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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/intervalMapping/IntervalMappingPage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/intervalMapping/IntervalMappingPage.py')
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diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py
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+# 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 Zach 12/14/2010
+
+
+import time
+import string
+from math import *
+import piddle as pid
+import sys,os
+import httplib, urllib
+
+from htmlgen import HTMLgen2 as HT
+from utility import Plot
+from intervalAnalyst import GeneUtil
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base import webqtlConfig
+from dbFunction import webqtlDatabaseFunction
+from base.GeneralObject import GeneralObject
+
+#########################################
+# Inteval Mapping Plot Page
+#########################################
+class IntervalMappingPage(templatePage):
+ cMGraphInterval = 5
+ maxBootStrap = 50
+ GRAPH_MIN_WIDTH = 900
+ GRAPH_MAX_WIDTH = 10000 # Don't set this too high
+ GRAPH_DEFAULT_WIDTH = 1280
+ MULT_GRAPH_DEFAULT_WIDTH = 2000
+ MULT_GRAPH_MIN_WIDTH = 1400
+ MULT_GRAPH_DEFAULT_WIDTH = 1600
+ GRAPH_DEFAULT_HEIGHT = 600
+
+
+ # Display order:
+ # UCSC BAND =========
+ # ENSEMBL BAND -=-=-=
+ # ** GENES **********
+ BAND_SPACING = 4
+
+ #ENSEMBL_BAND_Y = UCSC_BAND_Y + UCSC_BAND_HEIGHT + BAND_SPACING
+ UCSC_BAND_HEIGHT = 10
+ ENSEMBL_BAND_HEIGHT = 10
+ WEBQTL_BAND_HEIGHT = 10
+
+ #GENE_START_Y = ENSEMBL_BAND_Y + ENSEMBL_BAND_HEIGHT + BAND_SPACING
+ NUM_GENE_ROWS = 10
+ EACH_GENE_HEIGHT = 6 # number of pixels tall, for each gene to display
+ EACH_GENE_ARROW_WIDTH = 5
+ EACH_GENE_ARROW_SPACING = 14
+ DRAW_DETAIL_MB = 4
+ DRAW_UTR_LABELS_MB = 4
+
+ MIN_PIXELS_BETWEEN_LABELS = 50
+
+ qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
+ # Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
+ # like the ones on the image, though, which is why we don't use it here.
+
+ HELP_WINDOW_NAME = 'helpWind'
+
+ ## BEGIN HaplotypeAnalyst
+ NR_INDIVIDUALS = 0
+ ## END HaplotypeAnalyst
+
+ ALEX_DEBUG_BOOL_COLORIZE_GENES = 1 # 0=don't colorize, 1=colorize
+ ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1
+
+ kWIDTH_DEFAULT=1
+
+ kONE_MILLION = 1000000
+
+ LODFACTOR = 4.61
+
+ SNP_COLOR = pid.orange # Color for the SNP "seismograph"
+ TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple
+
+ GENE_FILL_COLOR = pid.HexColor(0x6666FF)
+ GENE_OUTLINE_COLOR = pid.HexColor(0x000077)
+ BOOTSTRAP_BOX_COLOR = pid.yellow
+ LRS_COLOR = pid.HexColor(0x0000FF)
+ LRS_LINE_WIDTH = 2
+ SIGNIFICANT_COLOR = pid.HexColor(0xEBC7C7)
+ SUGGESTIVE_COLOR = pid.gainsboro
+ SIGNIFICANT_WIDTH = 5
+ SUGGESTIVE_WIDTH = 5
+ ADDITIVE_COLOR_POSITIVE = pid.green
+ ADDITIVE_COLOR_NEGATIVE = pid.red
+ ADDITIVE_COLOR = ADDITIVE_COLOR_POSITIVE
+ DOMINANCE_COLOR_POSITIVE = pid.darkviolet
+ DOMINANCE_COLOR_NEGATIVE = pid.orange
+
+ ## BEGIN HaplotypeAnalyst
+ HAPLOTYPE_POSITIVE = pid.green
+ HAPLOTYPE_NEGATIVE = pid.red
+ HAPLOTYPE_HETEROZYGOUS = pid.blue
+ HAPLOTYPE_RECOMBINATION = pid.darkgray
+ ## END HaplotypeAnalyst
+
+ QMARK_EDGE_COLOR = pid.HexColor(0x718118)
+ QMARK_FILL_COLOR = pid.HexColor(0xDEE3BB)
+
+ TOP_RIGHT_INFO_COLOR = pid.black
+ X_AXIS_LABEL_COLOR = pid.black #HexColor(0x505050)
+
+ MINI_VIEW_MAGNIFIED_REGION_COLOR = pid.HexColor(0xCC0000)
+ MINI_VIEW_OUTSIDE_REGION_COLOR = pid.HexColor(0xEEEEEE)
+ MINI_VIEW_BORDER_COLOR = pid.black
+
+ CLICKABLE_WEBQTL_REGION_COLOR = pid.HexColor(0xF5D3D3)
+ CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
+ CLICKABLE_WEBQTL_TEXT_COLOR = pid.HexColor(0x912828)
+
+ CLICKABLE_UCSC_REGION_COLOR = pid.HexColor(0xDDDDEE)
+ CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF)
+ CLICKABLE_UCSC_TEXT_COLOR = pid.HexColor(0x333366)
+
+ CLICKABLE_ENSEMBL_REGION_COLOR = pid.HexColor(0xEEEEDD)
+ CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = pid.HexColor(0xFEFEEE)
+ CLICKABLE_ENSEMBL_TEXT_COLOR = pid.HexColor(0x555500)
+
+ GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF)
+ GRAPH_BACK_DARK_COLOR = pid.HexColor(0xF1F1F9)
+
+ HELP_PAGE_REF = '/glossary.html'
+
+ DRAW_UTR_LABELS=0
+
+ def __init__(self,fd):
+
+ templatePage.__init__(self, fd)
+
+ if not self.openMysql():
+ return
+
+ #RISet and Species
+ if not fd.genotype:
+ fd.readGenotype()
+
+ fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
+
+ if ((fd.parentsf14regression == 'on') and fd.genotype_2):
+ fd.genotype = fd.genotype_2
+ else:
+ fd.genotype = fd.genotype_1
+ fd.strainlist = list(fd.genotype.prgy)
+
+ self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+ if self.species == "rat":
+ self._ucscDb = "rn3"
+ elif self.species == "mouse":
+ self._ucscDb = "mm9"
+ else:
+ self._ucscDb = ""
+
+ #####################################
+ # Options
+ #####################################
+ #Mapping options
+ self.plotScale = fd.formdata.getvalue('scale', 'physic')
+ if self.plotScale == 'physic' and not fd.genotype.Mbmap:
+ self.plotScale = 'morgan'
+ self.permChecked = fd.formdata.getvalue('permCheck')
+ self.bootChecked = fd.formdata.getvalue('bootCheck', '')
+ self.controlLocus = fd.formdata.getvalue('controlLocus', '')
+ try:
+ self.selectedChr = int(fd.formdata.getvalue('chromosomes', "-1"))
+ except:
+ self.selectedChr = -1
+
+ #whether include parents and F1 for InbredSet
+ fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
+ if ((fd.parentsf14regression == 'on') and fd.genotype_2):
+ fd.genotype = fd.genotype_2
+ else:
+ fd.genotype = fd.genotype_1
+ self.strainlist = list(fd.genotype.prgy)
+ self.genotype = fd.genotype
+
+ #Darwing Options
+ try:
+ if self.selectedChr > -1:
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(fd.formdata.getvalue('graphWidth'))))
+ else:
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(fd.formdata.getvalue('graphWidth'))))
+ except:
+ if self.selectedChr > -1:
+ self.graphWidth = self.GRAPH_DEFAULT_WIDTH
+ else:
+ self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH
+
+## BEGIN HaplotypeAnalyst
+ self.haplotypeAnalystChecked = fd.formdata.getvalue('haplotypeAnalystCheck')
+## END HaplotypeAnalyst
+
+
+ self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
+ self.additiveChecked = fd.formdata.getvalue('additiveCheck')
+ self.dominanceChecked = fd.formdata.getvalue('dominanceCheck')
+ self.LRS_LOD = fd.formdata.getvalue('LRSCheck', 'LRS')
+ self.intervalAnalystChecked = fd.formdata.getvalue('intervalAnalystCheck')
+ self.legendChecked = fd.formdata.getvalue('viewLegend')
+ self.geneChecked = fd.formdata.getvalue('showGenes')
+ self.SNPChecked = fd.formdata.getvalue('showSNP')
+ self.draw2X = fd.formdata.getvalue('draw2X')
