#Note that although this module gets imported a bit, the dict columnNames is never used outside this code. #Also note that snpBrowser also defines a columnNames dict; it's different. -KA from htmlgen import HTMLgen2 as HT import os import time import pyXLWriter as xl import GeneUtil from base.templatePage import templatePage from utility import webqtlUtil from base import webqtlConfig _scriptfile = "main.py?FormID=qtlminerresult" #A dictionary that lets us map the html form names "txStart_mm6" -> "Mb Start (mm8)" #the first item is the short name (column headers) and the second item is the long name (dropdown list) # [short name, long name, category] columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], "GeneDescription" : ["Description", "Gene Description", 'species'], # "probeset" : ["ProbeSet", "ProbeSet", 'gene'], # "probesetsymbolA" : ["ProbeSet Symbol A", "ProbeSetsymbolA", 'gene'], # "probesetchrA" : ["probesetchrA", "probesetchrA", 'gene'], "hassnp" : ["Has nsSNP", "Has nsSNP", 'gene'], "hasindel" : ["Has indel", "Has indel", 'gene'], "hasexpr" : ["Has expr", "Has expression", 'gene'], "hascis" : ["Has cis", "Has cis regulation", 'gene'], "score" : ["Score", "Score", 'gene'], "meanA" : ["Expression A", "Expression in dataset 1", 'gene'], "meanB" : ["Expression B", "Expression in dataset 2", 'gene'], "meanC" : ["Expression C", "Expression in dataset 3", 'gene'], "probesetcisA" : ["Cis A", "Cis regulation in dataset 1", 'gene'], "probesetcisB" : ["Cis B", "Cis regulation in dataset 2", 'gene'], "probesetcisC" : ["Cis C", "Cis regulation in dataset 3", 'gene'], "probesetA" : ["ProbeSet A", "ProbeSet in dataset 1", 'gene'], "probesetB" : ["ProbeSet B", "ProbeSet in dataset 2", 'gene'], "probesetC" : ["ProbeSet C", "ProbeSet in dataset 3", 'gene'], "goterms" : ["GO biological process", "GO biological process", 'gene'], "pathways" : ["KEGG PathwayIDs", "KEGG PathwayIDs", 'gene'], "pathwaynames" : ["KEGG Pathways", "KEGG Pathways", 'gene'], # "newlrsA" : ["Lrs A", "lrs A", 'gene'], # "probesetchrB" : ["probesetchrB", "probesetchrB", 'gene'], # "newlrsB" : ["lrs B", "lrs B", 'gene'], # "probesetchrC" : ["probesetchrC", "probesetchrC", 'gene'], # "newlrsC" : ["lrs C", "lrs C", 'gene'], 'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], 'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], 'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'], "ProteinID" : ["Prot ID", "Protein ID", 'protein'], "Chromosome" : ["Chr", "Chromosome", 'species'], "TxStart" : ["Start", "Mb Start", 'species'], "TxEnd" : ["End", "Mb End", 'species'], "GeneLength" : ["Length", "Kb Length", 'species'], "cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], "cdsEnd" : ["CDS End", "Mb CDS End", 'species'], "exonCount" : ["Num Exons", "Exon Count", 'species'], "exonStarts" : ["Exon Starts", "Exon Starts", 'species'], "exonEnds" : ["Exon Ends", "Exon Ends", 'species'], "Strand" : ["Strand", "Strand", 'species'], "GeneID" : ["Gene ID", "Gene ID", 'species'], "GenBankID" : ["GenBank", "GenBank ID", 'species'], "UnigenID" : ["Unigen", "Unigen ID", 'species'], "NM_ID" : ["NM ID", "NM ID", 'species'], "kgID" : ["kg ID", "kg ID", 'species'], "snpCountall" : ["SNPs", "SNP Count", 'species'], "snpCountmis": ["nsSNPs all", "nsSNP Count all strains", 'species'], "snpCountmissel": ["nsSNPs selected", "nsSNP Count selected strains", 'species'], "snpDensity" : ["SNP Density", "SNP Density", 'species'], "indelCountBXD" : ["Indels in BXD mice", "Indel Count in BXD mice", 'species'], "lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], "lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], "pearson" : ["Pearson", "Pearson Product Moment", 'misc'], "literature" : ["Lit Corr", "Literature Correlation", 'misc'], } ###Species Freeze speciesFreeze = {'mouse':'mm9', 'rat':'rn3', 'human':'hg19'} for key in speciesFreeze.keys(): speciesFreeze[speciesFreeze[key]] = key class QTLminer (templatePage): ### filename = webqtlUtil.genRandStr("Itan_") javascript_content = """ <SCRIPT language="JAVASCRIPT"> function update4(self,form) { self.database='leeg'; } </SCRIPT> """ def __init__(self, fd): templatePage.