()) - intervalTable.append(HT.TR(intTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#intmap', target='_blank', text='Interval Mapping'), - ' computes linkage maps for the entire genome or single',HT.BR(),' chromosomes.', - ' The ',HT.Href(url='/glossary.html#permutation', target='_blank', text='Permutation Test'),' estimates suggestive and significant ',HT.BR(),' linkage scores. \ - The ',HT.Href(url='/glossary.html#bootstrap', target='_blank', text='Bootstrap Test'), ' estimates the precision of the QTL location.' - ,Class="fs12"), HT.BR(), valign="top"))) - - interval_container.append(intervalTable) - interval_div.append(interval_container) - mapping_container.append(interval_div) - - # Marker Regression - - marker_div = HT.Div(id="mappingtabs-2") - marker_container = HT.Span() - - markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - markerTD.append(markerMenu,HT.BR()) - - markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) - - markerTable.append(HT.TR(markerTD),HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#',target='_blank',text='Marker regression'), - ' computes and displays LRS values for individual markers.',HT.BR(), - 'This function also lists additive effects (phenotype units per allele) and', HT.BR(), - 'dominance deviations for some datasets.', HT.BR(),Class="fs12"), HT.BR(), valign="top"))) - - marker_container.append(markerTable) - marker_div.append(marker_container) - mapping_container.append(marker_div) - - # Composite interval mapping - composite_div = HT.Div(id="mappingtabs-3") - composite_container = HT.Span() - - compositeTable = HT.TableLite(cellspacing=0, cellpadding=3, width="100%") - compTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - compTD.append(compMappingMenu,HT.BR()) - - compTD.append(permCheck2, 'Permutation Test (n=2000)',HT.BR(), - bootCheck2,'Bootstrap Test (n=2000)', HT.BR(), - optionbox3, 'Use Parents', HT.BR(), HT.BR(), CompositeMappingButton, HT.BR(), HT.BR()) - compositeTable.append(HT.TR(compTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Composite',target='_blank',text='Composite Interval Mapping'), - " allows you to control for a single marker as",HT.BR()," a cofactor. ", - "To find a control marker, run the ",HT.Bold("Marker Regression")," function."), - HT.BR(), valign="top"))) - - composite_container.append(compositeTable) - composite_div.append(composite_container) - mapping_container.append(composite_div) - - # Pair Scan - - pairscan_div = HT.Div(id="mappingtabs-4") - pairscan_container = HT.Span() - - pairScanTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - pairScanTD = HT.TD(NOWRAP='ON', Class="fs12 fwn") - pairScanTD.append(pairScanMenus,HT.BR()) - pairScanTD.append(directPlotPermu, directPlotPermuText, HT.BR(), HT.BR(), - directPlotButton,HT.BR(),HT.BR()) - pairScanTable.append(HT.TR(pairScanTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Pair_Scan', target="_blank", text='Pair-Scan'), - ' searches for pairs of chromosomal regions that are',HT.BR(), - 'involved in two-locus epistatic interactions.'), HT.BR(), valign="top"))) - - pairscan_container.append(pairScanTable) - pairscan_div.append(pairscan_container) - mapping_container.append(pairscan_div) - - mapping_row.append(HT.TD(mapping_container)) - - # Treat Interval Mapping and Marker Regression and Pair Scan as a group for displaying - #disable Interval Mapping and Marker Regression and Pair Scan for human and the dataset doesn't have genotype file - mappingMethodId = webqtlDatabaseFunction.getMappingMethod(cursor=self.cursor, groupName=RISetgp) - - mapping_script = HT.Script(language="Javascript") - mapping_script_text = """$(function() { $("#mapping_tabs").tabs(); });""" - mapping_script.append(mapping_script_text) - - submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - - if mappingMethodId != None: - if int(mappingMethodId) == 1: - submitTable.append(mapping_row) - submitTable.append(mapping_script) - elif int(mappingMethodId) == 4: - # NL; 09-26-2011 testing for Human Genome Association function - mapping_row=HT.TR() - mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") - - mapping_tab_list = [HT.Href(text="Genome Association", url="#mappingtabs-1")] - mapping_tabs = HT.List(mapping_tab_list) - mapping_container.append(mapping_tabs) - - # Genome Association - markerSuggestiveText = HT.Span(HT.Bold("P Value:"), Class="ffl fwb fs12") - - markerSuggestive = HT.Input(name='pValue', value='0.001', size=10, maxlength=20,onClick="this.value='';",onBlur="if(this.value==''){this.value='0.001'};") - markerMenu = HT.TableLite(HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive),HT.TD(HT.Italic(' (e.g. 0.001 or 1e-3 or 1E-3 or 3)'))),cellspacing=0, width="400px", cellpadding=2) - MarkerRegressionButton=HT.Input(type='button',name='computePlink', value=' Compute