+ self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0))
+
+ self.startMb = fd.formdata.getvalue('startMb', "-1")
+ self.endMb = fd.formdata.getvalue('endMb', "-1")
+ try:
+ self.startMb = float(self.startMb)
+ self.endMb = float(self.endMb)
+ if self.startMb > self.endMb:
+ temp = self.startMb
+ self.startMb = self.endMb
+ self.endMb = temp
+ #minimal distance 10bp
+ if self.endMb - self.startMb < 0.00001:
+ self.endMb = self.startMb + 0.00001
+ except:
+ self.startMb = self.endMb = -1
+ #Trait Infos
+ self.identification = fd.formdata.getvalue('identification', "")
+
+ ################################################################
+ # Generate Chr list and Retrieve Length Information
+ ################################################################
+ self.ChrList = [("All", -1)]
+ for i, indChr in enumerate(self.genotype):
+ self.ChrList.append((indChr.name, i))
+
+ self.cursor.execute("""
+ Select
+ Length from Chr_Length, InbredSet
+ where
+ Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+ InbredSet.Name = '%s' AND
+ Chr_Length.Name in (%s)
+ Order by
+ OrderId
+ """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
+
+ self.ChrLengthMbList = self.cursor.fetchall()
+ self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
+ self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
+ if self.ChrLengthMbList:
+ self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
+ else:
+ self.MbGraphInterval = 1
+
+ self.ChrLengthCMList = []
+ for i, _chr in enumerate(self.genotype):
+ self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
+ self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)
+
+ if self.plotScale == 'physic':
+ self.GraphInterval = self.MbGraphInterval #Mb
+ else:
+ self.GraphInterval = self.cMGraphInterval #cM
+
+
+ ################################################################
+ # Get Trait Values and Infomation
+ ################################################################
+ #input from search page or selection page
+ self.searchResult = fd.formdata.getvalue('searchResult')
+ #convert single selection into a list
+ if type("1") == type(self.searchResult):
+ self.searchResult = string.split(self.searchResult,'\t')
+
+ self.traitList = []
+ if self.searchResult and len(self.searchResult) > webqtlConfig.MULTIPLEMAPPINGLIMIT:
+ heading = 'Multiple Interval Mapping'
+ detail = ['In order to get clear result, do not select more than %d traits for \
+ Multiple Interval Mapping analysis.' % webqtlConfig.MULTIPLEMAPPINGLIMIT]
+ self.error(heading=heading,detail=detail)
+ return
+ elif self.searchResult:
+ self.dataSource = 'selectionPage'
+ for item in self.searchResult:
+ thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+ thisTrait.retrieveInfo()
+ thisTrait.retrieveData(fd.strainlist)
+ self.traitList.append(thisTrait)
+ else:
+ #input from data editing page
+ fd.readData()
+ if not fd.allTraitData:
+ heading = "Mapping"
+ detail = ['No trait data was selected for %s data set. No mapping attempted.' % fd.RISet]
+ self.error(heading=heading,detail=detail)
+ return
+
+ self.dataSource = 'editingPage'
+ fullname = fd.formdata.getvalue('fullname', '')
+ if fullname:
+ thisTrait = webqtlTrait(fullname=fullname, data=fd.allTraitData, cursor=self.cursor)
+ thisTrait.retrieveInfo()
+ else:
+ thisTrait = webqtlTrait(data=fd.allTraitData)
+ self.traitList.append(thisTrait)
+
+
+
+
+
+
+
+## BEGIN HaplotypeAnalyst
+## count the amount of individuals to be plotted, and increase self.graphHeight
+ if self.haplotypeAnalystChecked and self.selectedChr > -1:
+ thisTrait = self.traitList[0]
+ _strains, _vals, _vars = thisTrait.exportInformative()
+ smd=[]
+ for ii, _val in enumerate(_vals):
+ temp = GeneralObject(name=_strains[ii], value=_val)
+ smd.append(temp)
+ bxdlist=list(self.genotype.prgy)
+ for j,_geno in enumerate (self.genotype[0][1].genotype):
+ for item in smd:
+ if item.name == bxdlist[j]:
+ self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
+## default:
+ self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
+## for paper:
+ #self.graphHeight = self.graphHeight + 1 * self.NR_INDIVIDUALS * self.EACH_GENE_HEIGHT - 180
+
+
+
+## END HaplotypeAnalyst
+
+ ################################################################
+ # Calculations QTL goes here
+ ################################################################
+ self.multipleInterval = len(self.traitList) > 1
+ errorMessage = self.calculateAllResult(fd)
+ if errorMessage:
+ heading = "Mapping"
+ detail = ['%s' % errorMessage]
+ self.error(heading=heading,detail=detail)
+ return
+
+ if self.multipleInterval:
+ self.colorCollection = Plot.colorSpectrum(len(self.qtlresults))
+ else:
+ self.colorCollection = [self.LRS_COLOR]
+
+
+ #########################
+ ## Get the sorting column
+ #########################
+ RISet = fd.RISet
+ if RISet in ('AXB', 'BXA', 'AXBXA'):
+ self.diffCol = ['B6J', 'A/J']
+ elif RISet in ('BXD', 'BXD300', 'B6D2F2', 'BDF2-2005', 'BDF2-1999', 'BHHBF2'):
+ self.diffCol = ['B6J', 'D2J']
+ elif RISet in ('CXB'):
+ self.diffCol = ['CBY', 'B6J']
+ elif RISet in ('BXH', 'BHF2'):
+ self.diffCol = ['B6J', 'C3H']
+ elif RISet in ('B6BTBRF2'):
+ self.diffCol = ['B6J', 'BTB']
+ elif RISet in ('LXS'):
+ self.diffCol = ['ILS', 'ISS']
+ else:
+ self.diffCol= []
+
+ for i, strain in enumerate(self.diffCol):
+ self.cursor.execute("select Id from Strain where Symbol = %s", strain)
+ self.diffCol[i] = self.cursor.fetchone()[0]
+ #print self.diffCol
+
+ ################################################################
+ # GeneCollection goes here
+ ################################################################
+ if self.plotScale == 'physic':
+ #StartMb or EndMb
+ if self.startMb < 0 or self.endMb < 0:
+ self.startMb = 0
+ self.endMb = self.ChrLengthMbList[self.selectedChr]
+
+ geneTable = ""
+ if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked):
+ chrName = self.genotype[0].name
+ # Draw the genes for this chromosome / region of this chromosome
+ if self.traitList and self.traitList[0] and len(self.traitList) == 1 and self.traitList[0].db:
+ webqtldatabase = self.traitList[0].db.name
+ else:
+ webqtldatabase = None
+
+ self.geneCol = None
+
+ if self.species == "mouse":
+ self.geneCol = GeneUtil.loadGenes(self.cursor, chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
+ elif self.species == "rat":
+ self.geneCol = GeneUtil.loadGenes(self.cursor, chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
+ else:
+ self.geneCol = None
+
+ if self.geneCol and self.intervalAnalystChecked:
+ #######################################################################
+ #Nick use GENEID as RefGene to get Literature Correlation Informations#
+ #For Interval Mapping, Literature Correlation isn't useful, so skip it#