__init__(self, fd) if not self.openMysql(): return self.species = fd.formdata.getvalue("species", "mouse") try: self.startMb = float(fd.formdata.getvalue("startMb")) except: self.startMb = 173 try: self.endMb = float(fd.formdata.getvalue("endMb")) except: self.endMb = self.startMb + 1 self.Chr = fd.formdata.getvalue("chromosome", "1") ######################################################### FOR A ###### species self.cursor.execute(""" Select Name, Id from Species Order by Id """ ) res = self.cursor.fetchall() self.spA = res self.spAsel = fd.formdata.getvalue("myspeciesA", "mouse") if not hasattr(self,"spA"): self.spA = res2 self.spAsel = 'mouse' ###### group self.cursor.execute(""" select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name """ % self.spAsel) res = self.cursor.fetchall() if not hasattr(self,"grA"): self.grA = res self.grAsel = 'BXD' if fd.formdata.getvalue('submitter') == 'a1': self.grA = res self.grAsel = self.grA[0][0] else: self.grAsel = fd.formdata.getvalue("groupA","BXD") ###### type self.cursor.execute(""" select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name """ % (self.grAsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"tyA"): self.tyA = res self.tyAsel = 'Hippocampus' if fd.formdata.getvalue('submitter') in ['a1','a2'] : self.tyA = res self.tyAsel = self.tyA[0][0] else: self.tyAsel = fd.formdata.getvalue("typeA","Hippocampus") ###### database self.cursor.execute(""" select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc """ % (self.grAsel,self.tyAsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"daA"): self.daA = res self.daAsel = 'HC_M2_0606_P' if fd.formdata.getvalue('submitter') in ['a1','a2','a3'] : self.daA = res self.daAsel = self.daA[0][0] else: self.daAsel = fd.formdata.getvalue("databaseA","HC_M2_0606_P") ######################################################### FOR B ###### species self.cursor.execute(""" Select Name, Id from Species Order by Id """ ) res = self.cursor.fetchall() self.spB = res self.spBsel = fd.formdata.getvalue("myspeciesB", "mouse") if not hasattr(self,"spB"): self.spB = res self.spBsel = 'mouse' ###### group self.cursor.execute(""" select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name """ % self.spBsel) res = self.cursor.fetchall() if not hasattr(self,"grB"): self.grB = res self.grBsel = 'CXB' if fd.formdata.getvalue('submitter') == 'b1': self.grB = res self.grBsel = self.grB[0][0] else: self.grBsel = fd.formdata.getvalue("groupB","CXB") ###### type self.cursor.execute(""" select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name """ % (self.grBsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"tyB"): self.tyB = res self.tyBsel = 'Hippocampus' if fd.formdata.getvalue('submitter') in ['b1','b2'] : self.tyB = res self.tyBsel = self.tyB[0][0] else: self.tyBsel = fd.formdata.getvalue("typeB","Hippocampus") ###### database self.cursor.execute(""" select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc """ % (self.grBsel,self.tyBsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"daB"): self.daB = res self.daBsel = 'HC_M2CB_1205_R' if fd.formdata.getvalue('submitter') in ['b1','b2','b3'] : self.daB = res self.daBsel = self.daB[0][0] else: self.daBsel = fd.formdata.getvalue("databaseB","HC_M2CB_1205_R") ######################################################### FOR C ###### species self.cursor.execute(""" Select Name, Id from Species Order by Id """ ) res = self.cursor.fetchall() self.spC = res self.spCsel = fd.formdata.getvalue("myspeciesC", "mouse") if not hasattr(self,"spC"): self.spC = res self.spCsel = 'mouse' ###### group self.cursor.execute(""" select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name """ % self.spCsel) res = self.cursor.fetchall() if not hasattr(self,"grC"): self.grC = res self.grCsel = 'LXS' if fd.formdata.getvalue('submitter') == 'c1': self.grC = res self.grCsel = self.grC[0][0] else: self.grCsel = fd.formdata.getvalue("groupC","LXS") ###### type self.cursor.execute(""" select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name """ % (self.grCsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"tyC"): self.tyC = res self.tyCsel = 'Hippocampus' if fd.formdata.getvalue('submitter') in ['c1','c2'] : self.tyC = res self.tyCsel = self.tyC[0][0] else: self.tyCsel = fd.formdata.getvalue("typeC","Hippocampus") ###### database self.cursor.execute(""" select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc """ % (self.grCsel,self.tyCsel,webqtlConfig.PUBLICTHRESH)) res = self.cursor.fetchall() if not hasattr(self,"daC"): self.daC = res self.daCsel = 'Illum_LXS_Hipp_loess0807' if fd.formdata.getvalue('submitter') in ['c1','c2','c3'] : self.daC = res self.daCsel = self.daC[0][0] else: self.daCsel = fd.formdata.getvalue("databaseC","Illum_LXS_Hipp_loess0807") # self.myspeciesA = fd.formdata.getvalue("myspeciesA", "mouse") # self.groupA = fd.formdata.getvalue("groupA", "BXD") # self.typeA = fd.formdata.getvalue("typeA", "Spleen") # self.databaseA = fd.formdata.getvalue("databaseA", "IoP_SPL_RMA_0509")# # self.myspeciesB = fd.formdata.getvalue("myspeciesB", "mouse") # self.groupB = fd.formdata.getvalue("groupB", "BXD") # self.typeB = fd.formdata.getvalue("typeB", "Spleen") # self.databaseB = fd.formdata.getvalue("databaseB", "IoP_SPL_RMA_0509") self.xls = fd.formdata.getvalue("xls", "1") try: s1 = int(fd.formdata.getvalue("s1")) s2 = int(fd.formdata.getvalue("s2")) self.diffColDefault = self.diffCol = [s1, s2] except: self.diffColDefault = self.diffCol = [] if self.species != 'mouse': self.diffColDefault = [2, 3]#default is B6 and D2 for other species self.str1 = fd.formdata.getvalue("str1", "C57BL/6J") self.str2 = fd.formdata.getvalue("str2", "DBA/2J") self.sorton = fd.formdata.getvalue("sorton", "Position") controlFrm, dispFields, dispFields2 = self.genControlForm(fd) ## if not fd.formdata.getvalue('submitter') in ['a1','a2','a3''a4'] : self.cursor.execute("""select Id from Strain where Name='%s' """ % self.str1 ) strain1 = self.cursor.fetchone()[0] self.cursor.execute("""select Id from Strain where Name='%s' """ % self.str2 ) strain2 = self.cursor.fetchone()[0] filename='' if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"): geneTable, filename = self.genGeneTable(fd, dispFields, strain1, strain2) infoTD = HT.TD(width=400, valign= "top") infoTD.append(HT.Paragraph("QTLminer : Chr %s" % self.Chr, Class="title"), # HT.Strong("Species : "), self.species.title(), HT.BR(), # HT.Strong("myspeciesA : "), self.myspeciesA, HT.BR(), # HT.Strong("groupA : "), self.groupA, HT.BR(), # HT.Strong("typeA : "), self.typeA, HT.BR(), # HT.Strong("databaseA : "), self.databaseA, HT.BR(), # HT.Strong("myspeciesB : "), self.myspeciesB, HT.BR(), # HT.Strong("groupB : "), self.groupB, HT.BR(), # HT.Strong("typeB : "), self.typeB, HT.BR(), # HT.Strong("databaseB : "), self.databaseB, HT.BR(), # HT.Strong("spAsel : "), self.spAsel, HT.BR(), # HT.Strong("grAsel : "), self.grAsel, HT.BR(), # HT.Strong("tyAsel : "), self.tyAsel, HT.BR(), # HT.Strong("daAsel : "), self.daAsel, HT.BR(), # HT.Strong("spBsel : "), self.spBsel, HT.BR(), # HT.Strong("grBsel : "), self.grBsel, HT.BR(), # HT.Strong("tyBsel : "), self.tyBsel, HT.BR(), # HT.Strong("daBsel : "), self.daBsel, HT.BR(), # HT.Strong("chr : "), self.Chr, HT.BR(), # HT.Strong("formdata.submitter :"), fd.formdata.getvalue("submitter"), HT.BR(), # HT.Strong("formdata.myspeciesA : "), fd.formdata.getvalue("myspeciesA"), HT.BR(), # HT.Strong("formdata.groupA: "), fd.formdata.getvalue("groupA") , HT.BR(), # HT.Strong("formdata.myspeciesB : "), fd.formdata.getvalue("myspeciesB"), HT.BR(), # HT.Strong("formdata.groupB: "), fd.formdata.getvalue("groupB") , HT.BR(), # HT.Strong("formdata.type: "), fd.formdata.getvalue("type") , HT.BR(), # HT.Strong("formdata.database: "), fd.formdata.getvalue("database") , HT.BR(), # HT.Strong("Database : "), "UCSC %s" % speciesFreeze[self.species], HT.BR(), HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(), ) if filename: infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize") , " output in MS excel format.") mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD(" ", width="")), cellpadding=10) if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"): mainTable.append(HT.TR(HT.TD(geneTable, colspan=3))) self.dict['body'] = HT.TD(mainTable) self.dict['title'] = "QTLminer" self.cursor.close(); def genGeneTable(self, fd, dispFields, strain1, strain2): filename = "" if self.xls: #import pyXLWriter as xl filename = "IntAn_Chr%s_%2.6f-%2.6f" % (self.Chr, self.startMb, self.endMb) filename += ".xls" # Create a new Excel workbook workbook = xl.Writer(os.path.join(webqtlConfig.TMPDIR, filename)) worksheet = workbook.add_worksheet() titleStyle = workbook.add_format(align = 'left', bold = 0, size=18, border = 1, border_color="gray") headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, fg_color = 0x1E, color="white", border = 1, border_color="gray") ##Write title Info worksheet.write([0, 0], "GeneNetwork Interval Analyst Table", titleStyle) worksheet.write([1, 0], "%s%s" % (webqtlConfig.PORTADDR, os.path.join(webqtlConfig.CGIDIR, _scriptfile))) # worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime())) worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime())) worksheet.write([4, 0], "Search by : %s" % fd.remote_ip) worksheet.write([5, 0], "view region : Chr %s %2.6f - %2.6f Mb" % (self.Chr, self.startMb, self.endMb)) nTitleRow = 7 geneTable = HT.TableLite(Class="collap", cellpadding=5) headerRow = HT.TR(HT.TD(" ", Class="fs13 fwb ffl b1 cw cbrb", width="1")) if self.xls: worksheet.write([nTitleRow, 0], "Index", headingStyle) for ncol, column in enumerate(dispFields): if