def traitInfo(self, fd, specialStrains = None):
        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
        heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (species.title(), fd.RISet) , HT.BR())
        if self.Trait:
            trait_url = HT.Href(text=self.Trait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \
                            "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (self.Trait.db.name, self.Trait.name), \
                            target='_blank', Class="fs13 fwn")
            heading2.append(HT.Strong("Database: "),
                    HT.Href(text=self.Trait.db.fullname, url = webqtlConfig.INFOPAGEHREF % self.Trait.db.name ,
                            target='_blank',Class="fs13 fwn"),HT.BR())
            if self.Trait.db.type == 'ProbeSet':
                heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(),
                        HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.symbol,id="green"),HT.BR())
                if self.Trait.chr and self.Trait.mb:
                    heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb))
            elif self.Trait.db.type == 'Geno':
                heading2.append(HT.Strong('Locus : '), trait_url, HT.BR())
                #heading2.append(HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.Symbol,id="green"),HT.BR())
                if self.Trait.chr and self.Trait.mb:
                    heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb))
            elif self.Trait.db.type == 'Publish':
                heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR())
                heading2.append(HT.Strong('Phenotype: '), self.Trait.phenotype, HT.BR())
                heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR())
            elif self.Trait.db.type == 'Temp':
                heading2.append(HT.Strong('Description: '), self.Trait.description, HT.BR())
                #heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR())
            else:
                pass
        else:
            heading2.append(HT.Strong("Trait Name: "), fd.identification)

        if specialStrains:
            mdpform = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='MDP_Form',submit=HT.Input(type='hidden'))
            mdphddn = {'FormID':'dataEditing', 'submitID':'basicStatistics','RISet':fd.RISet, "allstrainlist":string.join(fd.allstrainlist, " "), "ptype":self.plotType, 'identification':fd.identification, "incparentsf1":1}
            if self.fullname:  mdphddn['fullname'] = self.fullname
            webqtlUtil.exportData(mdphddn, fd.allTraitData)
            for key in mdphddn.keys():
                mdpform.append(HT.Input(name=key, value=mdphddn[key], type='hidden'))
            btn0 = HT.Input(type='button' ,name='',value='All Cases',onClick="this.form.ptype.value=0;submit();", Class="button")
            btn1 = HT.Input(type='button' ,name='',value='%s Only' % fd.RISet,onClick="this.form.ptype.value=1;submit();", Class="button")
            btn2 = HT.Input(type='button' ,name='',value='MDP Only', onClick="this.form.ptype.value=2;submit();", Class="button")
            mdpform.append(btn0)
            mdpform.append(btn1)
            mdpform.append(btn2)
            heading2.append(HT.P(), mdpform)

        return HT.Span(heading2)
Ejemplo n.º 2
0
	def gentextfile(self, db, text):
		#
		db.getRISet()
		info = self.getinfo(db.name)
		#
		group = db.riset
		species = webqtlDatabaseFunction.retrieveSpecies(self.cursor, group)
		type = info[4]
		database = db.fullname
		#
		metadatainfofile = "http://www.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s" % info[1]
		originaldata = "http://datafiles.genenetwork.org/download/GN%s/" % info[1]
		contactinformation = "%s %s, %s, %s, %s, %s %s %s, Tel. %s, %s" % (info[22], info[23], info[33], info[24], info[25], info[26], info[27], info[28], info[29], info[30])
		#
		attachment = ""
		attachment += ("Data source: GeneNetwork http://www.genenetwork.org/\n")
		attachment += ("Citations: http://www.genenetwork.org/reference.html\n")
		
		attachment += ("Species: %s\n" % species)
		attachment += ("Group: %s\n" % group)
		attachment += ("Type: %s\n" % type)
		attachment += ("Database: %s\n" % database)
		
		attachment += ("Metadata info file: %s\n" % metadatainfofile)
		attachment += ("Original data: %s\n" % originaldata)
		attachment += ("Contact Information: %s\n" % contactinformation)
		