Using PLINK ', onClick= "validatePvalue(this.form);", Class="button") - - marker_div = HT.Div(id="mappingtabs-1") - marker_container = HT.Span() - markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") - markerTD.append(markerMenu,HT.BR()) - markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) - markerTable.append(HT.TR(markerTD)) - - marker_container.append(markerTable) - marker_div.append(marker_container) - - mapping_container.append(marker_div) - mapping_row.append(HT.TD(mapping_container)) - submitTable.append(mapping_row) - submitTable.append(mapping_script) - else: - submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("mappingMethodId %s has not been implemented for this dataset yet." % mappingMethodId), id="mapping_tabs", Class="ui-tabs")))) - submitTable.append(mapping_script) - - else: - submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("Mapping options are disabled for data not matched with genotypes."), id="mapping_tabs", Class="ui-tabs")))) - submitTable.append(mapping_script) - - title4Body.append(submitTable) - - - def natural_sort(strain_list): - - sorted = [] - for strain in strain_list: - try: - strain = int(strain) - try: sorted[-1] = sorted[-1] * 10 + strain - except: sorted.append(strain) - except: - sorted.append(strain) - return sorted - - ########################################## - ## Function to display trait tables - ########################################## - def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait): - traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") - resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") - blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") - blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") - showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') - blockMenuSpan = HT.Span(Id="blockMenuSpan") - blockMenu = HT.Select(name='block_method') - - if fd.genotype.type == "riset": - allstrainlist_neworder = fd.f1list + fd.strainlist - else: - allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist - - 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))) - 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) - - for attribute in self.cursor.fetchall(): - attribute_ids.append(attribute[0]) - attribute_names.append(attribute[1]) - for this_attr_name in attribute_names: - exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttribute.Name = '%s' AND - CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) - try: - distinct_values = self.cursor.fetchall() - attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - attr_value_menu = HT.Select(name=this_attr_name) - attr_value_menu.append(("None", "show_all")) - for value in distinct_values: - attr_value_menu.append((str(value[0]), value[0])) - attr_value_menu_div.append(attr_value_menu) - dropdown_menus.append(attr_value_menu_div) - except: - pass - except: - pass - - other_strains = [] - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - other_strains.append(strain) - - if other_strains: - blockMenu.append(('%s Only' % fd.RISet,'1')) - blockMenu.append(('Non-%s Only' % fd.RISet,'0')) - blockMenuSpan.append(blockMenu) - else: - pass - - showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') - showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") - if other_strains: - showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockMenuSpan, " ", blockSamplesButton, HT.BR()) - else: - showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockSamplesButton, HT.BR()) - - exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') - if len(attribute_names) > 0: - excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') - showHideMenuOptions.append(HT.Bold(" Block samples by group:"), " "*5, exclude_menu, " "*5) - for menu in dropdown_menus: - showHideMenuOptions.append(menu) - showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) - showHideMenuOptions.append(HT.Bold(" Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) - - traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) - traitTableOptions.append(HT.Span(" Outliers highlighted in ", HT.Bold(" yellow ", style="background-color:yellow;"), " can be hidden using the ", - HT.Strong(" Hide Outliers "), " button,",HT.BR()," and samples with no value (x) can be hidden by clicking ", - HT.Strong(" Hide No Value "), "."), HT.BR()) - - - dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;") - - table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work - container = HT.Div() #This will contain everything and be put into a cell of the table defined above - - container.append(dispintro, traitTableOptions, HT.BR()) - - primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter") - primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object - - other_strainsExist = False - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - other_strainsExist = True - break - - primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') - - primary_table.append(primary_header) - for i in range(len(primary_body)): - primary_table.append(primary_body[i]) - - other_strains = [] - for strain in thisTrait.data.keys(): - if strain not in allstrainlist_neworder: - allstrainlist_neworder.append(strain) - other_strains.append(strain) - - if other_strains: - other_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable2", Class="tablesorter") #Table object with other (for example, non-BXD / MDP) traits - other_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for other table object; same function is used as the one used for the primary table, since the header is the same - other_strains.sort() #Sort other strains - other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #Append F1 and parent strains to the beginning of the sorted list of other strains - - MDPText = HT.Span("Samples:", Class="ffl fwb fs12") - MDPMenu1 = HT.Select(name='MDPChoice1') - MDPMenu2 = HT.Select(name='MDPChoice2') - MDPMenu3 = HT.Select(name='MDPChoice3') - MDPMenu1.append(('%s Only' % fd.RISet,'1')) - MDPMenu2.append(('%s Only' % fd.RISet,'1')) - MDPMenu3.append(('%s Only' % fd.RISet,'1')) - MDPMenu1.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu2.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu3.append(('Non-%s Only' % fd.RISet,'2')) - MDPMenu1.append(('All Cases','0')) - MDPMenu2.append(('All Cases','0')) - MDPMenu3.append(('All Cases','0')) - self.MDPRow1.append(HT.TD(MDPText),HT.TD(MDPMenu1)) - self.MDPRow2.append(HT.TD(MDPText),HT.TD(MDPMenu2)) - self.MDPRow3.append(HT.TD(MDPText),HT.TD(MDPMenu3)) - - other_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='other') - - other_table.append(other_header) - for i in range(len(other_body)): - other_table.append(other_body[i]) - else: - pass - - if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ - or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): - fd.allstrainlist = allstrainlist_neworder - - if nCols == 6 and fd.varianceDispName != 'Variance': - mainForm.append(HT.Input(name='isSE', value="yes", type='hidden')) - - primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values - container.append(primary_div) - - if other_strains: - other_div = HT.Div(other_table, Id="other") #Container for table with other (for example, Non-BXD/MDP) strain values - container.append(HT.Div(' ', height=30)) - container.append(other_div) - - table.append(HT.TR(HT.TD(container))) - title5Body.append(table) - - def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'): - #XZ, Aug 23, 2010: I commented the code related to the display of animal case - #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo - - table_body = [] - vals = [] - - for i, strainNameOrig in enumerate(strainlist): - strainName = strainNameOrig.replace("_2nd_", "") - - try: - thisval = thisTrait.data[strainName].val - thisvar = thisTrait.data[strainName].var - thisValFull = [strainName,thisval,thisvar] - except: - continue - - vals.append(thisValFull) - - upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - - for i, strainNameOrig in enumerate(strainlist): - - trId = strainNameOrig - selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") - - strainName = strainNameOrig.replace("_2nd_", "") - strainNameAdd = '' - if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): - strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") - - try: - thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N - if thisNP: - mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) - else: - pass - except: - thisval = thisvar = 'x' - - try: - traitVal = thisval - dispVal = "%2.3f" % thisval - except: - traitVal = '' - dispVal = 'x' - - strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') - - if varianceDataPage: - try: - traitVar = thisvar - dispVar = "%2.3f" % thisvar - except: - traitVar = '' - dispVar = 'x' - - if thisval == 'x': - traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" - - className = 'fs13 b1 c222 ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = 'novalue ' - else: - if (thisval >= upperBound) or (thisval <= lowerBound): - className = 'fs13 b1 c222 outlier ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = 'outlier' - else: - className = 'fs13 b1 c222 ' - valueClassName = 'fs13 b1 c222 valueField ' - rowClassName = ' ' - - if varianceDataPage: - varClassName = valueClassName + str(traitVar) - valueClassName += str(traitVal) - - if strainNameOrig == strainName: - if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list): - ######################################################################################################################################################## - # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user - # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. - ######################################################################################################################################################### - - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, - onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) - else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) - else: - valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, - onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) - if varianceDataPage: - seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, - onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) - - if (strains == 'primary'): - table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) - else: - table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) - - if varianceDataPage: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - table_row.append(HT.TD("±", width=20, align='center', Class=className)) - table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) - else: - table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) - table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) - table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) - - if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': - if len(attribute_ids) > 0: - - #ZS: Get StrainId value for the next query - self.cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSet - WHERE Strain.Name = '%s' and - StrainXRef.StrainId = Strain.Id and - InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (strainName, fd.RISet)) - - strain_id = self.cursor.fetchone()[0] - - attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). - for attribute_id in attribute_ids: - - #ZS: Add extra case attribute values (if any) - self.cursor.execute("""SELECT Value - FROM CaseAttributeXRef - WHERE ProbeSetFreezeId = '%s' AND - StrainId = '%s' AND - CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id))) - - attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any - - #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) - try: - attributeValue = int(attributeValue) - except: - pass - - span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1) - attr_container = HT.Span(attributeValue, Id=span_Id) - attr_className = str(attributeValue) + " " + className - table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) - attr_counter += 1 - - table_body.append(table_row) - return table_body - - def getTableHeader(self, fd, thisTrait, nCols, attribute_names): - - table_header = HT.TR() - - col_class = "fs13 fwb ff1 b1 cw cbrb" - - if nCols == 6: - try: - if fd.varianceDispName: - pass - except: - fd.varianceDispName = 'Variance' - - table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), - HT.TH('Sample', align='right', width=100, Class=col_class), - HT.TH('Value', align='right', width=70, Class=col_class), - HT.TH(' ', width=20, Class=col_class), - HT.TH(fd.varianceDispName, align='right', width=80, Class=col_class)) - - elif nCols == 4: - table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), - HT.TH('Sample', align='right', width=100, Class=col_class), - HT.TH('Value', align='right', width=70, Class=col_class)) - - else: - pass - - if len(attribute_names) > 0: - i=0 - for attribute in attribute_names: - char_count = len(attribute) - cell_width = char_count * 14 - table_header.append(HT.TH(attribute, align='right', width=cell_width, Class="attribute_name " + col_class)) - i+=1 - - return table_header - - - def getSortByValue(self): - - sortby = ("", "") - - return sortby - - diff --git a/web/webqtl/showTrait/ShowBestTrait.py b/web/webqtl/showTrait/ShowBestTrait.py deleted file mode 100755 index 9eb42923..00000000 --- a/web/webqtl/showTrait/ShowBestTrait.py +++ /dev/null @@ -1,195 +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 - -#from base.templatePage import templatePage -#from basicStatistics.BasicStatisticsPage import BasicStatisticsPage -from htmlgen import HTMLgen2 as HT - -from base import webqtlConfig -from utility import webqtlUtil -from base.webqtlTrait import webqtlTrait -from base.templatePage import templatePage -from DataEditingPage import DataEditingPage - - -#class ShowBestTrait(BasicStatisticsPage, templatePage): - -class ShowBestTrait(DataEditingPage): - def __init__(self,fd): - - ########## geneName means symbol ########## - geneName = fd.formdata.getvalue('gene') - if geneName: - geneName = string.strip(geneName) - - refseq = fd.formdata.getvalue('refseq') - if refseq: - refseq = string.strip(refseq) - - genbankid = fd.formdata.getvalue('genbankid') - if genbankid: - genbankid = string.strip(genbankid) - - geneid = fd.formdata.getvalue('geneid') - if geneid: - geneid = string.strip(geneid) - - species = fd.formdata.getvalue('species') - tissue = fd.formdata.getvalue('tissue') - database = fd.formdata.getvalue('database') - - ########## searchAlias is just a singal, so it doesn't need be stripped ########## - searchAlias = fd.formdata.getvalue('searchAlias') - - if not self.openMysql(): - return - - if database: - if geneName: - if searchAlias: - self.cursor.execute(""" SELECT ProbeSetXRef.