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-rwxr-xr-xweb/webqtl/genomeGraph/__init__.py0
-rwxr-xr-xweb/webqtl/genomeGraph/cmdGenomeScanPage.py532
-rwxr-xr-xweb/webqtl/genomeGraph/genAllDbResultPage.py309
3 files changed, 841 insertions, 0 deletions
diff --git a/web/webqtl/genomeGraph/__init__.py b/web/webqtl/genomeGraph/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/genomeGraph/__init__.py
diff --git a/web/webqtl/genomeGraph/cmdGenomeScanPage.py b/web/webqtl/genomeGraph/cmdGenomeScanPage.py
new file mode 100755
index 00000000..d880ce69
--- /dev/null
+++ b/web/webqtl/genomeGraph/cmdGenomeScanPage.py
@@ -0,0 +1,532 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import string
+import piddle as pid
+import os
+import math
+
+from htmlgen import HTMLgen2 as HT
+
+from utility import svg
+from base import webqtlConfig
+from utility import Plot
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.templatePage import templatePage
+
+
+#########################################
+# Genome Scan PAGE
+#########################################
+class cmdGenomeScanPage(templatePage):
+ def __init__(self,fd):
+ templatePage.__init__(self,fd)
+ if not self.openMysql():
+ return
+ self.database = fd.formdata.getvalue('database', '')
+ db = webqtlDataset(self.database, self.cursor)
+
+ try:
+ self.openURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + \
+ '?FormID=showDatabase&database=%s&incparentsf1=1&ProbeSetID=' % self.database
+
+ if db.type != "ProbeSet" or not db.id:
+ raise DbNameError
+
+ self.cursor.execute("""
+ Select
+ InbredSet.Name
+ From
+ ProbeSetFreeze, ProbeFreeze, InbredSet
+ whERE
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+ ProbeFreeze.InbredSetId = InbredSet.Id AND
+ ProbeSetFreeze.Id = %d
+ """ % db.id)
+ thisRISet = self.cursor.fetchone()[0]
+ if thisRISet =='BXD300':
+ thisRISet = 'BXD'
+
+ ##################################################
+ # exon data is too huge for GenoGraph, skip it #
+ ##################################################
+ self.cursor.execute('select count(*) from ProbeSetXRef where ProbeSetFreezeId=%d' % db.id)
+ amount = self.cursor.fetchall()
+ if amount:
+ amount = amount[0][0]
+ if amount>100000:
+ heading = "Whole Transcriptome Mapping"
+ detail = ["Whole Transcriptome Mapping is not available for this data set."]
+ self.error(heading=heading,detail=detail)
+ return
+
+ self.cursor.execute("""
+ Select
+ ProbeSet.Id, ProbeSet.Name, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus, ProbeSetXRef.pValue
+ From
+ ProbeSet, ProbeSetXRef
+ whERE
+ ProbeSetXRef.ProbeSetFreezeId = %d AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetXRef.Locus is not NULL
+ """ % db.id)
+ results = self.cursor.fetchall()
+
+ if results:
+ self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
+
+ import reaper
+ markerGMb = {}
+ genotype_1 = reaper.Dataset()
+ genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
+ for chr in genotype_1:
+ chrlen = self.mouseChrLengthDict[chr.name]
+
+ for locus in chr:
