diff options
Diffstat (limited to 'web/webqtl/genomeGraph')
| -rwxr-xr-x | web/webqtl/genomeGraph/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/genomeGraph/cmdGenomeScanPage.py | 532 | ||||
| -rwxr-xr-x | web/webqtl/genomeGraph/genAllDbResultPage.py | 309 |
3 files changed, 0 insertions, 841 deletions
diff --git a/web/webqtl/genomeGraph/__init__.py b/web/webqtl/genomeGraph/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/genomeGraph/__init__.py +++ /dev/null diff --git a/web/webqtl/genomeGraph/cmdGenomeScanPage.py b/web/webqtl/genomeGraph/cmdGenomeScanPage.py deleted file mode 100755 index d880ce69..00000000 --- a/web/webqtl/genomeGraph/cmdGenomeScanPage.py +++ /dev/null @@ -1,532 +0,0 @@ -# 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 deleted file mode 100755 index f0663a7c..00000000 --- a/web/webqtl/genomeGraph/genAllDbResultPage.py +++ /dev/null @@ -1,309 +0,0 @@ -# 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 |