+ #through set GENEID is None #
+ ########################################################################
+
+ #GENEID = fd.formdata.getvalue('GeneId') or None
+ GENEID = None
+ geneTable = self.geneTables(self.geneCol,GENEID)
+
+ else:
+ self.geneCol = None
+
+ ################################################################
+ # Plots goes here
+ ################################################################
+ if self.plotScale != 'physic' or self.multipleInterval:
+ showLocusForm = webqtlUtil.genRandStr("fm_")
+ else:
+ showLocusForm = ""
+ intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
+ gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
+
+ filename= webqtlUtil.genRandStr("Itvl_")
+ intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+ intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
+
+ if self.draw2X:
+ intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
+ gifmapX2 = self.plotIntMapping(fd, intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
+ intCanvasX2.save(os.path.join(webqtlConfig.IMGDIR, filename+"X2"), format='png')
+ DLintImgX2=HT.Href(text='Download',url = '/image/'+filename+'X2.png', Class='smallsize', target='_blank')
+
+ textUrl = self.writeQTL2Text(fd, filename)
+
+ ################################################################
+ # Info tables goes here
+ ################################################################
+ traitInfoTD = self.traitInfoTD(fd)
+
+ if self.draw2X:
+ traitInfoTD.append(HT.P(), DLintImgX2, ' a higher resolution 2X image. ')
+ else:
+ traitInfoTD.append(HT.P())
+
+ if textUrl:
+ traitInfoTD.append(HT.BR(), textUrl, ' results in tab-delimited text format.')
+ traitRemapTD = self.traitRemapTD(self.cursor, fd)
+
+ topTable = HT.TableLite(HT.TR(traitInfoTD, HT.TD("&nbsp;", width=25), traitRemapTD), border=0, cellspacing=0, cellpadding=0)
+
+ ################################################################
+ # Outputs goes here
+ ################################################################
+ #this form is used for opening Locus page or trait page, only available for genetic mapping
+ if showLocusForm:
+ showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
+ name=showLocusForm, submit=HT.Input(type='hidden'))
+ hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+ for key in hddn.keys():
+ showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+ showLocusForm.append(intImg)
+ else:
+ showLocusForm = intImg
+
+ ################################################################
+ # footnote goes here
+ ################################################################
+ btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
+
+ if (self.additiveChecked):
+ btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
+
+ if self.traitList and self.traitList[0].db and self.traitList[0].db.type == 'Geno':
+ btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
+
+ TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
+
+ if geneTable:
+ iaForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=intervalAnalyst"), enctype='multipart/form-data',
+ name="iaForm", submit=HT.Input(type='hidden'))
+ hddn = {'chromosome':self.genotype[0].name, 'species':self.species,'startMb':self.startMb,'endMb':self.endMb}
+ if self.diffCol:
+ hddn['s1'] = self.diffCol[0]
+ hddn['s2'] = self.diffCol[1]
+ for key in hddn.keys():
+ iaForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+ iaForm.append(HT.Paragraph("Interval Analyst : Chr %s from %2.6f to %2.6f Mb" % (self.genotype[0].name, self.startMb, self.endMb),
+ HT.Input(name='customize', value='Customize', onClick= "formInNewWindow(this.form);", type='button', Class="button"), Class="subtitle"))
+ TD_LR.append(HT.Blockquote(iaForm, geneTable))
+
+ self.dict['body'] = TD_LR
+ self.dict['title'] = "Mapping"
+
+ def writeQTL2Text(self, fd, filename):
+ if self.multipleInterval:
+ return ""
+ _dominance = (self.genotype.type == 'intercross')
+ _Mb = self.genotype.Mbmap
+
+ ###Write to text file
+ fpText = open(os.path.join(webqtlConfig.TMPDIR, filename) + '.txt','wb')
+
+ fpText.write("Source: WebQTL, The GeneNetwork (%s)\n" % webqtlConfig.PORTADDR)
+ #
+ fpText.write("Site: %s\n" % webqtlConfig.SITENAME)
+ fpText.write("Page: Map Viewer\n")
+ fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime()))
+ fpText.write("Trait ID: %s\n" % fd.identification)
+ fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive)
+ fpText.write("Significant LRS = %0.2f\n" % self.significance)
+ """
+ if fd.traitInfo:
+ writeSymbol, writeChromosome, writeMb = string.split(fd.traitInfo)
+ else:
+ writeSymbol, writeChromosome, writeMb = (" ", " ", " ")
+ fpText.write("Gene Symbol: %s\n" % writeSymbol)
+ fpText.write("Location: Chr %s @ %s Mb\n" % (writeChromosome, writeMb))
+ selectedChr = self.indexToChrName(int(fd.formdata.getvalue('chromosomes', -1)))
+ fpText.write("Chromosome: %s\n" % selectedChr)
+ fpText.write("Region: %0.6f-%0.6f Mb\n\n" % (self.startMb, self.endMb))
+ """
+
+ if hasattr(self, 'LRSArray'):
+ if _dominance:
+ fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\tDominance\n')
+ else:
+ fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\n')
+ else:
+ if _dominance:
+ fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\tDominance\n')
+ else:
+ fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\n')
+
+ i = 0
+ for qtlresult in self.qtlresults[0]:
+ if _Mb:
+ locusMb = '%2.3f' % qtlresult.locus.Mb
+ else:
+ locusMb = 'N/A'
+
+ if hasattr(self, 'LRSArray'):
+ P_value = self.calculatePValue(qtlresult.lrs, self.LRSArray)
+
+ if _dominance:
+ fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+ qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value, qtlresult.additive, qtlresult.dominance))
+ else:
+ fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+ qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value, qtlresult.additive))
+ else:
+ if _dominance:
+ fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+ qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive, qtlresult.dominance))
+ else:
+ fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+ qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive))
+
+ i += 1
+
+ fpText.close()
+ textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='smallsize')
+ return textUrl
+
+ def plotIntMapping(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+ #calculating margins
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ if self.multipleInterval:
+ yTopOffset = max(80, yTopOffset)
+ else:
+ if self.legendChecked:
+ yTopOffset = max(80, yTopOffset)
+ else:
+ pass
+
+ if self.plotScale != 'physic':
+ yBottomOffset = max(120, yBottomOffset)
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ xLeftOffset = int(xLeftOffset*fontZoom)