+ markerGMb[locus.name] = locus.Mb + chrlen
+
+ try:
+ FDR = float(fd.formdata.getvalue("fdr", ""))
+ except:
+ FDR = 0.2
+ self.grid = fd.formdata.getvalue("grid", "")
+
+ NNN = len(results)
+ results = list(results)
+ results.sort(self.cmppValue)
+
+ MbCoord = []
+ MbCoord2 = []
+
+ for j in range(NNN, 0, -1):
+ if results[j-1][-1] <= (FDR*j)/NNN:
+ break
+
+ if j > 0:
+ for i in range(j-1, -1, -1):
+ _Id, _probeset, _chr, _Mb, _marker, _pvalue = results[i]
+ try:
+ MbCoord.append([markerGMb[_marker], _Mb+self.mouseChrLengthDict[string.strip(_chr)], _probeset, _chr, _Mb, _marker, _pvalue])
+ except:
+ pass
+
+ filename=webqtlUtil.genRandStr("gScan_")
+ canvas = pid.PILCanvas(size=(1280,880))
+ self.drawGraph(canvas, MbCoord, cLength=sum)
+
+ canvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+
+ canvasSVG = self.drawSVG(MbCoord, cLength=sum, size=(1280,880))
+ canvasSVG.toXml(os.path.join(webqtlConfig.IMGDIR, filename+'.svg')) #and write it to file
+
+ img = HT.Embed(src='/image/'+filename+'.png', width=1280, height=880, border=0, alt='Genome Scan')
+ img2 = HT.Embed(src='/image/'+filename+'.svg', width=1280, height=880, border=0)
+ TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
+
+ heading = HT.Paragraph('Whole Transcriptome Mapping')
+ heading.__setattr__("class","title")
+ intro = HT.Blockquote()
+ intro.append('The plot below is the Whole Transcriptome Mapping of Database ')
+ intro.append(HT.Href(text=db.fullname, url = webqtlConfig.INFOPAGEHREF % db.name ,target='_blank',Class="normalsize"))
+ intro.append(". %d from a total of %d ProbeSets were utilized to generate this graph." % (len(MbCoord), len(results)))
+
+ mainfm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', \
+ name=webqtlUtil.genRandStr("fm_"), submit=HT.Input(type='hidden'))
+ mainfm.append(HT.Input(name='database', value=self.database, type='hidden'))
+ mainfm.append(HT.Input(name='FormID', value='transciptMapping', type='hidden'))
+
+ mainfm.append("<BLOCKQUOTE>")
+ mainfm.append("0 < FDR <= 1.0 ")
+ mainfm.append(HT.Input(name='fdr', value=FDR, type='text'))
+
+ mainfm.append(HT.Input(name='submit', value='Redraw Graph', type='submit', Class='button'))
+ mainfm.append("</BLOCKQUOTE>")
+ mainfm.append("""
+<center>
+<div id="gallery">
+<div class="on" title="img1"><span>Static</span></div>
+<div class="off" title="img2"><span>Interactive</span></div>
+</div>
+
+<div id="img1" class="show">
+""")
+ mainfm.append(img)
+ mainfm.append("""
+</div>
+
+<div id="img2" class="hide">
+""")
+ mainfm.append(img2)
+ mainfm.append("""
+</div>
+</center>
+""")
+
+ TD_LR.append(heading, intro, HT.Paragraph(mainfm))
+
+ self.dict['title'] = 'Whole Transcriptome Mapping'
+ self.dict['body'] = TD_LR
+ else:
+ heading = "Whole Transcriptome Mapping"
+ detail = ["Database calculation is not finished."]
+ self.error(heading=heading,detail=detail)
+ return
+ except:
+ heading = "Whole Transcriptome Mapping"
+ detail = ["Whole Transcriptome Mapping only apply to Microarray database."]
