diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 412 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 128 |
2 files changed, 318 insertions, 222 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index b89f6b97..e0007455 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -203,9 +203,9 @@ class MarkerRegression(object): # #self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) - if self.dataset.species == "rat": + if self.dataset.group.species == "rat": self._ucscDb = "rn3" - elif self.dataset.species == "mouse": + elif self.dataset.group.species == "mouse": self._ucscDb = "mm9" else: self._ucscDb = "" @@ -295,7 +295,7 @@ class MarkerRegression(object): self.dominanceChecked = False self.LRS_LOD = start_vars['LRSCheck'] self.cutoff = start_vars['cutoff'] - self.intervalAnalystChecked = False + self.intervalAnalystChecked = True self.draw2X = False if 'additiveCheck' in start_vars.keys(): self.additiveChecked = start_vars['additiveCheck'] @@ -514,34 +514,35 @@ class MarkerRegression(object): self.geneCol = None if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked): - chrName = self.selectedChr - # Draw the genes for this chromosome / region of this chromosome - webqtldatabase = self.dataset.name + chrName = self.selectedChr + # Draw the genes for this chromosome / region of this chromosome + webqtldatabase = self.dataset.name - if self.dataset.group.species == "mouse": + if self.dataset.group.species == "mouse": self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse") - elif self.dataset.group.species == "rat": + elif self.dataset.group.species == "rat": self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat") - # - # if self.geneCol and self.intervalAnalystChecked: - # ####################################################################### - # #Nick use GENEID as RefGene to get Literature Correlation Informations# - # #For Interval Mapping, Literature Correlation isn't useful, so skip it# - # #through set GENEID is None # - # ####################################################################### - # - # #GENEID = fd.formdata.getvalue('GeneId') or None - # GENEID = None - # - # geneTableContainer = HT.Div(Id="sortable") #Div to hold table - # geneTable = self.geneTable(self.geneCol,GENEID) - # geneTableContainer.append(geneTable) - # - # mainfmName = webqtlUtil.genRandStr("fm_") - # tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden')) - # tableForm.append(HT.Input(name='FormID', value='', type='hidden')) - # tableForm.append(geneTableContainer) + + if self.geneCol and self.intervalAnalystChecked: + ####################################################################### + #Nick use GENEID as RefGene to get Literature Correlation Informations# + #For Interval Mapping, Literature Correlation isn't useful, so skip it# + #through set GENEID is None # + ####################################################################### + + #GENEID = fd.formdata.getvalue('GeneId') or None + GENEID = None + + geneTableContainer = HT.Div(Id="sortable") #Div to hold table + self.geneTable(self.geneCol, GENEID) + #geneTable = self.geneTable(self.geneCol, GENEID) + #geneTableContainer.append(geneTable) + + #mainfmName = webqtlUtil.genRandStr("fm_") + #tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden')) + #tableForm.append(HT.Input(name='FormID', value='', type='hidden')) + #tableForm.append(geneTableContainer) ################################################################ @@ -1643,7 +1644,7 @@ class MarkerRegression(object): canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT)) - if self.species == "mouse": + if self.dataset.group.species == "mouse": UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) @@ -1653,7 +1654,7 @@ class MarkerRegression(object): canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT)) - if self.species == "mouse": + if self.dataset.group.species == "mouse": ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) @@ -2634,113 +2635,141 @@ class MarkerRegression(object): def geneTable(self, geneCol, refGene=None): #SNPLink = 0 #Not sure what this is used for - if self.species == 'mouse' or self.species == 'rat': - - gene_tblobj = {} - gene_tblobj["header"] = self.getGeneTableHeader(refGene=None) - gene_tblobj["body"] = self.getGeneTableBody(geneCol, refGene=None) - - sortby = self.getSortByValue() + if self.dataset.group.species == 'mouse' or self.dataset.group.species == 'rat': + #gene_tblobj = {} + self.gene_table_header = self.getGeneTableHeader(refGene=None) + self.gene_table_body = self.getGeneTableBody(geneCol, refGene=None) + #gene_tblobj["header"] = self.getGeneTableHeader(refGene=None) + #gene_tblobj["body"] = self.getGeneTableBody(geneCol, refGene=None) - filename= webqtlUtil.genRandStr("Mapping_") + #sortby = self.getSortByValue() - objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') - cPickle.dump(gene_tblobj, objfile) - objfile.close() + #filename= webqtlUtil.genRandStr("Mapping_") - gene_table = webqtlUtil.genTableObj(tblobj=gene_tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="0") + #objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') + #cPickle.dump(gene_tblobj, objfile) + #objfile.close() + #gene_table = webqtlUtil.genTableObj(tblobj=gene_tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="0") else: - gene_table = "" + self.gene_table_header = None + self.gene_table_body = None + #gene_table = "" - return gene_table - - def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None): - if not geneId1 or not geneId2: - return None - if geneId1 == geneId2: - return 1.0 - geneId1 = str(geneId1) - geneId2 = str(geneId2) - lCorr = None - try: - query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' - for x,y in [(geneId1,geneId2),(geneId2,geneId1)]: - cursor.execute(query,(x,y)) - lCorr = cursor.fetchone() - if lCorr: - lCorr = lCorr[0] - break - except: raise #lCorr = None - return lCorr + #return gene_table def getGeneTableHeader(self, refGene=None): gene_tblobj_header = [] + + gene_table_header_list = [] col_class = "fs14 fwb ffl b1 cw cbrb" - if self.species == "mouse": + if self.dataset.group.species == "mouse": if