		attachment += ("Date: %s\n" % time.strftime("%B %d, %Y", time.gmtime()))
		attachment += ("Time: %s\n" % time.strftime("%H:%M", time.gmtime()))
		
		attachment += "\n"
		attachment += ("Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)\n")
		attachment += ("PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE\n")
		attachment += "\n"
		
		rowindex = 0
		for row in text:
			if rowindex == 0:
				row.insert(0, 'Index')
			else:
				row.insert(0, rowindex)
			rowindex += 1
			attachment += string.join(map(lambda cell : str(cell).replace("\r\n", " ").strip(), row), '\t') + "\n"
		
		self.content_type = 'text/plain'
		self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
		self.attachment = attachment
Ejemplo n.º 3
0
    def __init__(self, fd):

        templatePage.__init__(self, fd)

        if not self.openMysql():
            return

        searchResult = fd.formdata.getvalue("searchResult")

        if not searchResult:
            heading = "Partial Correlation"
            detail = ["You need to select at least three traits in order to calculate partial correlation."]
            self.error(heading=heading, detail=detail)
            return

        ## Adds the Trait instance for each trait name from the collection
        traits = []

        for item in searchResult:
            traits.append(webqtlTrait(fullname=item, cursor=self.cursor))

        RISet = fd.formdata.getvalue("RISet")
        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)

        # XZ: HTML part
        TD_LR = HT.TD(colspan=2, height=200, width="100%", bgColor="#eeeeee")
        TD_LR.append(
            "Please select one primary trait, one to three control traits, and at least one target trait.", HT.P()
        )

        mainFormName = "showDatabase"
        mainForm = HT.Form(
            cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
            name=mainFormName,
            submit=HT.Input(type="hidden"),
        )

        # XZ: Add hidden form values
        hddn = {
            "FormID": "calPartialCorrTrait",
            "database": "",
            "ProbeSetID": "",
            "CellID": "",  # XZ: These four parameters are required by javascript function showDatabase2.
            "controlTraits": "",
            "primaryTrait": "",
            "targetTraits": "",
            "pcMethod": "",
            "RISet": RISet,
        }

        for key in hddn.keys():
            mainForm.append(HT.Input(type="hidden", name=key, value=hddn[key]))

        radioNames = []

        for thisTrait in traits:
            oneRadioName = thisTrait.getName()
            radioNames.append(oneRadioName)

        radioNamesString = ",".join(radioNames)

        # Creates the image href that runs the javascript setting all traits as target or ignored
        setAllTarget = HT.Href(
            url="#redirect",
            onClick="setAllAsTarget(document.getElementsByName('showDatabase')[0], '%s');" % radioNamesString,
        )
        setAllTargetImg = HT.Image("/images/select_all.gif", alt="Select All", title="Select All", style="border:none;")
        setAllTarget.append(setAllTargetImg)
        setAllIgnore = HT.Href(
            url="#redirect",
            onClick="setAllAsIgnore(document.getElementsByName('showDatabase')[0], '%s');" % radioNamesString,
        )
        setAllIgnoreImg = HT.Image("/images/select_all.gif", alt="Select All", title="Select All", style="border:none;")
        setAllIgnore.append(setAllIgnoreImg)

        tblobj = {}
        tblobj["header"] = self.getCollectionTableHeader()

        sortby = self.getSortByValue()

        tblobj["body"] = self.getCollectionTableBody(traitList=traits, formName=mainFormName, species=species)

        filename = webqtlUtil.genRandStr("Search_")

        objfile = open("%s.obj" % (webqtlConfig.TMPDIR + filename), "wb")
        cPickle.dump(tblobj, objfile)
        objfile.close()

        div = HT.Div(
            webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="1"),
            Id="sortable",
        )

        mainForm.append(div)