+ self.error(heading=heading,detail=detail)
+ return
+
+ def drawSVG(self, data, cLength = 2500, offset= (80, 160, 60, 60), size=(1280,880),
+ XLabel="Marker GMb", YLabel="Transcript GMb"):
+ entities = {
+ "colorText" : "fill:darkblue;",
+ "strokeText" : ";stroke:none;stroke-width:0;",
+ "allText" : "font-family:Helvetica;",
+ "titleText" : "font-size:22;font-weight:bold;",
+ "subtitleText" : "font-size:18;font-weight:bold;",
+ "headlineText" : "font-size:14;font-weight:bold;",
+ "normalText" : "font-size:12;",
+ "legendText" : "font-size:11;text-anchor:end;",
+ "valuesText" : "font-size:12;",
+ "boldValuesText" : "font-size:12;font-weight:bold;",
+ "smallText" : "font-size:10;",
+ "vText" : "writing-mode:tb-rl",
+ "rightText" : "text-anchor:end;",
+ "middleText" : "text-anchor:middle;",
+ "bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;",
+ "rectstyle" : "fill:lightblue;stroke:none;opacity:0.2;",
+ "fillUnbebaut" : "fill:#CCFFD4;stroke:none;",
+ "fillNodata" : "fill:#E7E7E7;stroke:black;stroke-width:2;stroke-antialiasing:true;",
+ "fillNodataLegend" : "fill:#E7E7E7;stroke:black;stroke-width:0.5;stroke-antialiasing:true;",
+ "grundzeitstyle" : "fill:none;stroke:#E00004;stroke-width:60;stroke-antialiasing:true;",
+ "bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;",
+ "mapAuthor" : "A. Neumann",
+ }
+ cWidth, cHeight = size
+ canvasSVG = svg.drawing(entities) #create a drawing
+ drawSpace=svg.svg((0, 0, cWidth, cHeight), cWidth, cHeight, xml__space="preserve",
+ zoomAndPan="disable", onload="initMap(evt);",
+ xmlns__a3="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/",
+ a3__scriptImplementation="Adobe") #create a svg drawingspace
+ canvasds=svg.description('Genome Graph') #define a description
+ drawSpace.addElement(canvasds) #add the description to the svg
+
+ #need to be modified or deleted
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = cWidth - xLeftOffset - xRightOffset
+ plotHeight = cHeight - yTopOffset - yBottomOffset
+ drawSpace.addElement(svg.script("", language="javascript", xlink__href="/javascript/svg.js"))
+
+ #add defs
+ defs = svg.defs()
+ symbol1= svg.symbol(id="magnifyer", overflow="visible",
+ style="fill:white;stroke:orange;stroke-width:2;")
+ symbol1.addElement(svg.line(0, 0, -8, 20))
+ symbol1.addElement(svg.circle(0, 0, 8))
+ symbol1.addElement(svg.line(-4, 0, 4, 0, style="stroke:orange;stroke-width:2;"))
+ defs.addElement(symbol1)
+ symbol2= svg.symbol(id="magnifyerZoomIn",overflow="visible")
+ symbol2.addElement(svg.use(link="#magnifyer", id="zoomIn"))
+ symbol2.addElement(svg.line(0, -4, 0, 4, style="stroke:orange;stroke-width:2;"))
+ defs.addElement(symbol2)
+ drawSpace.addElement(defs)
+
+ symbol3= svg.symbol(id="msgbox", overflow="visible",
+ style="fill:white;stroke:orange;stroke-width:1;opacity:0.8;")
+ symbol3.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
+ symbol3.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
+ symbol3.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
+ symbol3.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+ symbol3.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+ symbol3.addElement(svg.text(-60, -90, "LRS ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+ symbol3.addElement(svg.text(-60, -55, "P value ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+ defs.addElement(symbol3)
+
+ g = svg.group("title")
+ g.addElement(svg.text(cWidth-40, 30, "Genome Graph", style="&colorText; &allText; &titleText; &rightText;"))
+ g.addElement(svg.text(cWidth-40, 50, "Whole Transcriptome Mapping", style="&colorText; &allText; &subtitleText; &rightText;"))
+ drawSpace.addElement(g)
+
+ #draw Main display area border
+ mainSquare = cHeight-60
+ cordZOOM = 10