+ xRightOffset = int(xRightOffset*fontZoom)
+ yBottomOffset = int(yBottomOffset*fontZoom)
+
+ cWidth = canvas.size[0]
+ cHeight = canvas.size[1]
+ plotWidth = cWidth - xLeftOffset - xRightOffset
+ plotHeight = cHeight - yTopOffset - yBottomOffset
+ startPixelX = xLeftOffset
+ endPixelX = (xLeftOffset + plotWidth)
+
+ #Drawing Area Height
+ drawAreaHeight = plotHeight
+ if self.plotScale == 'physic' and self.selectedChr > -1:
+ drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
+ if self.geneChecked:
+ drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
+ else:
+ if self.selectedChr > -1:
+ drawAreaHeight -= 20
+ else:
+ drawAreaHeight -= 30
+
+## BEGIN HaplotypeAnalyst
+ if self.haplotypeAnalystChecked and self.selectedChr > -1:
+ drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS+10) * 2 * zoom
+## END HaplotypeAnalyst
+
+ #Image map
+ gifmap = HT.Map(name='WebQTLImageMap')
+
+ newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
+ # Draw the alternating-color background first and get plotXScale
+ plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+
+ #draw bootstap
+ if self.bootChecked and not self.multipleInterval:
+ self.drawBootStrapResult(canvas, fd.nboot, drawAreaHeight, plotXScale, offset=newoffset)
+
+ # Draw clickable region and gene band if selected
+ if self.plotScale == 'physic' and self.selectedChr > -1:
+ self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ if self.geneChecked and self.geneCol:
+ self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ if self.SNPChecked:
+ self.drawSNPTrackNew(canvas, offset=newoffset, zoom= 2*zoom, startMb=startMb, endMb = endMb)
+## BEGIN HaplotypeAnalyst
+ if self.haplotypeAnalystChecked:
+ self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+## END HaplotypeAnalyst
+ # Draw X axis
+ self.drawXAxis(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ # Draw QTL curve
+ self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+
+ #draw legend
+ if self.multipleInterval:
+ self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
+ elif self.legendChecked:
+ self.drawLegendPanel(fd, canvas, offset=newoffset)
+ else:
+ pass
+
+ #draw position, no need to use a separate function
+ if fd.genotype.Mbmap:
+ self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset)
+
+ return gifmap
+
+ def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ bootHeightThresh = drawAreaHeight*3/4
+
+ #break bootstrap result into groups
+ BootCoord = []
+ i = 0
+ startX = xLeftOffset
+ for j, _chr in enumerate(self.genotype):
+ BootCoord.append( [])
+ for _locus in _chr:
+ if self.plotScale == 'physic':
+ Xc = startX + (_locus.Mb-self.startMb)*plotXScale
+ else:
+ Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
+ BootCoord[-1].append([Xc, self.bootResult[i]])
+ i += 1
+ startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale
+
+ #reduce bootResult
+ if self.selectedChr > -1:
+ maxBootBar = 80.0
+ else:
+ maxBootBar = 200.0
+ stepBootStrap = plotWidth/maxBootBar
+ reducedBootCoord = []
+ maxBootCount = 0
+
+ for BootChrCoord in BootCoord:
+ nBoot = len(BootChrCoord)
+ bootStartPixX = BootChrCoord[0][0]
+ bootCount = BootChrCoord[0][1]
+ for i in range(1, nBoot):
+ if BootChrCoord[i][0] - bootStartPixX < stepBootStrap:
+ bootCount += BootChrCoord[i][1]
+ continue
+ else:
+ if maxBootCount < bootCount:
+ maxBootCount = bootCount
+ # end if
+ reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount])
+ bootStartPixX = BootChrCoord[i][0]
+ bootCount = BootChrCoord[i][1]
+ # end else
+ # end for
+ #add last piece
+ if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap/2.0:
+ reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount])
+ else:
+ reducedBootCoord[-1][2] += bootCount
+ reducedBootCoord[-1][1] = BootChrCoord[-1][0]
+ # end else
+ if maxBootCount < reducedBootCoord[-1][2]:
+ maxBootCount = reducedBootCoord[-1][2]
+ # end if
+ for item in reducedBootCoord:
+ if item[2] > 0:
+ if item[0] < xLeftOffset:
+ item[0] = xLeftOffset
+ if item[0] > xLeftOffset+plotWidth:
+ item[0] = xLeftOffset+plotWidth
+ if item[1] < xLeftOffset:
+ item[1] = xLeftOffset
+ if item[1] > xLeftOffset+plotWidth:
+ item[1] = xLeftOffset+plotWidth
+ if item[0] != item[1]:
+ canvas.drawRect(item[0], yZero, item[1], yZero - item[2]*bootHeightThresh/maxBootCount,
+ fillColor=self.BOOTSTRAP_BOX_COLOR)
+
+ ###draw boot scale
+ highestPercent = (maxBootCount*100.0)/nboot
+ bootScale = Plot.detScale(0, highestPercent)
+ bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1]/bootScale[2])
+ bootScale = bootScale[:-1] + [highestPercent]
+
+ bootOffset = 50*fontZoom
+ bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0)
+ canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow)
+ canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black)
+ canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black)
+ for item in bootScale:
+ if item == 0:
+ continue
+ bootY = yZero-bootHeightThresh*item/highestPercent
+ canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=pid.black)
+ canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=pid.black)
+
+ if self.legendChecked:
+ startPosY = 30
+ nCol = 2
+ smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
+ leftOffset = xLeftOffset+(nCol-1)*200
+ canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=pid.yellow)
+ canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=pid.black)
+
+ def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ if len(self.traitList) != 1:
+ return
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ try:
+ Chr = self.traitList[0].chr
+ Mb = self.traitList[0].mb
+ except:
+ return
+
+ if self.plotScale == 'physic':
+ if self.selectedChr > -1:
+ if self.genotype[0].name != Chr or Mb < self.startMb or Mb > self.endMb:
+ return
+ else:
+ locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
+ else:
+ locPixel = xLeftOffset
+ for i, _chr in enumerate(self.genotype):
+ if _chr.name != Chr:
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ else:
+ locPixel += Mb*plotXScale
+ break
+ else:
+ if self.selectedChr > -1:
+ if self.genotype[0].name != Chr:
+ return
+ else:
+ for i, _locus in enumerate(self.genotype[0]):
+ #the trait's position is on the left of the first genotype
+ if i==0 and _locus.Mb >= Mb:
+ locPixel=-1
+ break
+
+ #the trait's position is between two traits
+ if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
+ locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
+ break
+
+ #the trait's position is on the right of the last genotype
+ if i==len(self.genotype[0]) and Mb>=_locus.Mb:
+ locPixel = -1
+ else:
+ locPixel = xLeftOffset
+ for i, _chr in enumerate(self.genotype):
+ if _chr.name != Chr:
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ else:
+ locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+ break
+ if locPixel >= 0:
+ traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
+ canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
+
+ if self.legendChecked:
+ startPosY = 15
+ nCol = 2
+ smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
+ leftOffset = xLeftOffset+(nCol-1)*200
+ canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
+ canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)
+
+
+ def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
+ return
+
+ SNP_HEIGHT_MODIFIER = 18.0
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ drawSNPLocationY = yTopOffset + plotHeight
+ chrName = self.genotype[0].name
+
+ stepMb = (endMb-startMb)/plotWidth
+ strainId1, strainId2 = self.diffCol
+ SNPCounts = []
+
+ while startMb<endMb:
+ self.cursor.execute("""
+ select
+ count(*) from BXDSnpPosition
+ where
+ Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
+ StrainId1 = %d AND StrainId2 = %d
+ """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2))
+ SNPCounts.append(self.cursor.fetchone()[0])
+ startMb += stepMb
+
+ if (len(SNPCounts) > 0):
+ maxCount = max(SNPCounts)
+ if maxCount>0:
+ for i in range(xLeftOffset, xLeftOffset + plotWidth):
+ snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
+ canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1)
+
+ def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
+ nameWidths = []
+ yPaddingTop = 10
+ colorFont=pid.Font(ttf="trebuc",size=12,bold=1)
+ if len(self.qtlresults) >20 and self.selectedChr > -1:
+ rightShift = 20
+ rightShiftStep = 60
+ rectWidth = 10
+ else:
+ rightShift = 40
+ rightShiftStep = 80
+ rectWidth = 15
+
+ for k, thisTrait in enumerate(self.traitList):
+ thisLRSColor = self.colorCollection[k]
+ kstep = k % 4
+ if k!=0 and kstep==0:
+ if nameWidths:
+ rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20
+ rightShift += rightShiftStep
+
+ name = thisTrait.displayName()
+ nameWidth = canvas.stringWidth(name,font=colorFont)
+ nameWidths.append(nameWidth)
+
+ canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor)
+ canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black)
+ if thisTrait.db:
+
+ COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+ HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
+ Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+ gifmap.areas.append(Areas)
+
+
+ def drawLegendPanel(self, fd, canvas, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+
+ labelFont=pid.Font(ttf="trebuc",size=12, bold=1)
+ startPosY = 15
+ stepPosY = 12
+ canvas.drawLine(xLeftOffset,startPosY,xLeftOffset+32,startPosY,color=self.LRS_COLOR, width=2)
+ canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=pid.black)
+ startPosY += stepPosY
+
+ if self.additiveChecked:
+ startPosX = xLeftOffset
+ canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.ADDITIVE_COLOR_POSITIVE, width=2)
+ canvas.drawLine(startPosX+18,startPosY,startPosX+32,startPosY,color=self.ADDITIVE_COLOR_NEGATIVE, width=2)
+ canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=pid.black)
+
+ if self.genotype.type == 'intercross' and self.dominanceChecked:
+ startPosX = xLeftOffset
+ startPosY += stepPosY
+ canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.DOMINANCE_COLOR_POSITIVE, width=4)
+ canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.DOMINANCE_COLOR_NEGATIVE, width=4)
+ canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=pid.black)
+
+ if self.haplotypeAnalystChecked:
+ startPosY += stepPosY
+ startPosX = xLeftOffset
+ canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.HAPLOTYPE_POSITIVE, width=4)
+ canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.HAPLOTYPE_NEGATIVE, width=4)
+ canvas.drawLine(startPosX+36,startPosY,startPosX+53,startPosY,color=self.HAPLOTYPE_HETEROZYGOUS, width=4)
+ canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4)
+ canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black)
+
+ if self.permChecked:
+ startPosY += stepPosY
+ startPosX = xLeftOffset
+ canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
+ canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
+ lod = 1
+ if self.LRS_LOD == 'LOD':
+ lod = self.LODFACTOR
+ canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significance/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
+ canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive/lod),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
+
+
+
+ labelFont=pid.Font(ttf="verdana",size=12)
+ labelColor = pid.black
+ if self.selectedChr == -1:
+ string1 = 'Mapping for Dataset: %s, mapping on All Chromosomes' % fd.RISet
+ else:
+ string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (fd.RISet,self.genotype[0].name)
+ if self.controlLocus:
+ string2 = 'Using %s as control' % self.controlLocus
+ else:
+ string2 = 'Using Haldane mapping function with no control for other QTLs'
+ d = 4+ max(canvas.stringWidth(string1,font=labelFont),canvas.stringWidth(string2,font=labelFont))
+ if fd.identification:
+ identification = "Trait ID: %s" % fd.identification
+ canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20,font=labelFont,color=labelColor)
+
+ canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35,font=labelFont,color=labelColor)
+ canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50,font=labelFont,color=labelColor)
+
+
+ def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
+ return
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ yPaddingTop = yTopOffset
+
+ displayStartInBases = startMb*self.kONE_MILLION
+ displayEndInBases = endMb*self.kONE_MILLION
+
+ for gIndex, theGO in enumerate(self.geneCol):
+ geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s'
+ if self.species == "mouse":
+ txStart = theGO["TxStart"]
+ txEnd = theGO["TxEnd"]
+ geneLength = (txEnd - txStart)*1000.0
+ tenPercentLength = geneLength*0.0001
+ SNPdensity = theGO["snpCount"]/geneLength
+
+ exonStarts = map(float, theGO['exonStarts'].split(",")[:-1])
+ exonEnds = map(float, theGO['exonEnds'].split(",")[:-1])
+ cdsStart = theGO['cdsStart']
+ cdsEnd = theGO['cdsEnd']
+ accession = theGO['NM_ID']
+ geneId = theGO['GeneID']
+ geneSymbol = theGO["GeneSymbol"]
+ strand = theGO["Strand"]
+ exonCount = theGO["exonCount"]
+
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+
+ if (geneEndPix < xLeftOffset):
+ return; # this gene is not on the screen
+ elif (geneEndPix > xLeftOffset + plotWidth):
+ geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ if (geneStartPix > xLeftOffset + plotWidth):
+ return; # we are outside the valid on-screen range, so stop drawing genes
+ elif (geneStartPix < xLeftOffset):
+ geneStartPix = xLeftOffset; # clip the first in-range gene
+