        # XZ: Add button
        radioNamesString = ",".join(radioNames)
        jsCommand_1 = "validateTrait(this.form, '" + radioNamesString + "', 0, 1);"
        jsCommand_2 = "validateTrait(this.form, '" + radioNamesString + "', 0, 2);"
        partialCorrTraitButton_1 = HT.Input(
            type="button",
            name="submitPartialCorrTrait_1",
            value="Pearson's r",
            onClick="%s" % jsCommand_1,
            Class="button",
        )
        partialCorrTraitButton_2 = HT.Input(
            type="button",
            name="submitPartialCorrTrait_2",
            value="Spearman's rho",
            onClick="%s" % jsCommand_2,
            Class="button",
        )
        mainForm.append(
            HT.BR(),
            "Compute partial correlation for target selected above:",
            HT.BR(),
            partialCorrTraitButton_1,
            partialCorrTraitButton_2,
            HT.BR(),
            HT.BR(),
            HT.HR(color="gray", size=3),
        )

        jsCommand = "validateTrait(this.form, '" + radioNamesString + "', 1);"
        partialCorrDBButton = HT.Input(
            type="button", name="submitPartialCorrDB", value="Calculate", onClick="%s" % jsCommand, Class="button"
        )

        methodText = HT.Span("Calculate:", Class="ffl fwb fs12")

        methodMenu = HT.Select(name="method")
        methodMenu.append(("Genetic Correlation, Pearson's r", "1"))
        methodMenu.append(("Genetic Correlation, Spearman's rho", "2"))
        methodMenu.append(("SGO Literature Correlation", "3"))
        methodMenu.append(("Tissue Correlation, Pearson's r", "4"))
        methodMenu.append(("Tissue Correlation, Spearman's rho", "5"))

        databaseText = HT.Span("Choose Database:", Class="ffl fwb fs12")
        databaseMenu = HT.Select(name="database2")

        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'
            % (RISet, webqtlConfig.PUBLICTHRESH)
        )
        for item in self.cursor.fetchall():
            databaseMenu.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'
            % (RISet, webqtlConfig.PUBLICTHRESH)
        )
        for item in self.cursor.fetchall():
            databaseMenu.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, RISet)
            )
            for item2 in self.cursor.fetchall():
                databaseMenuSub.append(item2)
                nmenu += 1
            databaseMenu.append(databaseMenuSub)

        if nmenu:
            criteriaText = HT.Span("Return:", Class="ffl fwb fs12")
            criteriaMenu = HT.Select(name="criteria", selected="500")
            criteriaMenu.append(("top 100", "100"))
            criteriaMenu.append(("top 200", "200"))
            criteriaMenu.append(("top 500", "500"))
            criteriaMenu.append(("top 1000", "1000"))
            criteriaMenu.append(("top 2000", "2000"))
            criteriaMenu.append(("top 5000", "5000"))
            criteriaMenu.append(("top 10000", "10000"))
            criteriaMenu.append(("top 15000", "15000"))
            criteriaMenu.append(("top 20000", "20000"))

            self.MPDCell = HT.TD()
            correlationMenus = HT.TableLite(
                HT.TR(HT.TD(databaseText, HT.BR(), databaseMenu, colspan=4)),
                HT.TR(HT.TD(methodText, HT.BR(), methodMenu), self.MPDCell, HT.TD(criteriaText, HT.BR(), criteriaMenu)),
                border=0,
                cellspacing=4,
                cellpadding=0,
            )
        else:
            correlationMenus = ""

        mainForm.append(
            HT.Font("or", color="red", size=4),
            HT.BR(),
            HT.BR(),
            "Compute partial correlation for each trait in the database selected below:",
            HT.BR(),
        )
        mainForm.append(partialCorrDBButton, HT.BR(), HT.BR(), correlationMenus)