+ drawSpace.addElement(svg.rect(8, 8, mainSquare+4, mainSquare+4,'none',"orange",0.5, rx="5", ry="5"))
+ drawSpace.addElement(svg.text(10+mainSquare/2, 40+mainSquare,'Marker GMb',
+ style="&colorText; &allText; &titleText; &middleText;", id="XLabel"))
+ drawSpace.addElement(svg.text(mainSquare + 80, 10+mainSquare/2,'Transcript GMb',
+ style="&colorText; &allText; &titleText; &middleText; &vText;", id="YLabel"))
+
+ #draw overview display area
+ drawSpace.addElement(svg.rect(cWidth-40-260, 60, 260, 260,'none',"orange",0.5, rx="5", ry="5"))
+ drawSpaceThumb= svg.svg(id="overviewPlot",x=cWidth-40-260,y="60",width="260",
+ height="260",viewBox=(0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM))
+ g = svg.group(style="&bezgrenzstyle;")
+ g.addElement(svg.use("#grid"))
+ drawSpaceThumb.addElement(g)
+ drawSpaceThumb.addElement(svg.rect(id="overviewRect",style="&rectstyle;",
+ x="0",y="0",width=mainSquare*cordZOOM,height=mainSquare*cordZOOM,
+ onmouseover="statusChange('click and drag rectangle to change extent');",
+ onmousedown="beginPan(evt);", onmousemove="doPan(evt);",
+ onmouseup="endPan();", onmouseout="endPan();"))
+ drawSpace.addElement(drawSpaceThumb)
+
+ #draw navigator
+ g = svg.group(id="navigatorElements")
+ g.addElement(svg.use("#magnifyerZoomIn", id="zoomIn", transform="translate(%d,350)" % (cWidth-40-130-20),
+ onmouseover="magnify(evt,1.3,'in');", onmouseout="magnify(evt,1,'in');", onclick="zoomIt('in');"))
+ g.addElement(svg.use("#magnifyer", id="zoomOut", transform="translate(%d,350)" % (cWidth-40-130+20),
+ onmouseover="magnify(evt,1.3,'out');",onmouseout="magnify(evt,1,'out');", onclick="zoomIt('out');"))
+
+ drawSpace.addElement(g)
+
+ g = svg.group(id="statusBar")
+ g.addElement(svg.text(cWidth-40-260, 360, "ZOOM: 100%", style="fill:orange; font-size:14;", id="zoomValueObj"))
+ g.addElement(svg.text(cWidth-40-260, 380, "Status:", style="&colorText; &allText; &smallText;"))
+ g.addElement(svg.text(cWidth-40-260, 395, "Loading Plot", style="&colorText; &allText; &smallText;", id="statusText"))
+ drawSpace.addElement(g)
+
+ #draw main display area
+ drawSpaceMain= svg.svg((0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM), mainSquare, mainSquare,
+ id="mainPlot",x="10",y="10")
+ mPlotWidth = mPlotHeight = 0.8*mainSquare*cordZOOM
+
+ drawSpaceMain.addElement(svg.rect(mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1, mPlotWidth, mPlotHeight,style="fill:white",
+ onmousemove="showChr(evt);", onmouseover="showChr(evt);", onmouseout="showNoChr(evt);"))
+ #draw grid
+ g = svg.group("grid", style="stroke:lightblue;stroke-width:3",
+ transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
+
+ if 1: #self.grid == "on":
+ js = []
+ for key in self.mouseChrLengthDict.keys():
+ length = self.mouseChrLengthDict[key]
+ js.append(mPlotWidth*length/cLength)
+ if length != 0:
+ yCoord = mPlotHeight*(1.0-length/cLength)
+ l = svg.line(0,yCoord ,mPlotWidth, yCoord)
+ g.addElement(l)
+ xCoord = mPlotWidth*length/cLength
+ l = svg.line(xCoord, 0 ,xCoord, mPlotHeight)
+ g.addElement(l)
+ js.sort()
+ drawSpace.addElement(svg.script("",language="javascript", cdata="var openURL=\"%s\";\nvar chrLength=%s;\n" % (self.openURL, js)))
+
+ g.addElement(svg.rect(0, 0, mPlotWidth, mPlotHeight,'none','black',10))
+ drawSpaceMain.addElement(g)
+
+ #draw Scale
+ g = svg.group("scale", style="stroke:black;stroke-width:0",
+ transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
+ i = 100
+ scaleFontSize = 11*cordZOOM
+ while i < cLength:
+ yCoord = mPlotHeight - mPlotHeight*i/cLength
+ l = svg.line(0,yCoord ,-5*cordZOOM, yCoord)
+ g.addElement(l)
+ t = svg.text(-40*cordZOOM, yCoord +5*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag Y