column[0]=='meanA': headerRow.append(HT.TD("Expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='meanB': headerRow.append(HT.TD("Expression in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='meanC': headerRow.append(HT.TD("Expression in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetcisA': headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetcisB': headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetcisC': headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetA': headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetB': headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='probesetC': headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='hasexpr': headerRow.append(HT.TD("Has expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='hascis': headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='snpCountmis': headerRow.append(HT.TD("nsSNPs" , HT.BR(), "all strains", HT.BR(), " ", Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif column[0]=='snpCountmissel': headerRow.append(HT.TD("nsSNPs" , HT.BR(), self.str1, " vs", HT.BR(), self.str2, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) elif len(column) == 1: # header headerRow.append(HT.TD(columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) else: # header headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), " (%s)" % speciesFreeze[column[1]], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center")) if self.xls: colTitle = columnNames[column[0]][0] + " (%s)" % speciesFreeze[column[1]] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) #headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), # "(%s %s)" % (column[1].title(), speciesFreeze[column[1]]), # Class="colorBlue", NOWRAP=1, align="Center")) geneTable.append(headerRow) geneColnul = GeneUtil.loadGenesForQTLminer(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species, databaseA=self.daAsel, databaseB=self.daBsel, databaseC=self.daCsel, str1=self.str1, str2=self.str2) # scores = [] # for gIndex, theGO in enumerate(geneCol): # keyValue = "" # fieldName = 'score' # if theGO.has_key(fieldName): # keyValue = theGO[fieldName] # scores.append(keyValue) sort_on = "TxStart" myrev = False if self.sorton == "Score": sort_on = "score" myrev = True geneColeen = [(dict_[sort_on], dict_) for dict_ in geneColnul] geneColeen.sort(reverse=myrev) geneCol = [dict_ for (key, dict_) in geneColeen] for gIndex, theGO in enumerate(geneCol): geneRow = HT.TR(HT.TD(gIndex+1, Class="fs12 fwn b1", align="right")) if self.xls: nTitleRow += 1 worksheet.write([nTitleRow, 0], gIndex + 1) for ncol, column in enumerate(dispFields): if len(column) == 1 or column[1]== self.species: keyValue = "" fieldName = column[0] curSpecies = self.species curGO = theGO if theGO.has_key(fieldName): keyValue = theGO[fieldName] else: fieldName , othSpec = column curSpecies = othSpec subGO = '%sGene' % othSpec keyValue = "" curGO = theGO[subGO] if theGO[subGO].has_key(fieldName): keyValue = theGO[subGO][fieldName] if self.xls: worksheet.write([nTitleRow, ncol+1], keyValue) geneRow.append(self.formatTD(keyValue, fieldName, curSpecies, curGO, strain1, strain2)) geneTable.append(geneRow) if self.xls: workbook.close() return geneTable, filename def formatTD(self, keyValue, fieldName, Species, theGO, strain1, strain2): if keyValue is None: keyValue = "" if keyValue != "": if fieldName in ("exonStarts", "exonEnds"): keyValue = string.replace(keyValue, ',', ' ') return HT.TD(HT.Span(keyValue, Class="code", Id="green"), width=350, Class="fs12 fwn b1") elif fieldName in ("GeneDescription"): if keyValue == "---": keyValue = "" return HT.TD(keyValue, Class="fs12 fwn b1", width=300) elif fieldName in ("GeneSymbol"): webqtlLink = HT.Href("./%s/%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, keyValue, Species), HT.Image("/images/webqtl_search.gif", border=0, valign="top"), target="_blank") if theGO['GeneID']: geneSymbolLink = HT.Href(webqtlConfig.NCBI_LOCUSID % theGO['GeneID'], keyValue, Class="normalsize", target="_blank") else: geneSymbolLink = keyValue return HT.TD(webqtlLink, geneSymbolLink, Class="fs12 fwn b1",NOWRAP=1) elif fieldName == 'UnigenID': try: gurl = HT.Href(webqtlConfig.UNIGEN_ID % tuple(string.split(keyValue,'.')