+ #color the gene based on SNP density
+
+
+ #found earlier, needs to be recomputed as snps are added
+
+ #always apply colors now, even if SNP Track not checked - Zach 11/24/2010
+
+ densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
+ if SNPdensity < densities[0]:
+ myColor = pid.black
+ elif SNPdensity < densities[1]:
+ myColor = pid.purple
+ elif SNPdensity < densities[2]:
+ myColor = pid.darkblue
+ elif SNPdensity < densities[3]:
+ myColor = pid.darkgreen
+ elif SNPdensity < densities[4]:
+ myColor = pid.gold
+ elif SNPdensity < densities[5]:
+ myColor = pid.darkorange
+ else:
+ myColor = pid.darkred
+
+ outlineColor = myColor
+ fillColor = myColor
+
+ TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
+ # NL: 06-02-2011 Rob required to change this link for gene related
+ HREF=geneNCBILink %geneSymbol
+
+ elif self.species == "rat":
+ exonStarts = []
+ exonEnds = []
+ txStart = theGO["TxStart"]
+ txEnd = theGO["TxEnd"]
+ cdsStart = theGO["TxStart"]
+ cdsEnd = theGO["TxEnd"]
+ geneId = theGO["GeneID"]
+ geneSymbol = theGO["GeneSymbol"]
+ strand = theGO["Strand"]
+ exonCount = 0
+
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+
+ if (geneEndPix < xLeftOffset):
+ return; # this gene is not on the screen
+ elif (geneEndPix > xLeftOffset + plotWidth):
+ geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ if (geneStartPix > xLeftOffset + plotWidth):
+ return; # we are outside the valid on-screen range, so stop drawing genes
+ elif (geneStartPix < xLeftOffset):
+ geneStartPix = xLeftOffset; # clip the first in-range gene
+
+ outlineColor = pid.darkblue
+ fillColor = pid.darkblue
+ TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
+ # NL: 06-02-2011 Rob required to change this link for gene related
+ HREF=geneNCBILink %geneSymbol
+ else:
+ outlineColor = pid.orange
+ fillColor = pid.orange
+ TITLE = "Gene: %s" % geneSymbol
+
+ #Draw Genes
+ geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
+
+ if 1:#drawClickableRegions:
+ geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+ else:
+ geneYLocation += self.BAND_SPACING
+
+ #draw the detail view
+ if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
+ utrColor = pid.Color(0.66, 0.66, 0.66)
+ arrowColor = pid.Color(0.7, 0.7, 0.7)
+
+ #draw the line that runs the entire length of the gene
+ #canvas.drawString(str(geneStartPix), 300, 400)
+ canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
+
+ #draw the arrows
+ for xCoord in range(0, geneEndPix-geneStartPix):
+
+ if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
+ if strand == "+":
+ canvas.drawLine(geneStartPix + xCoord, geneYLocation, geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+ canvas.drawLine(geneStartPix + xCoord, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH, geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom, color=arrowColor, width=1)
+ else:
+ canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation, geneStartPix + xCoord, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+ canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord, geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+
+ #draw the blocks for the exon regions
+ for i in range(0, len(exonStarts)):
+ exonStartPix = (exonStarts[i]-startMb)*plotXScale + xLeftOffset
+ exonEndPix = (exonEnds[i]-startMb)*plotXScale + xLeftOffset
+ if (exonStartPix < xLeftOffset):
+ exonStartPix = xLeftOffset
+ if (exonEndPix < xLeftOffset):
+ exonEndPix = xLeftOffset
+ if (exonEndPix > xLeftOffset + plotWidth):
+ exonEndPix = xLeftOffset + plotWidth
+ if (exonStartPix > xLeftOffset + plotWidth):
+ exonStartPix = xLeftOffset + plotWidth
+ canvas.drawRect(exonStartPix, geneYLocation, exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+
+ #draw gray blocks for 3' and 5' UTR blocks
+ if cdsStart and cdsEnd:
+
+ utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
+ utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
+ if (utrStartPix < xLeftOffset):
+ utrStartPix = xLeftOffset
+ if (utrEndPix < xLeftOffset):
+ utrEndPix = xLeftOffset
+ if (utrEndPix > xLeftOffset + plotWidth):
+ utrEndPix = xLeftOffset + plotWidth
+ if (utrStartPix > xLeftOffset + plotWidth):
+ utrStartPix = xLeftOffset + plotWidth
+ canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+
+ if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ if strand == "-":
+ labelText = "3'"
+ else:
+ labelText = "5'"
+ canvas.drawString(labelText, utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+
+ #the second UTR region
+
+ utrStartPix = (cdsEnd-startMb)*plotXScale + xLeftOffset
+ utrEndPix = (txEnd-startMb)*plotXScale + xLeftOffset
+ if (utrStartPix < xLeftOffset):
+ utrStartPix = xLeftOffset
+ if (utrEndPix < xLeftOffset):
+ utrEndPix = xLeftOffset
+ if (utrEndPix > xLeftOffset + plotWidth):
+ utrEndPix = xLeftOffset + plotWidth
+ if (utrStartPix > xLeftOffset + plotWidth):
+ utrStartPix = xLeftOffset + plotWidth
+ canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+
+ if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ if tstrand == "-":
+ labelText = "5'"
+ else:
+ labelText = "3'"
+ canvas.drawString(labelText, utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+
+ #draw the genes as rectangles
+ else:
+ canvas.drawRect(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+
+ COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
+ # NL: 06-02-2011 Rob required to display NCBI info in a new window
+ gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+
+## BEGIN HaplotypeAnalyst
+ def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
+ return
+
+
+ fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb')
+
+ clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ widthMultiplier = 1
+
+ yPaddingTop = yTopOffset
+
+ exprdrawn = 0
+
+ thisTrait = self.traitList[0]
+ _strains, _vals, _vars = thisTrait.exportInformative()
+
+ smd=[]
+ for ii, _val in enumerate(_vals):
+ temp = GeneralObject(name=_strains[ii], value=_val)
+ smd.append(temp)
+
+ smd.sort(lambda A, B: cmp(A.value, B.value))
+
+ bxdlist=list(self.genotype.prgy)
+
+ oldgeneEndPix = -1
+ #Initializing plotRight, error before
+ plotRight = xRightOffset
+
+#### find out PlotRight
+ for i, _locus in enumerate(self.genotype[0]):
+ txStart = self.genotype[0][i].Mb
+ txEnd = self.genotype[0][i].Mb
+
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
+
+ drawit = 1
+ if (geneStartPix < xLeftOffset):
+ drawit = 0;
+ if (geneStartPix > xLeftOffset + plotWidth):
+ drawit = 0;
+
+ if drawit == 1:
+
+ if self.genotype[0][i].name != " - " :
+
+ plotRight = geneEndPix + 4
+
+
+
+#### end find out PlotRight
+
+ firstGene = 1
+ lastGene = 0
+
+ #Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype"
+ #was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped.