* - FROM - ProbeSet, ProbeSetXRef, DBList - WHERE - ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - (DBList.Name=%s or DBList.Code=%s) AND - MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE) - ORDER BY ProbeSetXRef.mean DESC - """ , (database, database, geneName)) - else: - self.cursor.execute(""" SELECT ProbeSetXRef.* - FROM - ProbeSet, ProbeSetXRef, DBList - WHERE - ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - (DBList.Name=%s or DBList.Code=%s) AND - ProbeSet.symbol = %s - ORDER BY ProbeSetXRef.mean DESC - """ , (database, database, geneName)) - elif refseq: - self.cursor.execute(""" SELECT ProbeSetXRef.* - FROM - ProbeSet, ProbeSetXRef, DBList - WHERE - ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - (DBList.Name=%s or DBList.Code=%s) AND - ProbeSet.RefSeq_TranscriptId = %s - ORDER BY ProbeSetXRef.mean DESC - """ , (database, database, refseq)) - elif genbankid: - self.cursor.execute(""" SELECT ProbeSetXRef.* - FROM - ProbeSet, ProbeSetXRef, DBList - WHERE - ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - (DBList.Name=%s or DBList.Code=%s) AND - ProbeSet.GenbankId = %s - ORDER BY ProbeSetXRef.mean DESC - """ , (database, database, genbankid)) - elif geneid: - self.cursor.execute(""" SELECT ProbeSetXRef.* - FROM - ProbeSet, ProbeSetXRef, DBList - WHERE - ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - (DBList.Name=%s or DBList.Code=%s) AND - ProbeSet.GeneId = %s - ORDER BY ProbeSetXRef.mean DESC - """ , (database, database, geneid)) - - Results = self.cursor.fetchone() - - - - ########## select the Data that match the selection(currently, only max mean available) ########## - if Results: - ProbeSetFreezeId = Results[0] - ProbeSetId = Results[1] - DataId = Results[2] - - self.cursor.execute(""" - select - InbredSet.Name - from - InbredSet, ProbeFreeze, ProbeSetFreeze - where - InbredSet.Id=ProbeFreeze.InbredSetId and - ProbeFreeze.Id=ProbeSetFreeze.ProbeFreezeId and - ProbeSetFreeze.Id=%s - """, ProbeSetFreezeId) - fd.RISet = self.cursor.fetchone()[0] - #fd.RISet = Results[0] - - self.cursor.execute("select Name, FullName from ProbeSetFreeze where Id=%s", ProbeSetFreezeId) - fd.database, fd.identification = self.cursor.fetchone() - - self.cursor.execute("select Name, symbol, description from ProbeSet where Id=%s", ProbeSetId) - fd.ProbeSetID, fd.symbol, fd.description = self.cursor.fetchone() - - fd.identification += ' : '+fd.ProbeSetID - fd.formdata['fullname'] = fd.database+'::'+fd.ProbeSetID - - #XZ, 03/03/2009: Xiaodong changed Data to ProbeSetData - self.cursor.execute("select Strain.Name, ProbeSetData.Value from Strain, ProbeSetData where Strain.Id=ProbeSetData.StrainId and ProbeSetData.Id=%s", DataId) - Results = self.cursor.fetchall() - - fd.allstrainlist = [] - for item in Results: - fd.formdata[item[0]] = item[1] - fd.allstrainlist.append(item[0]) - - #XZ, 03/12/2009: Xiaodong changed SE to ProbeSetSE - self.cursor.execute("select Strain.Name, ProbeSetSE.error from Strain, ProbeSetSE where Strain.Id = ProbeSetSE.StrainId and ProbeSetSE.DataId=%s", DataId) - Results = self.cursor.fetchall() - for item in Results: - fd.formdata['V'+item[0]] = item[1] - else: - fd.RISet = 'BXD' - fd.database = 'KI_2A_0405_Rz' - fd.ProbeSetID = '1367452_at' - else: - fd.RISet = 'BXD' - fd.database = 'KI_2A_0405_Rz' - fd.ProbeSetID = '1367452_at' - - - #BasicStatisticsPage.__init__(self, fd) - - - thisTrait = webqtlTrait(db=fd.database, name=fd.ProbeSetID, cursor=self.cursor) - thisTrait.retrieveInfo() - thisTrait.retrieveData() - DataEditingPage.