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authorzsloan2016-04-25 23:13:35 +0000
committerzsloan2016-04-25 23:13:35 +0000
commite2bdde9488c02603caee5b19644135cac23e9daf (patch)
treec37b500abba3069c2efa3d0d0a25c3bab645cd58
parent1fcdd76716d76d6f24c62df3009b0a1fc648e692 (diff)
downloadgenenetwork2-e2bdde9488c02603caee5b19644135cac23e9daf.tar.gz
Interval Analyst table mostly working, just need to work out a few more things
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py412
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html128
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"), "&nbsp;", 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__() + "&nbsp;" + 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"), "&nbsp;", 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"), "&nbsp;", 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__() + "&nbsp;" + 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"), "&nbsp;", 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 -->