+ g.addElement(t)
+ xCoord = mPlotWidth*i/cLength
+ l = svg.line(xCoord, mPlotHeight, xCoord, mPlotHeight+5*cordZOOM)
+ g.addElement(l)
+ if i%200 == 0:
+ t = svg.text(xCoord, mPlotHeight+10*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag X
+ g.addElement(t)
+ i += 100
+
+ drawSpaceMain.addElement(g)
+ #draw Points
+ finecolors = Plot.colorSpectrumSVG(12)
+ finecolors.reverse()
+ g = preColor = ""
+ for item in data:
+ _probeset, _chr, _Mb, _marker, _pvalue = item[2:]
+ try:
+ _idx = int((-math.log10(_pvalue))*12/6.0) # add module name
+ _color = finecolors[_idx]
+ except:
+ _color = finecolors[-1]
+ if _color != preColor:
+ preColor = _color
+ if g:
+ drawSpaceMain.addElement(g)
+ g = svg.group("points", style="stroke:%s;stroke-width:5" % _color,
+ transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1),
+ onmouseover="mvMsgBox(evt);", onmouseout="hdMsgBox();", onmousedown="openPage(evt);")
+ else:
+ pass
+ px = mPlotWidth*item[0]/cLength
+ py = mPlotHeight*(1.0-item[1]/cLength)
+ l = svg.line("%2.1f" % (px-3*cordZOOM), "%2.1f" % py, "%2.1f" % (px+3*cordZOOM), "%2.1f" % py, ps=_probeset, mk=_marker)
+ g.addElement(l)
+
+ drawSpaceMain.addElement(g)
+
+ """
+ #draw spectrum
+ i = 0
+ j = 0
+ middleoffsetX = 40
+ labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
+ for dcolor in finecolors:
+ drawSpace.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \
+ xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
+ if i % 50 == 0:
+ drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
+ xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
+ drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
+ j += 1
+ i += 1
+ drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \
+ xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)
+ drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
+ labelFont=pid.Font(ttf="tahoma",size=14,bold=1)
+ drawSpace.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
+
+ labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+ drawSpace.drawString(XLabel, xLeftOffset + (plotWidth -drawSpace.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
+ drawSpace.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -drawSpace.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)
+ """
+ drawSpace.addElement(drawSpaceMain)
+
+ g= svg.group(id="dispBox", overflow="visible",
+ style="fill:white;stroke:orange;stroke-width:1;opacity:0.85;",
+ transform="translate(%d,650)" % (cWidth-40-300), visibility="hidden")
+ g.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
+ g.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
+ g.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
+ g.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_probeset"))
+ g.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_marker"))
+
+ drawSpace.addElement(g)
+
+ canvasSVG.setSVG(drawSpace) #set the svg of the drawing to the svg
+ return canvasSVG
+
+
+ def drawGraph(self, canvas, data, cLength = 2500, offset= (80, 160, 60, 60), XLabel="QTL location (GMb)", YLabel="Gene location (GMb)"):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+
+ #draw Frame
+ canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
+
+ #draw Scale
+ i = 100
+ scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ while i < cLength:
+ yCoord = plotHeight + yTopOffset - plotHeight*i/cLength
+ canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset-5, yCoord)
+ canvas.drawString("%d"% i, xLeftOffset -40, yCoord +5,font=scaleFont)
+ xCoord = xLeftOffset + plotWidth*i/cLength
+ canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, plotHeight + yTopOffset+5)
+ canvas.drawString("%d"% i, xCoord -10, plotHeight + yTopOffset+15,font=scaleFont)
+ i += 100