__init__(self, fd, thisTrait) - self.dict['title'] = '%s: Display Trait' % fd.identification - - 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 - - - diff --git a/web/webqtl/showTrait/ShowTraitPage.py b/web/webqtl/showTrait/ShowTraitPage.py deleted file mode 100644 index 82511228..00000000 --- a/web/webqtl/showTrait/ShowTraitPage.py +++ /dev/null @@ -1,170 +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 - -from htmlgen import HTMLgen2 as HT - -from base import webqtlConfig -from utility import webqtlUtil -from base.webqtlTrait import webqtlTrait -from base.templatePage import templatePage -from DataEditingPage import DataEditingPage - - - -class ShowTraitPage(DataEditingPage): - - def __init__(self, fd, traitInfos = []): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - if traitInfos: - database,ProbeSetID,CellID = traitInfos - else: - database = fd.formdata.getfirst('database') - ProbeSetID = fd.formdata.getfirst('ProbeSetID') - CellID = fd.formdata.getfirst('CellID') - try: - thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor) - except: - heading = "Trait Data and Analysis Form" - detail = ["The trait isn't available currently."] - self.error(heading=heading,detail=detail,error="Error") - return - - if thisTrait.db.type == "ProbeSet": - - self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers - FROM ProbeSetFreeze WHERE Name = "%s"''' % database) - - indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0] - - if confidential == 1: - access_to_confidential_dataset = 0 - - #for the dataset that confidentiality is 1 - #1. 'admin' and 'root' can see all of the dataset - #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table) - if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']: - access_to_confidential_dataset = 1 - else: - AuthorisedUsersList=AuthorisedUsers.split(',') - if AuthorisedUsersList.__contains__(self.userName): - access_to_confidential_dataset = 1 - - if not access_to_confidential_dataset: - #Error, Confidential Database - heading = "Show Database" - detail = ["The %s database you selected is not open to the public \ - at this time, please go back and select other database." % indFullName] - self.error(heading=heading,detail=detail,error="Confidential Database") - return - - user_ip = fd.remote_ip - query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \ - UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400" - self.cursor.execute(query,user_ip) - daycount = self.cursor.fetchall() - if daycount: - daycount = daycount[0][0] - if daycount > webqtlConfig.DAILYMAXIMUM: - heading = "Retrieve Data" - detail = ['For security reasons, the maximum access to a database is \ - %d times per day per ip address. You have reached the limit, please \ - try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM] - self.error(heading=heading,detail=detail) - return - else: - pass - else: - pass - - if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid: - heading = "Retrieve Data" - detail = ['The Record you requested doesn\'t exist!'] - self.error(heading=heading,detail=detail) - return - - #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore - # check if animal information are available - """ - self.cursor.execute(''' - SELECT - SampleXRef.ProbeFreezeId - FROM - SampleXRef, ProbeSetFreeze - WHERE - SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % thisTrait.db.name) - - sampleId = self.cursor.fetchall() - if sampleId: - thisTrait.strainInfo = 1 - else: - thisTrait.strainInfo = None - """ - - ##identification, etc. - fd.identification = '%s : %s'%(thisTrait.db.shortname,ProbeSetID) - thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ - &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database,ProbeSetID,fd.RISet) - - if CellID: - fd.identification = '%s/%s'%(fd.identification, CellID) - thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) - - #retrieve trait information - try: - thisTrait.retrieveInfo() - thisTrait.retrieveData() - self.updMysql() - self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)" ,user_ip) - self.openMysql() - except: - heading = "Retrieve Data" - detail = ["The information you requested is not avaiable at this time."] - self.error(heading=heading,detail=detail) - return - - ##read genotype file - fd.RISet = thisTrait.riset - fd.readGenotype() - - if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): - fd.displayVariance = 1 - fd.varianceDispName = 'SE' - fd.formID = 'varianceChoice' - - self.dict['body']= thisTrait - DataEditingPage.__init__(self, fd, thisTrait) - self.dict['title'] = '%s: Display Trait' % fd.identification - - diff --git a/web/webqtl/showTrait/__init__.py b/web/webqtl/showTrait/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/showTrait/__init__.py +++ /dev/null diff --git a/web/webqtl/showTrait/exportPage.py b/web/webqtl/showTrait/exportPage.py deleted file mode 100755 index ff3f12a1..00000000 --- a/web/webqtl/showTrait/exportPage.py +++ /dev/null @@ -1,141 +0,0 @@ -import string -import os -import re -import cPickle -import pyXLWriter as xl - -from base import webqtlConfig -from utility import webqtlUtil -from base.templatePage import templatePage - -class ExportPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - filename = webqtlUtil.genRandStr("Export_") - workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+filename)) - style_formats = [] #Array with Excel style formats - Zach 9/2/2011 - heading = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white") #Style for the header cells - right = workbook.add_format(align = 'right') #Style to align cell contents to the right - style_formats.append(heading) - style_formats.append(right) - worksheet = workbook.add_worksheet() - - primaryStrainNames = fd.formdata.getvalue('strainNames', '').split(',') - primaryVals = fd.formdata.getvalue('strainVals', '').split(',') - primaryVars = fd.formdata.getvalue('strainVars', '').split(',') - otherStrainNames = fd.formdata.getvalue('otherStrainNames', '').split(',') - otherVals = fd.formdata.getvalue('otherStrainVals', '').split(',') - otherVars = fd.formdata.getvalue('otherStrainVars', '').split(',') - attributeData = fd.formdata.getvalue('extra_attributes', '') - otherAttributeData = fd.formdata.getvalue('other_extra_attributes', '') - - #ZS: This section is to parse the attribute formdata string - attributeTypes = attributeData.split('/') - otherAttributeTypes = otherAttributeData.split('/') - - attributeNames = [] - attributeVals = [] - for i in range(len(attributeTypes)): - if i < len(attributeTypes) - 1: - attributeNames.append(attributeTypes[i].split(':')[0]) - attributeVals.append(attributeTypes[i].split(':')[1].split(',')) - else: - break - - otherAttributeNames = [] - otherAttributeVals = [] - for i in range(len(otherAttributeTypes)): - if i < len(otherAttributeTypes) - 1: - otherAttributeNames.append(otherAttributeTypes[i].split(':')[0]) - otherAttributeVals.append(otherAttributeTypes[i].split(':')[1].split(',')) - else: - break - - varsExist = 0 #ZS: Even if there are no variances "primaryVars" would still be populated with empty values, so we need to check if there really are any - for i in range(len(primaryVars)): - if primaryVars[i] != '': - varsExist = 1 - break - - otherStrainsExist = 0 #ZS: Same as above; checking to see if there's a set of "other" (non-primary) strains - for i in range(len(otherStrainNames)): - if otherStrainNames[i] != '': - otherStrainsExist = 1 - break - - if varsExist == 1: - column_headers = ["Sample", "Value", " SE "] #ZS: Names of the header for each column in the excel worksheet - else: - column_headers = ["Sample", "Value"] - - - for attr_name in attributeNames: - column_headers.append(attr_name) - - start_line = 0 #Gets last line of "primary" strain values to define a start-point for "other" strain values - for ncol, item in enumerate(column_headers): - worksheet.write([start_line, ncol], item, style_formats[0]) - worksheet.set_column([ncol, ncol], 2*len(item)) - - start_line += 1 - last_line = start_line - - for i in range(len(primaryStrainNames)): - ncol = 0 - if varsExist == 1: - for ncol, item in enumerate([primaryStrainNames[i], primaryVals[i], primaryVars[i]]): - worksheet.write([start_line + i, ncol], item, style_formats[1]) - ncol += 1 - else: - for ncol, item in enumerate([primaryStrainNames[i], primaryVals[i]]): - worksheet.write([start_line + i, ncol], item, style_formats[1]) - ncol += 1 - - for attribute_type in attributeVals: - worksheet.write([start_line + i, ncol], attribute_type[i], style_formats[1]) - ncol += 1 - - last_line += 1 - - if otherStrainsExist == 1: - start_line = last_line + 2 - - for ncol, item in enumerate(column_headers): - worksheet.write([start_line, ncol], item, style_formats[0]) - worksheet.set_column([ncol, ncol], 2*len(item)) - start_line += 1 - - for i in range(len(otherStrainNames)): - ncol = 0 - if varsExist == 1: - for ncol, item in enumerate([otherStrainNames[i], otherVals[i], otherVars[i]]): - worksheet.write([start_line + i, ncol], item, style_formats[1]) - ncol += 1 - else: - for ncol, item in enumerate([otherStrainNames[i], otherVals[i]]): - worksheet.write([start_line + i, ncol], item, style_formats[1]) - - for attribute_type in otherAttributeVals: - worksheet.write([start_line + i, ncol], attribute_type[i], style_formats[1]) - ncol += 1 - - workbook.close() - - full_filename = os.path.join(webqtlConfig.TMPDIR, '%s.xls' % filename) - fp = open(full_filename, 'rb') - text = fp.read() - fp.close() - - self.content_type = 'application/xls' - self.content_disposition = 'attachment; filename=%s' % ('%s.xls' % filename) - self.attachment = text - - - - - - - diff --git a/web/webqtl/showTrait/testTraitPage.py b/web/webqtl/showTrait/testTraitPage.py deleted file mode 100755 index 322bf3dc..00000000 --- a/web/webqtl/showTrait/testTraitPage.py +++ /dev/null @@ -1,36 +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 - -from base.webqtlFormData import webqtlFormData -from DataEditingPage import DataEditingPage - -def testTraitPage(): - fd = webqtlFormData() - fd.Sample() - page = DataEditingPage(fd) - return page - - |