refGene: - gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), - THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), - THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), - THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), - THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - THCell(HT.TD('Literature',HT.BR(),'Correlation', align='left', width=100, Class=col_class), text="lit_corr", idx=9), - THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=10), - THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), - align='left', width=100, Class=col_class), sort=0, idx=11), - THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), - align='left', width=110, Class=col_class), sort=0, idx=12), - ]] + gene_table_header_list = ["Index", + "Symbol", + "Mb Start", + "Length (Kb)", + "SNP Count", + "SNP Density", + "Avg Expr", + "Human Chr", + "Mb Start (hg19)", + "Literature Correlation", + "Gene Description", + "PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(), + "Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()] + + # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), + # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), + # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), + # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), + # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), + # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), + # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), + # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), + # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), + # THCell(HT.TD('Literature',HT.BR(),'Correlation', align='left', width=100, Class=col_class), text="lit_corr", idx=9), + # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=10), + # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), + # align='left', width=100, Class=col_class), sort=0, idx=11), + # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), + # align='left', width=110, Class=col_class), sort=0, idx=12), + # ]] else: - gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), - THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), - THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), - THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), - THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=9), - THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), - align='left', width=100, Class=col_class), sort=0, idx=10), - THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), - align='left', width=110, Class=col_class), sort=0, idx=11), - ]] - - elif self.species == "rat": - - gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - THCell(HT.TD('Mb Start',HT.BR(),'(rn3)', align='left', width=100, Class=col_class), text="mb_start_rn3", idx=2), - THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=4), - THCell(HT.TD('Mouse',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="mouse_chr", idx=5), - THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=6), - THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', Class=col_class), text="description", idx=9)]] + gene_table_header_list = ["", + "Index", + "Symbol", + "Mb Start", + "Length (Kb)", + "SNP Count", + "SNP Density", + "Avg Expr", + "Human Chr", + "Mb Start (hg19)", + "Gene Description", + "PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(), + "Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()] + + # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), + # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), + # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), + # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), + # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), + # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), + # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), + # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), + # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), + # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=9), + # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), + # align='left', width=100, Class=col_class), sort=0, idx=10), + # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), + # align='left', width=110, Class=col_class), sort=0, idx=11), + # ]] + + elif self.dataset.group.species == "rat": + + gene_table_header_list = ["", + "Index", + "Symbol", + "Mb Start", + "Length (Kb)", + "Avg Expr", + "Mouse Chr", + "Mb Start (mm9)", + "Human Chr", + "Mb Start (hg19)", + "Gene Description"] + + # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), + # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), + # THCell(HT.TD('Mb Start',HT.BR(),'(rn3)', align='left', width=100, Class=col_class), text="mb_start_rn3", idx=2), + # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), + # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=4), + # THCell(HT.TD('Mouse',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="mouse_chr", idx=5), + # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=6), + # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), + # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), + # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', Class=col_class), text="description", idx=9)]] else: pass - return gene_tblobj_header + return gene_table_header_list + #return gene_tblobj_header def getGeneTableBody(self, geneCol, refGene=None): tblobj_body = [] #contains table rows className = "fs13 b1 c222" + + gene_table_body = [] tableIterationsCnt = 0 - if self.species == "mouse": + if self.dataset.group.species == "mouse": # polymiRTS # http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125 @@ -2779,8 +2808,8 @@ class MarkerRegression(object): allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"]) if theGO["snpCount"]: - snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), - theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]), + snpString = HT.Href(url="http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (theGO["Chromosome"], + theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]), text=theGO["snpCount"], target="_blank", Class="normalsize") else: snpString = 0 @@ -2817,7 +2846,7 @@ class MarkerRegression(object): geneDescription = theGO["GeneDescription"] if len(geneDescription) > 26: geneDescription = geneDescription[:26]+"..." - probeSetSearch = HT.Href(allProbeString, HT.Image("/images/webqtl_search.gif", border=0), target="_blank") + probeSetSearch = HT.Href(allProbeString, ">>", target="_blank") if theGO["snpDensity"] < 0.000001: snpDensityStr = "0" @@ -2844,37 +2873,69 @@ class MarkerRegression(object): literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A") - this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) - this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) - this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) - this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) - this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) - this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) - this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) - this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) - this_row.append(TDCell(HT.TD(literatureCorrelationString, align='right', Class=className), literatureCorrelationString, literatureCorrelation)) - this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) - this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) - this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) + this_row = [selectCheck.__str__(), + str(tableIterationsCnt), + HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__() + " " + probeSetSearch.__str__(), + HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(), + HT.Href("javascript:rangeView('%s', %f, %f)" % (str(int(theGO["Chromosome"])-1), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(), + snpString, + snpDensityStr, + avgExpr, + humanChr, + HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), + literatureCorrelationString, + geneDescription, + polymiRTS, + ""] + + # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) + # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) + # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) + # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) + # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) + # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) + # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) + # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) + # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) + # this_row.append(TDCell(HT.TD(literatureCorrelationString, align='right', Class=className), literatureCorrelationString, literatureCorrelation)) + # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) + # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) + # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) else: - this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) - this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) - this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) - this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) - this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) - this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) - this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) - this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) - this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) - this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) - this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) - - tblobj_body.append(this_row) - - elif self.species == 'rat': + + this_row = [selectCheck.__str__(), + str(tableIterationsCnt), + HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__() + " " + probeSetSearch.__str__(), + HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(), + HT.Href("javascript:rangeView('%s', %f, %f)" % (str(int(theGO["Chromosome"])-1), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(), + snpString, + snpDensityStr, + avgExpr, + humanChr, + HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), + geneDescription, + polymiRTS, + ""] + + + # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) + # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) + # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) + # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) + # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) + # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) + # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) + # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) + # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) + # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) + # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) + # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) + + gene_table_body.append(this_row) + #tblobj_body.append(this_row) + + elif self.dataset.group.species == 'rat': for gIndex, theGO in enumerate(geneCol): @@ -2922,32 +2983,57 @@ class MarkerRegression(object): if geneDesc == "---": geneDesc = "" - """ - if len(geneDesc) > 40: - geneDesc = gene0So apparently Angola prison (which used to be a slave plantation) has a rodeo that they invite the general public to. -The prisoners are not trained before hand -But its cool because its completely voluntary. -And by voluntary, according to HFG when I talked to him, they have a choice between doing it or door number two and "door number 2 is... rather worse than volunteering"Desc[:37] + "..." - """ - - this_row.append(TDCell(HT.TD(gIndex + 1, selectCheck, align='left', Class=className), str(gIndex+1), gIndex+1)) - this_row.append(TDCell(HT.TD(webqtlSearch, geneSymbolNCBI, align='left', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - this_row.append(TDCell(HT.TD(theGO["TxStart"], align='left', Class=className), theGO["TxStart"], theGO["TxStart"])) - this_row.append(TDCell(HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)), align='left', Class=className), "%0.3f" % (geneLength*1000.0), (geneLength*1000.0))) - this_row.append(TDCell(HT.TD(avgExprVal, align='left', Class=className), "", "")) - this_row.append(TDCell(HT.TD(mouseChr, align='left', Class=className), mouseChr, mouseChr)) - this_row.append(TDCell(HT.TD(mouseTxStart, align='left', Class=className), mouseTxStart, mouseTxStart)) - this_row.append(TDCell(HT.TD(humanChr, align='left', Class=className), humanChr, humanChrSort)) - this_row.append(TDCell(HT.TD(humanTxStart, align='left', Class=className), humanTxStart, humanTxStart)) - this_row.append(TDCell(HT.TD(geneDesc, align='left', Class=className), geneDesc, geneDesc)) - - tblobj_body.append(this_row) + this_row = [selectCheck.