+
+ #draw Points
+ finecolors = Plot.colorSpectrum(300)
+ finecolors.reverse()
+ for item in data:
+ _pvalue = item[-1]
+ try:
+ _idx = int((-math.log10(_pvalue))*300/6.0) # XZ, 09/11/2008: add module name
+ _color = finecolors[_idx]
+ except:
+ _color = finecolors[-1]
+
+ canvas.drawCross(xLeftOffset + plotWidth*item[0]/cLength, plotHeight + yTopOffset - plotHeight*item[1]/cLength, color=_color,size=3)
+
+ #draw grid / always draw grid
+ if 1: #self.grid == "on":
+ for key in self.mouseChrLengthDict.keys():
+ length = self.mouseChrLengthDict[key]
+ if length != 0:
+ yCoord = plotHeight + yTopOffset - plotHeight*length/cLength
+ canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset+plotWidth, yCoord, color=pid.lightgrey)
+ xCoord = xLeftOffset + plotWidth*length/cLength
+ canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, yTopOffset, color=pid.lightgrey)
+
+ #draw spectrum
+ i = 0
+ j = 0
+ middleoffsetX = 40
+ labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
+ for dcolor in finecolors:
+ canvas.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \
+ xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
+ if i % 50 == 0:
+ canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
+ xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
+ canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
+ j += 1
+ i += 1
+ canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \
+ xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)
+ canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
+ labelFont=pid.Font(ttf="tahoma",size=14,bold=1)
+ canvas.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
+
+ labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+ canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
+ canvas.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)
+ return
+
+ def readMouseGenome(self, RISet):
+ ldict = {}
+ lengths = []
+ sum = 0
+ #####################################
+ # Retrieve Chr Length Information
+ #####################################
+ self.cursor.execute("""
+ Select
+ Chr_Length.Name, Length from Chr_Length, InbredSet
+ where
+ Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+ InbredSet.Name = '%s'
+ Order by
+ OrderId
+ """ % RISet)
+ lengths = self.cursor.fetchall()
+ ldict[lengths[0][0]] = 0
+ prev = lengths[0][1]/1000000.0
+ sum += lengths[0][1]/1000000.0
+ for item in lengths[1:]:
+ ldict[item[0]] = prev
+ prev += item[1]/1000000.0
+ sum += item[1]/1000000.0
+ return ldict, sum
+
+ def cmppValue(self, A,B):
+ if A[-1] < B[-1]:
+ return -1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return 1
+
diff --git a/web/webqtl/genomeGraph/genAllDbResultPage.py b/web/webqtl/genomeGraph/genAllDbResultPage.py
new file mode 100755
index 00000000..f0663a7c
--- /dev/null
+++ b/web/webqtl/genomeGraph/genAllDbResultPage.py
@@ -0,0 +1,309 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import string
+import os
+import time
+
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.templatePage import templatePage
+
+
+#########################################
+# Genome Scan PAGE
+#########################################
+class genAllDbResultPage(templatePage):
+
+ def __init__(self,fd):
+
+ templatePage.__init__(self,fd)
+
+ if not self.openMysql():
+ return
+
+ self.database = fd.formdata.getvalue('database', '')
+ db = webqtlDataset(self.database, self.cursor)
+
+ try:
+ if db.type != "ProbeSet" or not db.id:
+ raise DbNameError
+ except:
+ print 'Content-type: text/html\n'
+ heading = "Download Results"
+ detail = ["Only results of microarray database are available to download."]
+ self.error(heading=heading,detail=detail)
+ self.write()
+ return
+
+
+ #XZ, protect confidential dataset.
