# 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