[:2]), keyValue, Class="normalsize", target="_blank") except: gurl = keyValue return HT.TD(gurl, Class="fs12 fwn b1",NOWRAP=1) elif fieldName in ("exonCount", "Chromosome"): return HT.TD(keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("snpCount"): return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1) elif fieldName in ("snpCountmis"): snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"] ), text=theGO["snpCountmis"], target="_blank", Class="normalsize") return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1) elif fieldName in ("snpCountmissel"): snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP&customStrain=1&diffAlleles=1&chosenStrains=%s,%s" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], self.str1, self.str2 ), text=theGO["snpCountmissel"], target="_blank", Class="normalsize") return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1) # if keyValue: # snpString = HT.Href(url="%s?chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'snpBrowser.py'), theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), text=theGO["snpCount"], target="_blank", Class="normalsize") # else: # snpString = keyValue # return HT.TD(snpString, Class="fs12 fwn b1",align="right") elif fieldName in ("snpDensity", "GeneLength"): if keyValue: keyValue = "%2.3f" % keyValue else: keyValue = "" return HT.TD(keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("TxStart", "TxEnd"): return HT.TD("%2.6f" % keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("score"): return HT.TD("%1d" % keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("pathways", "pathwaynames", "goterms"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(kk,HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right",NOWRAP=1) elif fieldName in ("probesetA", "probesetB", "probesetC"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(kk,HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") elif fieldName in ("probesetsymbolA"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(kk,HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") elif fieldName in ("meanA", "meanB", "meanC"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(str(round(kk,1)),HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") elif fieldName in ("hassnp", "hasindel", "hasexpr","hascis"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(kk,HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") elif fieldName in ("newlrsA", "newlrsB", "newlrsC"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(str(round(kk,1)),HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") elif fieldName in ("probesetcisA", "probesetcisB", "probesetcisC"): html = HT.Paragraph(Class="fs12 fwn b1") for kk in keyValue: html.append(kk,HT.BR()) # if kk==0: # html.append('no',HT.BR()) # if kk==1: # html.append('yes',HT.BR()) return HT.TD(html, Class="fs12 fwn b1",align="right") else: return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1) else: return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1,align="right") # def getStrainNameList(self, strain_data): # return strain_data[1:] def getStrainNamePair(self): strainNamePair=[] 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:] for index, name in enumerate(strainsNameList): strainNamePair.append((name,name)) return strainNamePair def genControlForm(self, fd): ##desc GeneList self.cursor.execute("Desc GeneList") GeneListFields = self.cursor.fetchall() GeneListFields = map(lambda X: X[0], GeneListFields) #group columns by category--used for creating the dropdown list of possible columns categories = {} for item in columnNames.keys(): category = columnNames[item] if category[-1] not in categories.keys(): categories[category[-1]] = [item ] else: categories[category[-1]] = categories[category[-1]]+[item] ##List All Species in the Gene Table speciesDict = {} self.cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \ GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId order by Species.Id") results = self.cursor.fetchall() speciesField = categories.pop('species', []) categoriesOrder = ['gene', 'protein'] for item in results: specName, specId = item categoriesOrder.append(specName) speciesDict[specName] = specId AppliedField = [] for item2 in speciesField: if item2 in GeneListFields: self.cursor.execute("select %s from GeneList where SpeciesId = %d and %s is not NULL limit 1 " % (item2, specId, item2)) columnApply = self.cursor.fetchone() if not columnApply: continue elif specName != 'mouse' and item2 in ('snpCount', 'snpDensity'): continue else: pass AppliedField.append(item2) categories[specName] = AppliedField categoriesOrder += ['misc'] s1_data = self.getStrainNamePair() self.allStrainNames = s1_data[1:] ############################################################ ## Create the list of possible columns for the dropdown list ############################################################ allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox")#onChange="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)") for category in categoriesOrder: allFields = categories[category] if allFields: geneOpt = HT.Optgroup(label=category.title()) for item in allFields: if category in speciesFreeze.keys(): geneOpt.append(("%s (%s %s)" % (columnNames[item][1], category.title(), speciesFreeze[category]), "%s__%s" % (item, speciesFreeze[category]))) else: geneOpt.append((columnNames[item][1], item)) geneOpt.sort() allColumnsList.append(geneOpt) allColumnsList2 = HT.Select(name="allColumns2", Class="snpBrowserDropBox") for item in self.allStrainNames: allColumnsList2.append(item) ###################################### ## Create the list of selected columns ###################################### #cols contains the value of all the selected columns submitCols = cols = fd.formdata.getvalue("columns", "default") if cols == "default": if self.species=="mouse": #these are the same columns that are shown on intervalPage.py cols = ['GeneSymbol', 'GeneDescription', 'goterms', 'pathwaynames', 'Chromosome', 'TxStart', 'snpCountmis', 'snpCountmissel', 'meanA', 'meanB', 'meanC', 'probesetcisA','probesetcisB','probesetcisC', 'probesetA','probesetB','probesetC', 'indelCountBXD','hassnp','hasindel','hasexpr','hascis','score'] elif self.species=="rat": cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'GeneLength', 'Strand', 'GeneID', 'UnigenID'] else: #should not happen cols = [] else: if type(cols)==type(""): cols = [cols] colsLst = [] dispFields = [] for column in cols: if submitCols == "default" and column not in ('GeneSymbol') and (column in GeneListFields or column in speciesField): colsLst.append(("%s (%s %s)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), "%s__%s" % (column, speciesFreeze[self.species]))) dispFields.append([column, self.species]) else: column2 = column.split("__") if len(column2) == 1: colsLst.append((columnNames[column2[0]][1], column)) dispFields.append([column]) else: thisSpecies = speciesFreeze[column2[1]] colsLst.append(("%s (%s %s)" % (columnNames[column2[0]][1], thisSpecies.title(), column2[1]), column)) dispFields.append((column2[0], thisSpecies)) selectedColumnsList = HT.Select(name="columns", Class="snpBrowserSelectBox", multiple="true", data=colsLst, size=6) ######### now for the strains!!!!!! #cols contains the value of all the selected columns submitCols2 = cols2 = fd.formdata.getvalue("columns2", "default") if cols2 == "default": if self.species=="mouse": #these are the same columns that are shown on intervalPage.py cols2 = ['C57BL/6J', 'DBA/2J',] else: #should not happen cols2 = [] else: if type(cols2)==type(""): cols2 = [cols2] colsLst2 = [] dispFields2 = [] for column2 in cols2: # if submitCols2 == "default" and (column in GeneListFields or column in speciesField): # colsLst2.append(("%s (%s %s)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), # "%s__%s" % (column, speciesFreeze[self.species]))) # dispFields.append([column, self.species]) # else: # column2 = column.split("__") # if len(column2) == 1: colsLst2.append((column2, column2)) dispFields2.append([column2]) selectedColumnsList2 = HT.Select(name="columns2", Class="snpBrowserSelectBox", multiple="true", data=colsLst2, size=6) ######### now for the sorton #cols contains the value of all the selected columns submitCols3 = cols3 = fd.formdata.getvalue("columns3", "default") if cols3 == "default": if self.species=="mouse": #these are the same columns that are shown on intervalPage.py cols3 = ['Position', 'Score',] else: #should not happen cols3 = [] else: if type(cols3)==type(""): cols3 = [cols3] colsLst3 = [] dispFields3 = [] for column3 in cols3: colsLst3.append((column3, column3)) dispFields3.append([column3]) selectedColumnsList3 = HT.Select(name="columns3", Class="snpBrowserSelectBox", multiple="true", data=colsLst3, size=6) ########################## ## Create the columns form ########################## columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, _scriptfile), enctype="multipart/form-data") columnsForm.append(HT.Input(type="hidden", name="fromdatabase", value= fd.formdata.getvalue("fromdatabase", "unknown"))) columnsForm.append(HT.Input(type="hidden", name="species", value=self.species)) columnsForm.append(HT.Input(type="hidden", name="submitter", value="empty")) if self.diffCol: columnsForm.append(HT.Input(type="hidden", name="s1", value=self.diffCol[0])) columnsForm.append(HT.Input(type="hidden", name="s2", value=self.diffCol[1])) startBox = HT.Input(type="text", name="startMb", value=self.startMb, size=10) endBox = HT.Input(type="text", name="endMb", value=self.endMb, size=10) addButton = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)") # addButton2 = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns2.options[this.form.allColumns2.selectedIndex].text, this.form.allColumns2.options[this.form.allColumns2.selectedIndex].value, this.form.columns2)") removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)") # removeButton2 = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns2.selectedIndex, this.form.columns2)") upButton = HT.Input(type="button", name="up", value="Up", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex-1, this.form.columns)") downButton = HT.Input(type="button", name="down", value="Down", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex+1, this.form.columns)") clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)") submitButton = HT.Input(type="submit", value="Analyze QTL interval", Class="button", onClick="Javascript:this.form.submitter.value='refresh';selectAllElements(this.form.columns)") selectChrBox = HT.Select(name="chromosome") self.cursor.execute(""" Select Chr_Length.Name, Length from Chr_Length, Species where Chr_Length.SpeciesId = Species.Id AND Species.Name = '%s' Order by Chr_Length.OrderId """ % self.species) results = self.cursor.fetchall() for chrInfo in results: selectChrBox.append((chrInfo[0], chrInfo[0])) selectChrBox.selected.append(self.Chr) ############################################ 2 strain boxes selectstr1 = HT.Select(name="str1") for item in self.allStrainNames: selectstr1.append(item[0]) selectstr1.selected.append(self.str1) selectstr2 = HT.Select(name="str2") for item in self.allStrainNames: selectstr2.append(item[0]) selectstr2.selected.append(self.str2) ############################################ select sort on selectsorton = HT.Select(name="sorton") selectsorton.append('Position') selectsorton.append('Score') selectsorton.selected.append('Position') ############################################ selectSpeciesBoxA = HT.Select(name="myspeciesA",onChange="Javascript:this.form.submitter.value='s2';submit();") for speciesInfo in self.spA: name = '' if speciesInfo[0]=='mouse': name='Mouse' elif speciesInfo[0]=='rat': name='Rat' elif speciesInfo[0]=='arabidopsis': name='Arabidopsis thaliana' elif speciesInfo[0]=='human': name='Human' elif speciesInfo[0]=='barley': name='Barley' elif speciesInfo[0]=='drosophila': name='Drosophila' elif speciesInfo[0]=='macaque monkey': name='Macaque Monkey' selectSpeciesBoxA.append((name, speciesInfo[0])) selectSpeciesBoxA.selected.append(self.spAsel) selectGroupBoxA = HT.Select(name="groupA",onChange="Javascript:this.form.submitter.value='a2';submit();") for groupInfo in self.grA: selectGroupBoxA.append((groupInfo[1], groupInfo[0])) selectGroupBoxA.selected.append(self.grAsel) selectTypeBoxA = HT.Select(name="typeA",onChange="Javascript:this.form.submitter.value='a3';submit();") for typeInfo in self.tyA: selectTypeBoxA.append((typeInfo[0] + ' mRNA', typeInfo[0])) selectTypeBoxA.selected.append(self.tyAsel) selectDatabaseBoxA = HT.Select(name="databaseA",onChange="Javascript:this.form.submitter.value='a4';submit();") for databaseInfo in self.daA: selectDatabaseBoxA.append((databaseInfo[1], databaseInfo[0])) selectDatabaseBoxA.selected.append(self.daAsel) ############################# ############################################ selectSpeciesBoxB = HT.Select(name="myspeciesB",onChange="Javascript:this.form.submitter.value='b1';submit();") for speciesInfo in self.spB: name = '' if speciesInfo[0]=='mouse': name='Mouse' elif speciesInfo[0]=='rat': name='Rat' elif speciesInfo[0]=='arabidopsis': name='Arabidopsis thaliana' elif speciesInfo[0]=='human': name='Human' elif speciesInfo[0]=='barley': name='Barley' elif speciesInfo[0]=='drosophila': name='Drosophila' elif speciesInfo[0]=='macaque monkey': name='Macaque Monkey' selectSpeciesBoxB.append((name, speciesInfo[0])) selectSpeciesBoxB.selected.append(self.spBsel) selectGroupBoxB = HT.Select(name="groupB",onChange="Javascript:this.form.submitter.value='b2';submit();") for groupInfo in self.grB: selectGroupBoxB.append((groupInfo[1], groupInfo[0])) selectGroupBoxB.selected.append(self.grBsel) selectTypeBoxB = HT.Select(name="typeB",onChange="Javascript:this.form.submitter.value='b3';submit();") for typeInfo in self.tyB: selectTypeBoxB.append((typeInfo[0] + ' mRNA', typeInfo[0])) selectTypeBoxB.selected.append(self.tyBsel) selectDatabaseBoxB = HT.Select(name="databaseB",onChange="Javascript:this.form.submitter.value='b4';submit();") for databaseInfo in self.daB: selectDatabaseBoxB.append((databaseInfo[1], databaseInfo[0])) selectDatabaseBoxB.selected.append(self.daBsel) ############################################ ############################# ############################################ selectSpeciesBoxC = HT.Select(name="myspeciesC",onChange="Javascript:this.form.submitter.value='c1';submit();") for speciesInfo in self.spC: name = '' if speciesInfo[0]=='mouse': name='Mouse' elif speciesInfo[0]=='rat': name='Rat' elif speciesInfo[0]=='arabidopsis': name='Arabidopsis thaliana' elif speciesInfo[0]=='human': name='Human' elif speciesInfo[0]=='barley': name='Barley' elif speciesInfo[0]=='drosophila': name='Drosophila' elif speciesInfo[0]=='macaque monkey': name='Macaque Monkey' selectSpeciesBoxC.append((name, speciesInfo[0])) selectSpeciesBoxC.selected.append(self.spCsel) selectGroupBoxC = HT.Select(name="groupC",onChange="Javascript:this.form.submitter.value='c2';submit();") for groupInfo in self.grC: selectGroupBoxC.append((groupInfo[1], groupInfo[0])) selectGroupBoxC.selected.append(self.grCsel) selectTypeBoxC = HT.Select(name="typeC",onChange="Javascript:this.form.submitter.value='c3';submit();") for typeInfo in self.tyC: selectTypeBoxC.append((typeInfo[0] + ' mRNA', typeInfo[0])) selectTypeBoxC.selected.append(self.tyCsel) selectDatabaseBoxC = HT.Select(name="databaseC",onChange="Javascript:this.form.submitter.value='c4';submit();") for databaseInfo in self.daC: selectDatabaseBoxC.append((databaseInfo[1], databaseInfo[0])) selectDatabaseBoxC.selected.append(self.daCsel) ############################################ ############################# innerColumnsTable = HT.TableLite(border=0, Class="collap", cellpadding = 2) innerColumnsTable.append(HT.TR(HT.TD(selectedColumnsList)), HT.TR(HT.TD(clearButton, removeButton, upButton, downButton))) # innerColumnsTable2 = HT.TableLite(border=0, Class="collap", cellpadding = 2) # innerColumnsTable2.append(HT.TR(HT.TD(selectedColumnsList2)), # HT.TR(HT.TD(removeButton2))) columnsTable = HT.TableLite(border=0, cellpadding=2, cellspacing=0) columnsTable.append( HT.TR(HT.TD(HT.Font(" ")), HT.TD(HT.Strong("Select the QTL interval"))), HT.TR(HT.TD(HT.Font("Chr: ", size=-1)), HT.TD(selectChrBox)), HT.TR(HT.TD(HT.Font("View: ", size=-1)), HT.TD(startBox, HT.Font("Mb to ", size=-1), endBox, HT.Font("Mb", size=-1))), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(HT.Font(" ")), HT.TD(HT.Strong("Select two mouse strains for inclusion of nsSNP count"))), HT.TR(HT.TD(HT.Font("Strains: ", size=-1)), HT.TD(selectstr1,selectstr2)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(HT.Font(" ")), HT.TD(HT.Strong("Select 3 datasets for inclusion of expression and cis-activity data"))), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(" "), HT.TD(HT.Font("Dataset 1", size=-1))), HT.TR(HT.TD(HT.Font("Species: ", size=-1)), HT.TD(selectSpeciesBoxA)), HT.TR(HT.TD(HT.Font("Group: ", size=-1)), HT.TD(selectGroupBoxA)), HT.TR(HT.TD(HT.Font("Type: ", size=-1)), HT.TD(selectTypeBoxA)), HT.TR(HT.TD(HT.Font("Database: ", size=-1)), HT.TD(selectDatabaseBoxA)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(" "), HT.TD(HT.Font("Dataset 2", size=-1))), HT.TR(HT.TD(HT.Font("Species: ", size=-1)), HT.TD(selectSpeciesBoxB)), HT.TR(HT.TD(HT.Font("Group: ", size=-1)), HT.TD(selectGroupBoxB)), HT.TR(HT.TD(HT.Font("Type: ", size=-1)), HT.TD(selectTypeBoxB)), HT.TR(HT.TD(HT.Font("Database: ", size=-1)), HT.TD(selectDatabaseBoxB)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(" "), HT.TD(HT.Font("Dataset 3", size=-1))), HT.TR(HT.TD(HT.Font("Species: ", size=-1)), HT.TD(selectSpeciesBoxC)), HT.TR(HT.TD(HT.Font("Group: ", size=-1)), HT.TD(selectGroupBoxC)), HT.TR(HT.TD(HT.Font("Type: ", size=-1)), HT.TD(selectTypeBoxC)), HT.TR(HT.TD(HT.Font("Database: ", size=-1)), HT.TD(selectDatabaseBoxC)), # HT.TR(HT.TD(""), # HT.TD(innerColumnsTable2)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(HT.Font(" ")), HT.TD(HT.Strong("Optionally, choose additional data to display"))), HT.TR(HT.TD(HT.Font("Show: ", size=-1)), HT.TD(allColumnsList, addButton)), HT.TR(HT.TD(HT.Font("Selected:",size=-1)), HT.TD(innerColumnsTable)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(HT.Font("Sort by: ", size=-1)), HT.TD(selectsorton)), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(" ")), HT.TR(HT.TD(HT.Font(" ", size=-1)), HT.TD(submitButton)), ) columnsForm.append(columnsTable) #columnsForm.append(HT.Input(type="hidden", name="sort", value=diffCol), # HT.Input(type="hidden", name="identification", value=identification), # HT.Input(type="hidden", name="traitInfo", value=traitInfo)) return columnsForm, dispFields, dispFields2