+ userExist = None
+ self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' % self.database)
+ indId, indName, indFullName, indConfid, AuthorisedUsers = self.cursor.fetchall()[0]
+ if indConfid == 1 and userExist == None:
+ try:
+
+ userExist = self.userName
+
+ #for the dataset that confidentiality is 1
+ #1. 'admin' and 'root' can see all of the dataset
+ #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
+ if webqtlConfig.USERDICT[self.privilege] < webqtlConfig.USERDICT['admin']:
+ if not AuthorisedUsers:
+ userExist=None
+ else:
+ AuthorisedUsersList=AuthorisedUsers.split(',')
+ if not AuthorisedUsersList.__contains__(self.userName):
+ userExist=None
+ except:
+ pass
+
+ if not userExist:
+ #Error, Confidential Database
+ heading = "Correlation Table"
+ detail = ["The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName]
+ self.error(heading=heading,detail=detail,error="Confidential Database")
+ return
+
+ self.cursor.execute("""
+ Select
+ InbredSet.Name
+ From
+ ProbeSetFreeze, ProbeFreeze, InbredSet
+ whERE
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+ ProbeFreeze.InbredSetId = InbredSet.Id AND
+ ProbeSetFreeze.Id = %d
+ """ % db.id)
+ thisRISet = self.cursor.fetchone()[0]
+ if thisRISet =='BXD300':
+ thisRISet = 'BXD'
+
+ #XZ, 06/26/2009: It seems that this query is not neccessary. It doesn't return any result.
+ #XZ: It seems it is just for test purpose. The next try-except block does the real work.
+ #XZ: I think it should be deleted to shorten the response time.
+ #self.cursor.execute("""
+ # Select
+ # ProbeSet.Name, ProbeSet.symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus,
+ # ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.mean
+ # From
+ # ProbeSet, ProbeSetXRef
+ # whERE
+ # ProbeSetXRef.ProbeSetFreezeId = %d AND
+ # ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ # ProbeSetXRef.Locus is not NULL
+ # Order by
+ # ProbeSet.name_num
+ # """ % db.id)
+
+ filename = os.path.join(webqtlConfig.SECUREDIR, db.name+'.result.xls')
+
+ try:
+ import random234
+ if random.choice(range(10)) == 0:
+ raise "ReCalculate"
+ fp = open(filename, 'rb')
+ text = fp.read()
+ fp.close()
+ except:
+ self.cursor.execute("Select ProbeSetXRef.ProbeSetId from ProbeSetXRef where ProbeSetFreezeId=%d" % db.id)
+ ProbeSetIds = self.cursor.fetchall()
+ self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
+
+ if ProbeSetIds:
+ import reaper
+ markerGMb = {}
+ genotype_1 = reaper.Dataset()
+ genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
+ for chr in genotype_1:
+ chrlen = self.mouseChrLengthDict[chr.name]
+ for locus in chr:
+ markerGMb[locus.name] = [chr.name, locus.Mb, locus.Mb + chrlen]
+
+ text = []
+ text.append(['ProbeSetId', 'Symbol', 'Description', 'Target Description', 'Chr', 'TMb', 'TGMb', 'Locus', 'LRS', 'Additive', 'pvalue', 'markerChr', 'markerMb', 'markerGMb', 'meanExpression'])
+ ProbeSetIdList = []
+ for ProbeSetId in ProbeSetIds:
+ ProbeSetIdList.append(ProbeSetId[0])
+ if len(ProbeSetIdList)==1000:
+ ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
+ ProbeSetIdList = []
+
+ cmd = """
+ Select
+ ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description,ProbeSet.Chr, ProbeSet.Mb,
+ ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue,
+ ProbeSetXRef.additive, ProbeSetXRef.mean
+ From
+ ProbeSet, ProbeSetXRef
+ Where
+ ProbeSetXRef.ProbeSetFreezeId = %s AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetXRef.Locus is not NULL AND
+ ProbeSet.Id in (%s)
+ Order by
+ ProbeSet.name_num
+ """ % (db.id, ProbeSetIdStr)
+
+ self.cursor.execute(cmd)
+ results = self.cursor.fetchall()
+
+ for result in results:
+ _Id, _symbol, _desc,_targetDesc, _chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
+ if _marker == "-":
+ continue
+ if not _additive:
+ _additive = ""
+
+ try:
+ _TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
+ except:
+ _TGMb = ""
+
+ result2 = [_Id, _symbol, _desc, _targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
+ try:
+ result2 += markerGMb[_marker]
+ except:
+ result2 += ['', '', '']
+ result2 += [_mean]
+ text.append(map(str, result2))
+
+ #XZ, 06/29/2007: This block is dealing with the last several probesets that fall out of the 1000-probeset block.
