From b37f5cc857849a29ea13825b96fbb8ea7c24a807 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 8 Aug 2016 21:02:46 +0000
Subject: Fixed bug where Interval Analyst result wouldn't appear for
chromosome X in mice/rats
Fixed broken image link in Interval Analyst table for rats
Small change to column width of gene global search
---
.../marker_regression/marker_regression_gn1.py | 30 +++++++++++++++++-----
wqflask/wqflask/templates/gsearch_gene.html | 2 +-
.../wqflask/templates/marker_regression_gn1.html | 2 +-
3 files changed, 25 insertions(+), 9 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index d0509c75..4f52bd55 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -506,14 +506,21 @@ 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
if self.dataset.group.species == "mouse":
+ if self.selectedChr == 20:
+ chrName = "X"
+ else:
+ chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
elif self.dataset.group.species == "rat":
- self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
+ if self.selectedChr == 21:
+ chrName = "X"
+ else:
+ chrName = self.selectedChr
+ self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
if self.geneCol and self.intervalAnalystChecked:
#######################################################################
@@ -2856,6 +2863,10 @@ class MarkerRegression(object):
polymiRTS = dic[theGO["GeneID"]]
# If we have a referenceGene then we will show the Literature Correlation
+ if theGO["Chromosome"] == "X":
+ chr_as_int = 19
+ else:
+ chr_as_int = int(theGO["Chromosome"]) - 1
if refGene:
try:
literatureCorrelation = self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID'])
@@ -2868,7 +2879,7 @@ class MarkerRegression(object):
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__(),
+ HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
snpString,
snpDensityStr,
avgExpr,
@@ -2899,7 +2910,7 @@ class MarkerRegression(object):
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__(),
+ HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
snpString,
snpDensityStr,
avgExpr,
@@ -2931,15 +2942,20 @@ class MarkerRegression(object):
for gIndex, theGO in enumerate(geneCol):
this_row = [] #container for the cells of each row
- selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)") #checkbox for each row
+ selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
- webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], HT.Image("/images/webqtl_search.gif", border=0), target="_blank")
+ webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
if theGO["GeneID"] != "":
- geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blanK")
+ geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blank").__str__()
else:
geneSymbolNCBI = theGO["GeneSymbol"]
+ if theGO["Chromosome"] == "X":
+ chr_as_int = 20
+ else:
+ chr_as_int = int(theGO["Chromosome"]) - 1
+
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
#geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 70cafcfe..a50157ce 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -161,7 +161,7 @@
{ "type": "natural" },
{ "type": "natural", "width": "8%" },
{ "type": "natural" },
- { "type": "natural", "width": "5%" },
+ { "type": "natural" },
{ "type": "natural", "width": "8%" },
{ "type": "natural" }
],
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 5389978a..c5cb278c 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -216,7 +216,7 @@
{% endfor %}
- {% elif selectedChr > -1 %}
+ {% else %}
Interval Analyst