        TD_LR.append(mainForm)

        self.dict["body"] = str(TD_LR)
        self.dict["js1"] = ""
        self.dict["title"] = "Partial Correlation Input"
	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'] = ''
Ejemplo n.º 5
0
    def writeHTML(self,fd):
        TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top")
        pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
        tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left")
        seq = 1
        SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")

        mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}")
        mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
        mintmap.append(mintmap_img)
        mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}")
        mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;")
        mcorr.append(mcorr_img)
        cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}")
        cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
        cormatrix.append(cormatrix_img)
        networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}")
        networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;")
        networkGraph.append(networkGraph_img)
        heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}")
        heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
        heatmap.append(heatmap_img)
        partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}")
        partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
        partialCorr.append(partialCorr_img)

        BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}")
        networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;")
        BN.append(networkGraph_img)

        removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet)
        removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;")
        removeselect.append(removeselect_img)
        selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);")
        selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
        selectall.append(selectall_img)
        reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);")
        reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
        reset.append(reset_img)
        exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');")
        exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;")
        exportSelect.append(exportSelect_img)
        selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);")
        selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
        selectinvert.append(selectinvert_img)

        chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')

        importFile = HT.Input(type='file', name='importfile', size=15)
        importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button")
        exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button")
        importMenu = HT.Select(name='importmethod')
        importMenu.append(('append','append'))
        importMenu.append(('replace','replace'))

        GeneWeaver = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');")
        GeneWeaver_img = HT.Image("/images/ODE_logo_final.jpg", name="GeneWeaver", alt="GeneWeaver", title="GeneWeaver", style="border:none")
        GeneWeaver.append(GeneWeaver_img)

        GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');")
        GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
        GCATButton.append(GCATButton_img)

        GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');")
        GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
        GeneSet.append(GeneSet_img)
        
        BNW = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'BNW');")
        BNW_img = HT.Image("/images/bnw.jpg", name="BNW", alt="Bayesian Network Webserver", title="Bayesian Network Webserver", style="border:none; width:57px; height:55px;")
        BNW.append(BNW_img)

        #need to be refined
        if fd.genotype.Mbmap:
            scale = HT.Input(name="scale", value="physic", type="hidden")
        else:
            scale = ""

        formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))

        #XZ, July 22, 2011: I add parameters for interval mapping
        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None}
        for key in hddn.keys():
            formMain.append(HT.Input(name=key, value=hddn[key], type='hidden'))

        if not self.searchResult:
            SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
            formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton)
            TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain))
            self.dict['body'] = str(TD_LR)
            self.dict['title'] = "%s Trait Collection" % fd.RISet
            return

        #########################################
        # Creating table object for AJAX table  #
        #########################################
        tblobj = {}
        mainfmName = 'showDatabase'
        # NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py;
        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
        if species == 'human':
            chrMenu = scale = mintmap = heatmap = ""

        tblobj['header'] = self.getCollectionTableHeader()

        sortby = self.getSortByValue()

        thisRISet = fd.RISet
        tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species)

        filename= webqtlUtil.genRandStr("Search_")

        objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
        cPickle.dump(tblobj, objfile)
        objfile.close()


        div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable")


        containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
        postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")

        optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0, width="640", border=0, align="Left")
        optionsTable.append(HT.TR(
            HT.TD(selectall,	width="77", style="text-align:center"),
            HT.TD(reset,		width="77", style="text-align:center"),
            HT.TD(selectinvert, width="77", style="text-align:center"),
            HT.TD(removeselect, width="77", style="text-align:center"),
            HT.TD(exportSelect, width="77", style="text-align:center"),
			HT.TD("&nbsp;",		width="8"),
            HT.TD(GeneWeaver,	width="77", style="text-align:center"),
            HT.TD(GCATButton,	width="77", style="text-align:center"),
            HT.TD(GeneSet,		width="77", style="text-align:center"),
            HT.TD(BNW,			width="77", style="text-align:center")))
        optionsTable.append(HT.TR(
            HT.TD("Select",						style="text-align:center"),
            HT.TD("Deselect",					style="text-align:center"),
            HT.TD("Invert",						style="text-align:center"),
            HT.TD("Remove",						style="text-align:center"),
            HT.TD("Export",						style="text-align:center"),
			HT.TD("&nbsp;"),
            HT.TD("Gene", HT.BR(), "Weaver",	style="text-align:center"),
            HT.TD("GCAT",						style="text-align:center"),
            HT.TD("Gene Set",					style="text-align:center"),
            HT.TD("BNW",						style="text-align:center")))
        postContainerTable.append(HT.TR(HT.TD(optionsTable)))
        containerTable.append(HT.TR(HT.TD(optionsTable)))

        functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left")
        functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap))
        if species == "human":
            labelRow = HT.TR(HT.TD("&nbsp;"*2,HT.Text("Graph")), HT.TD("&nbsp;"*2,HT.Text("Matrix")), HT.TD("&nbsp;"*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
        else:
            labelRow = HT.TR(HT.TD("&nbsp;"*2,HT.Text("Graph")), HT.TD("&nbsp;"*2,HT.Text("Matrix")), HT.TD("&nbsp;"*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
        functionTable.append(functionRow, labelRow)
        postContainerTable.append(HT.TR(HT.TD(functionTable)))
        containerTable.append(HT.TR(HT.TD(functionTable)))
        containerTable.append(HT.TR(HT.TD("&nbsp;")))

        pageTable.append(HT.TR(HT.TD(containerTable)))
        chrMenu = scale = ""

        pageTable.append(HT.TR(HT.TD(div)))
        pageTable.append(HT.TR(HT.TD("&nbsp;")))
        if len(self.theseTraits) > 20:
            pageTable.append(HT.TR(HT.TD(postContainerTable)))
        pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, '&nbsp;'*10, exportButton)))
            #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010
        formMain.append(chrMenu,scale,pageTable)

        #Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js
        self.dict['js1'] = ''
        TD_LR.append(SelectionHeading,formMain)

        self.dict['body'] = str(TD_LR)
        self.dict['js2'] = 'onLoad="pageOffset()"'
        self.dict['layer'] = self.generateWarningLayer()
        self.dict['title'] = "%s Trait Collection" % thisRISet
Ejemplo n.º 6
0
	def __init__(self,fd):

		self.theseTraits = []
		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
		
		templatePage.__init__(self, fd)

		if not self.openMysql():
			return

		self.searchResult = fd.formdata.getvalue('searchResult', [])
		if type("1") == type(self.searchResult):
			self.searchResult = [self.searchResult]

		#XZ, self.theseTraits holds the "ProbeSet" traits.

		for item in self.searchResult:
			try:
				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
				thisTrait.retrieveInfo(QTL=1)
				if thisTrait.db.type == "ProbeSet":
					self.theseTraits.append(thisTrait)
			except:
				pass
				
		if self.theseTraits:
			pass
		else:
			templatePage.__init__(self, fd)
			heading = 'WebGestalt'
			detail = ['You need to select at least one microarray trait to submit.']
			self.error(heading=heading,detail=detail)
			return
			
		chipName = self.testChip(fd)

		#XZ, 8/24/2009: the name of arraylist is misleading. It holds the name of traits.
		arraylist, geneIdList = self.genGeneIdList(fd)
		
		target_url = "http://bioinfo.vanderbilt.edu/webgestalt/webgestalt.php"
		
		formWebGestalt = HT.Form(cgi=target_url, enctype='multipart/form-data', name='WebGestalt', submit = HT.Input(type='hidden'))

		id_type = chipName

		hddnWebGestalt = {'id_list':string.join(arraylist, ","),
				  'id_type':id_type}
		
		hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
		hddnWebGestalt['analysis_type'] = 'GO'
		hddnWebGestalt['significancelevel'] = '.05'
		hddnWebGestalt['stat'] = 'Hypergeometric'
		hddnWebGestalt['mtc'] = 'BH'
		hddnWebGestalt['min'] = '2'
		hddnWebGestalt['id_value'] = fd.formdata.getvalue('correlation') 
			
                species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)

                if species == 'rat':
                    hddnWebGestalt['org'] = 'Rattus norvegicus'
                elif species == 'human':
                    hddnWebGestalt['org'] = 'H**o sapiens'
                elif species == 'mouse':
                    hddnWebGestalt['org'] = 'Mus musculus'
                else:
                    hddnWebGestalt['org'] = ''

		hddnWebGestalt['org'] = hddnWebGestalt['org'].replace(' ','_')
		
		for key in hddnWebGestalt.keys():
				formWebGestalt.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
	
		TD_LR.append(formWebGestalt)

		TD_LR.append(HT.Paragraph("Your selection of %d traits is being submitted to GO Tree" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
		
		# updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
		#                moved unknownChipError() to webqtl.js and change it to unknownChipError(chipName)
		if chipName == 'mixed':
			methodName = "WebGestalt"
			self.dict['js1'] = """
				<SCRIPT LANGUAGE="JavaScript">		
					setTimeout("mixedChipError('%s')" ,1000);
				</SCRIPT>
			""" % methodName 
		elif chipName.find('_NA') > 0:
			chipName = chipName[0:-3]
			self.dict['js1'] = """
                <SCRIPT LANGUAGE="JavaScript">
                setTimeout("unknownChipError('%s')",1000);
                </SCRIPT>
            """ % chipName
		else:
			self.dict['js1'] = """
				<SCRIPT LANGUAGE="JavaScript">
					setTimeout('document.WebGestalt.submit()',1000);
				</SCRIPT>
			"""
			
		self.dict['body'] = TD_LR
Ejemplo n.º 7
0
    def __init__(self,fd):

        templatePage.__init__(self, fd)

        if not self.openMysql():
            return

        #XZ, self.theseTraits holds the "ProbeSet" traits.
        self.theseTraits = []

        self.searchResult = fd.formdata.getvalue('searchResult', [])
        if type("1") == type(self.searchResult):
            self.searchResult = [self.searchResult]

        for item in self.searchResult:
            try:
                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
                thisTrait.retrieveInfo(QTL=1)
                if thisTrait.db.type == "ProbeSet":
                    self.theseTraits.append(thisTrait)
            except:
                pass

        if self.theseTraits:
            pass
        else:
            heading = 'ODE'
            detail = ['You need to select at least one microarray trait to submit.']
            self.error(heading=heading,detail=detail)
            return

        chipName = self.getChipName(fd)
        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)

        if species == 'rat':
            species = 'Rattus norvegicus'
        elif species == 'human':
            species = 'H**o sapiens'
        elif species == 'mouse':
            species = 'Mus musculus'
        else:
            species = ''

        probesetNameList = self.getProbesetNameList(fd)

        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")

        formODE = HT.Form(cgi="http://ontologicaldiscovery.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))

        hddnODE = {}

        hddnODE['client'] = 'genenetwork'
        hddnODE['species'] = species
        hddnODE['idtype'] = chipName
        hddnODE['list'] = string.join(probesetNameList, ",")

        for key in hddnODE.keys():
            formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))

        TD_LR.append(formODE)

        TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
        # updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)		
        if chipName == 'mixed':
            methodName = "ODE" 	
            self.dict['js1'] = """
                <SCRIPT LANGUAGE="JavaScript">
                    setTimeout("mixedChipError('%s')",1000);
                </SCRIPT>
                        """ % methodName 
        else:
            self.dict['js1'] = """
                <SCRIPT LANGUAGE="JavaScript">
                    setTimeout('document.formODE.submit()',1000);
                </SCRIPT>
                """

        self.dict['body'] = TD_LR