__str__(), + str(gIndex+1), + webqtlSearch.__str__() + geneSymbolNCBI, + theGO["TxStart"], + HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), + avgExprVal, + mouseChr, + mouseTxStart, + humanChr, + humanTxStart, + geneDesc] + + + #this_row.append(TDCell(HT.TD(gIndex + 1, selectCheck, align='left', Class=className), str(gIndex+1), gIndex+1)) + #this_row.append(TDCell(HT.TD(webqtlSearch, geneSymbolNCBI, align='left', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) + #this_row.append(TDCell(HT.TD(theGO["TxStart"], align='left', Class=className), theGO["TxStart"], theGO["TxStart"])) + #this_row.append(TDCell(HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)), align='left', Class=className), "%0.3f" % (geneLength*1000.0), (geneLength*1000.0))) + #this_row.append(TDCell(HT.TD(avgExprVal, align='left', Class=className), "", "")) + #this_row.append(TDCell(HT.TD(mouseChr, align='left', Class=className), mouseChr, mouseChr)) + #this_row.append(TDCell(HT.TD(mouseTxStart, align='left', Class=className), mouseTxStart, mouseTxStart)) + #this_row.append(TDCell(HT.TD(humanChr, align='left', Class=className), humanChr, humanChrSort)) + #this_row.append(TDCell(HT.TD(humanTxStart, align='left', Class=className), humanTxStart, humanTxStart)) + #this_row.append(TDCell(HT.TD(geneDesc, align='left', Class=className), geneDesc, geneDesc)) + + gene_table_body.append(this_row) + #tblobj_body.append(this_row) else: pass - return tblobj_body - + return gene_table_body + #return tblobj_body + + def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None): + if not geneId1 or not geneId2: + return None + if geneId1 == geneId2: + return 1.0 + geneId1 = str(geneId1) + geneId2 = str(geneId2) + lCorr = None + try: + query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' + for x,y in [(geneId1,geneId2),(geneId2,geneId1)]: + cursor.execute(query,(x,y)) + lCorr = cursor.fetchone() + if lCorr: + lCorr = lCorr[0] + break + except: raise #lCorr = None + return lCorr def getSortByValue(self): diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 7d34e88f..7f269048 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -117,10 +117,10 @@ <span style="color:red;">*</span> <br> <input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br> - <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span><br> {% if plotScale != "morgan" %} - <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span> + <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span><br> {% endif %} + <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span> </div> <div class="col-xs-12" align="center" style="padding: 5px;"> <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span> @@ -165,65 +165,75 @@ </div> </form> - {% if selectedChr == -1 %} <div style="width:48%;"> - <h2> - Results - </h2> - <table id="qtl_results" class="table table-hover table-striped"> - <thead> - <tr> - <th></th> - <th>Index</th> - <th>{{ LRS_LOD }}</th> - <th>Chr</th> - {% if plotScale == "centimorgan" %} - <th>cM</th> - {% else %} - <th>Mb</th> - {% endif %} - <th>Locus</th> - </tr> - </thead> - <tbody> - {% for marker in trimmed_markers %} - <tr> - <td> - <input type="checkbox" name="selectCheck" - class="checkbox edit_sample_checkbox" - value="{{ marker.name }}" checked="checked"> - </td> - <td align="right">{{ loop.index }}</td> - {% if LRS_LOD == "LOD" %} - {% if 'lod_score' in marker %} - <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td> - {% else %} - <td>{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td> - {% endif %} - {% else %} - {% if 'lod_score' in marker %} - <td>{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td> - {% else %} - <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td> - {% endif %} - {% endif %} - <td>{{marker.chr}}</td> - <td>{{ '%0.6f' | format(marker.Mb|float) }}</td> - <td> - {{ marker.name }} - <!--<a href="{{ url_for('show_trait_page', - trait_id = marker.name, - dataset = dataset.name - )}}"> - {{ marker.name }} - </a>--> - </td> - </tr> - {% endfor %} - </tbody> - </table> + {% if selectedChr == -1 %} + <h2>Results</h2> + <table id="qtl_results" class="table table-hover table-striped"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>{{ LRS_LOD }}</th> + <th>Chr</th> + {% if plotScale == "centimorgan" %} + <th>cM</th> + {% else %} + <th>Mb</th> + {% endif %} + <th>Locus</th> + </tr> + </thead> + <tbody> + {% for marker in trimmed_markers %} + <tr> + <td> + <input type="checkbox" name="selectCheck" + class="checkbox edit_sample_checkbox" + value="{{ marker.name }}" checked="checked"> + </td> + <td align="right">{{ loop.index }}</td> + {% if LRS_LOD == "LOD" %} + {% if 'lod_score' in marker %} + <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td> + {% else %} + <td>{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td> + {% endif %} + {% else %} + {% if 'lod_score' in marker %} + <td>{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td> + {% else %} + <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td> + {% endif %} + {% endif %} + <td>{{marker.chr}}</td> + <td>{{ '%0.6f' | format(marker.Mb|float) }}</td> + <td>{{ marker.name }}</td> + </tr> + {% endfor %} + </tbody> + </table> + {% elif selectedChr > -1 %} + <h2>Interval Analyst</h2> + <table id="interval_analyst" class="table table-hover table-striped"> + <thead> + <tr> + {% for header in gene_table_header %} + <th>{{ header|safe }}</th> + {% endfor %} + </tr> + </thead> + <tbody> + {% for row in gene_table_body %} + <tr> + {% for n in range(row|length) %} + <td>{{ row[n]|safe }}</td> + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + {% endif %} </div> - {% endif %} </div> <!-- End of body --> |