+ if ProbeSetIdList:
+ ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
+
+ cmd = """
+ Select
+ ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description, ProbeSet.Chr, ProbeSet.Mb,
+ ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue,
+ ProbeSetXRef.additive, ProbeSetXRef.mean
+ From
+ ProbeSet, ProbeSetXRef
+ Where
+ ProbeSetXRef.ProbeSetFreezeId = %s AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetXRef.Locus is not NULL AND
+ ProbeSet.Id in (%s)
+ Order by
+ ProbeSet.name_num
+ """ % (db.id, ProbeSetIdStr)
+
+ self.cursor.execute(cmd)
+ results = self.cursor.fetchall()
+
+ for result in results:
+ _Id, _symbol, _desc, _targetDesc,_chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
+ if _marker == "-":
+ continue
+ if not _additive:
+ _additive = ""
+
+ try:
+ _TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
+ except:
+ _TGMb = ""
+
+ result2 = [_Id, _symbol, _desc,_targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
+ try:
+ result2 += markerGMb[_marker]
+ except:
+ result2 += ['', '', '']
+ result2 += [_mean]
+ text.append(map(str, result2))
+
+
+ import pyXLWriter as xl
+ # Create a new Excel workbook
+ workbook = xl.Writer(filename)
+ worksheet = workbook.add_worksheet()
+ heading = workbook.add_format(align = 'center', bold = 1, size=13, color = 'red')
+ titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
+
+ worksheet.write([0, 0], "Data source: The GeneNetwork at http://www.genenetwork.org", titleStyle)
+ worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
+ worksheet.write([2, 0], "Database : %s" % db.fullname, titleStyle)
+ worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
+ worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
+ worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
+
+ table_row_start_index = 7
+ nrow = table_row_start_index
+ for row in text:
+ for ncol, cell in enumerate(row):
+ if nrow == table_row_start_index:
+ worksheet.write([nrow, ncol], cell.strip(), heading)
+ worksheet.set_column([ncol, ncol], 20)
+ else:
+ worksheet.write([nrow, ncol], cell.strip())
+ nrow += 1
+
+ worksheet.write([1+nrow, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
+ worksheet.write([2+nrow, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
+
+ workbook.close()
+
+ fp = open(filename, 'rb')
+ text = fp.read()
+ fp.close()
+ else:
+ heading = "Download Results"
+ detail = ["Database calculation is not finished."]
+ self.error(heading=heading,detail=detail)
+ return
+
+ self.content_type = 'application/xls'
+ self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
+ self.attachment = text
+
+ def readMouseGenome(self, RISet):
+ ldict = {}
+ lengths = []
+ sum = 0
+ #####################################
+ # Retrieve Chr Length Information
+ #####################################
+ self.cursor.execute("""
+ Select
+ Chr_Length.Name, Length from Chr_Length, InbredSet
+ where
+ Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+ InbredSet.Name = '%s'
+ Order by
+ OrderId
+ """ % RISet)
+ lengths = self.cursor.fetchall()
+ ldict[lengths[0][0]] = 0
+ prev = lengths[0][1]/1000000.0
+ sum += lengths[0][1]/1000000.0
+ for item in lengths[1:]:
+ ldict[item[0]] = prev
+ prev += item[1]/1000000.0
+ sum += item[1]/1000000.0
+ return ldict, sum
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:46:29 +0000