+ #Now there should always be some value set for "oldgeno" - Zach 12/14/2010
+ oldgeno = [None]*len(self.strainlist)
+
+ for i, _locus in enumerate(self.genotype[0]):
+ txStart = self.genotype[0][i].Mb
+ txEnd = self.genotype[0][i].Mb
+
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0
+
+ if oldgeneEndPix >= xLeftOffset:
+ drawStart = oldgeneEndPix + 4
+ else:
+ drawStart = xLeftOffset + 3
+
+ drawEnd = plotRight - 9
+
+ drawit = 1
+
+ if (geneStartPix < xLeftOffset):
+ if firstGene == 1:
+ drawit = 1
+ else:
+ drawit = 0
+
+ elif (geneStartPix > (xLeftOffset + plotWidth - 3)):
+ if lastGene == 0:
+ drawit = 1
+ drawEnd = xLeftOffset + plotWidth - 6
+ lastGene = 1
+ else:
+ break
+
+ else:
+ firstGene = 0
+ drawit = 1
+
+ if drawit == 1:
+ myColor = pid.darkblue
+ outlineColor = myColor
+ fillColor = myColor
+
+ maxind=0
+
+ #Draw Genes
+
+ geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
+
+ if 1:#drawClickableRegions:
+ geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+ else:
+ geneYLocation += self.BAND_SPACING
+
+ if self.genotype[0][i].name != " - " :
+
+ if (firstGene == 1) and (lastGene != 1):
+ oldgeneEndPix = drawStart = xLeftOffset
+ oldgeno = self.genotype[0][i].genotype
+ continue
+
+ for j,_geno in enumerate (self.genotype[0][i].genotype):
+
+ plotbxd=0
+ for item in smd:
+ if item.name == bxdlist[j]:
+ plotbxd=1
+
+ if (plotbxd == 1):
+ ind = 0
+ counter = 0
+ for item in smd:
+ counter = counter + 1
+ if item.name == bxdlist[j]:
+ ind = counter
+ maxind=max(ind,maxind)
+
+ # lines
+ if (oldgeno[j] == -1 and _geno == -1):
+ mylineColor = self.HAPLOTYPE_NEGATIVE
+ elif (oldgeno[j] == 1 and _geno == 1):
+ mylineColor = self.HAPLOTYPE_POSITIVE
+ elif (oldgeno[j] == 0 and _geno == 0):
+ mylineColor = self.HAPLOTYPE_HETEROZYGOUS
+ else:
+ mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
+
+ canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+
+ fillColor=pid.black
+ outlineColor=pid.black
+ if lastGene == 0:
+ canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
+
+
+ COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
+ TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (bxdlist[j], self.genotype[0][i].name, float(txStart))
+ HREF = ''
+ gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+
+ # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
+ # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
+ if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
+ drawEnd = xLeftOffset + plotWidth - 6
+ mylineColor = self.HAPLOTYPE_RECOMBINATION
+ canvas.drawLine(plotRight, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+
+
+ if lastGene == 0:
+ canvas.drawString("%s" % (self.genotype[0][i].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)
+
+ oldgeneEndPix = geneEndPix;
+ oldgeno = self.genotype[0][i].genotype
+ firstGene = 0
+ else:
+ lastGene = 0
+
+ for j,_geno in enumerate (self.genotype[0][1].genotype):
+
+ plotbxd=0
+ for item in smd:
+ if item.name == bxdlist[j]:
+ plotbxd=1
+
+ if (plotbxd == 1):
+
+ ind = 0
+ counter = 0
+ expr = 0
+ for item in smd:
+ counter = counter + 1
+ if item.name == bxdlist[j]:
+ ind = counter
+ expr = item.value
+
+ # Place where font is hardcoded
+ canvas.drawString("%s" % (bxdlist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+ canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+
+ fpText.close()
+
+## END HaplotypeAnalyst
+
+ def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ if self.plotScale != 'physic' or self.selectedChr == -1:
+ return
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ # only draw this many clickable regions (if you set it higher, you get more precision in clicking,
+ # but it makes the HTML huge, and takes forever to render the page in the first place)
+ # Draw the bands that you can click on to go to UCSC / Ensembl
+ MAX_CLICKABLE_REGION_DIVISIONS = 100
+ clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
+ pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS))
+ # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
+
+ numBasesCurrentlyOnScreen = self.kONE_MILLION*abs(startMb - endMb) # Number of bases on screen now
+ flankingWidthInBases = int ( min( (float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION) ) )
+ webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
+ # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
+
+ currentChromosome = self.genotype[0].name
+ i = 0
+ for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
+
+ calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
+
+ xBrowse1 = pixel
+ xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
+
+ paddingTop = yTopOffset
+ ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+ ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
+
+ WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
+ bandWidth = xBrowse2 - xBrowse1
+ WEBQTL_HREF = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (currentChromosome, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
+
+ WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
+ gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+ canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
+ canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+
+ UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
+ if self.species == "mouse":
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, currentChromosome)
+ else:
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
+ gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+ canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
+ canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
+
+ ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
+ if self.species == "mouse":
+ ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ else:
+ ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
+ gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+ canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
+ canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
+ # end for
+
+ canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.WEBQTL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
+ canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.UCSC_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
+ canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.ENSEMBL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
+
+ #draw the gray text
+ chrFont = pid.Font(ttf="verdana", size=26, bold=1)
+ traitFont = pid.Font(ttf="verdana", size=14, bold=0)
+ chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont)
+ canvas.drawString("Chr %s" % currentChromosome, chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
+ traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
+ # end of drawBrowserClickableRegions
+
+ pass
+
+ def drawXAxis(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ yZero = canvas.size[1] - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ #Parameters
+ NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
+ X_MAJOR_TICK_THICKNESS = 2
+ X_MINOR_TICK_THICKNESS = 1
+ X_AXIS_THICKNESS = 1*zoom
+
+ # ======= Alex: Draw the X-axis labels (megabase location)
+ MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
+ xMajorTickHeight = 15 # How high the tick extends below the axis
+ xMinorTickHeight = 5*zoom
+ xAxisTickMarkColor = pid.black
+ xAxisLabelColor = pid.black
+ fontHeight = 12*fontZoom # How tall the font that we're using is
+ spacingFromLabelToAxis = 20
+ spacingFromLineToLabel = 3
+
+ if self.plotScale == 'physic':
+ strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
+ ###Physical single chromosome view
+ if self.selectedChr > -1:
+ graphMbWidth = endMb - startMb
+ XScale = Plot.detScale(startMb, endMb)
+ XStart, XEnd, XStep = XScale
+ if XStep < 8:
+ XStep *= 2
+ spacingAmtX = spacingAmt = (XEnd-XStart)/XStep
+
+ j = 0
+ while abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
+ j += 1
+ spacingAmtX *= 10
+
+ formatStr = '%%2.%df' % j
+
+ for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
+ if _Mb < startMb or _Mb > endMb:
+ continue
+ Xc = xLeftOffset + plotXScale*(_Mb - startMb)
+ if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
+ canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
+ labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
+ strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
+ drawStringXc = (Xc - (strWidth / 2.0))
+ canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
+ else:
+ canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
+ # end else
+
+ ###Physical genome wide view
+ else:
+ distScale = 0
+ startPosX = xLeftOffset
+ for i, distLen in enumerate(self.ChrLengthDistList):
+ if distScale == 0: #universal scale in whole genome mapping
+ if distLen > 75:
+ distScale = 25
+ elif distLen > 30:
+ distScale = 10
+ else:
+ distScale = 5
+ for tickdists in range(distScale, ceil(distLen), distScale):
+ canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
+ canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
+ startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
+
+ megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
+ canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
+ strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
+ pass
+ else:
+ ChrAInfo = []
+ preLpos = -1
+ distinctCount = 0.0
+ if len(self.genotype) > 1:
+ for i, _chr in enumerate(self.genotype):
+ thisChr = []
+ Locus0CM = _chr[0].cM
+ nLoci = len(_chr)
+ if nLoci <= 8:
+ for _locus in _chr:
+ if _locus.name != ' - ':
+ if _locus.cM != preLpos:
+ distinctCount += 1
+ preLpos = _locus.cM
+ thisChr.append([_locus.name, _locus.cM-Locus0CM])
+ else:
+ for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1):
+ while _chr[j].name == ' - ':
+ j += 1
+ if _chr[j].cM != preLpos:
+ distinctCount += 1
+ preLpos = _chr[j].cM
+ thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM])
+ ChrAInfo.append(thisChr)
+ else:
+ for i, _chr in enumerate(self.genotype):
+ thisChr = []
+ Locus0CM = _chr[0].cM
+ for _locus in _chr:
+ if _locus.name != ' - ':
+ if _locus.cM != preLpos:
+ distinctCount += 1
+ preLpos = _locus.cM
+ thisChr.append([_locus.name, _locus.cM-Locus0CM])
+ ChrAInfo.append(thisChr)
+
+ stepA = (plotWidth+0.0)/distinctCount
+
+ LRectWidth = 10
+ LRectHeight = 3
+ offsetA = -stepA
+ lineColor = pid.lightblue
+ startPosX = xLeftOffset
+ for j, ChrInfo in enumerate(ChrAInfo):
+ preLpos = -1
+ for i, item in enumerate(ChrInfo):
+ Lname,Lpos = item
+ if Lpos != preLpos:
+ offsetA += stepA
+ differ = 1
+ else:
+ differ = 0
+ preLpos = Lpos
+ Lpos *= plotXScale
+ if self.selectedChr > -1:
+ Zorder = i % 5
+ else:
+ Zorder = 0
+ if differ:
+ canvas.drawLine(startPosX+Lpos,yZero,xLeftOffset+offsetA,\
+ yZero+25, color=lineColor)
+ canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
+ yZero+40+Zorder*(LRectWidth+3),color=lineColor)
+ rectColor = pid.orange
+ else:
+ canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
+ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
+ rectColor = pid.deeppink
+ canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\
+ xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\
+ edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
+ COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
+ xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
+ HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
+ Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
+ gifmap.areas.append(Areas)
+ ##piddle bug
+ if j == 0:
+ canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
+ startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
+
+ canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself
+
+
+ def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ INTERCROSS = (self.genotype.type=="intercross")
+
+ LRSHeightThresh = drawAreaHeight
+ AdditiveHeightThresh = drawAreaHeight/2
+ DominanceHeightThresh = drawAreaHeight/2
+
+ #draw the LRS scale
+ #We first determine whether or not we are using a sliding scale.
+ #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax.
+ #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
+ #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.
+
+ if self.LRS_LOD == 'LOD':
+ lodm = self.LODFACTOR
+ else:
+ lodm = 1.0
+
+ if self.lrsMax <= 0: #sliding scale
+ LRSMax = max(map(max, self.qtlresults)).lrs
+ #genotype trait will give infinite LRS
+ LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
+ if self.permChecked and not self.multipleInterval:
+ self.significance = min(self.significance, webqtlConfig.MAXLRS)
+ self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
+ LRSMax = max(self.significance, LRSMax)
+ else:
+ LRSMax = self.lrsMax*lodm
+
+ if LRSMax/lodm > 100:
+ LRSScale = 20.0
+ elif LRSMax/lodm > 20:
+ LRSScale = 5.0
+ elif LRSMax/lodm > 7.5:
+ LRSScale = 2.5
+ else:
+ LRSScale = 1.0
+
+ LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale)
+ #make sure the user's value appears on the y-axis
+ #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460
+ LRSAxisList.append(round(LRSMax/lodm))
+
+ #draw the "LRS" or "LOD" string to the left of the axis
+ LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
+ LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
+ yZero = yTopOffset + plotHeight
+
+
+ canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \
+ yZero - 150, font=LRSLODFont, color=pid.black, angle=90)
+
+ for item in LRSAxisList:
+ yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh
+ canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom)
+ scaleStr = "%2.1f" % item
+ canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
+
+
+ #"Significant" and "Suggestive" Drawing Routine
+ # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
+ if self.permChecked and not self.multipleInterval:
+ significantY = yZero - self.significance*LRSHeightThresh/LRSMax
+ suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax
+ startPosX = xLeftOffset
+ for i, _chr in enumerate(self.genotype):
+ rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
+ canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
+ width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
+ canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
+ width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
+ sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
+ sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2)
+ if self.LRS_LOD == 'LRS':
+ sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
+ sig_title = "Significant LRS = %0.2f" % self.significance
+ else:
+ sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
+ sig_title = "Significant LOD = %0.2f" % (self.significance/4.61)
+ Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
+ Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
+ gifmap.areas.append(Areas1)
+ gifmap.areas.append(Areas2)
+
+ startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
+
+
+ if self.multipleInterval:
+ lrsEdgeWidth = 1
+ else:
+ additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
+ if INTERCROSS:
+ dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
+ else:
+ dominanceMax = -1
+ lrsEdgeWidth = 2
+ for i, qtlresult in enumerate(self.qtlresults):
+ m = 0
+ startPosX = xLeftOffset
+ thisLRSColor = self.colorCollection[i]
+ for j, _chr in enumerate(self.genotype):
+ LRSCoordXY = []
+ AdditiveCoordXY = []
+ DominanceCoordXY = []
+ for k, _locus in enumerate(_chr):
+ if self.plotScale == 'physic':
+ Xc = startPosX + (_locus.Mb-startMb)*plotXScale
+ else:
+ Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
+ # updated by NL 06-18-2011:
+ # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
+ # for any lrs is over than 460(LRS max in this system), it will be reset to 460
+ if qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf':
+ Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+ else:
+ Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax
+
+ LRSCoordXY.append((Xc, Yc))
+ if not self.multipleInterval and self.additiveChecked:
+ Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
+ AdditiveCoordXY.append((Xc, Yc))
+ if not self.multipleInterval and INTERCROSS and self.additiveChecked:
+ Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
+ DominanceCoordXY.append((Xc, Yc))
+ m += 1
+ canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ if not self.multipleInterval and self.additiveChecked:
+ plusColor = self.ADDITIVE_COLOR_POSITIVE
+ minusColor = self.ADDITIVE_COLOR_NEGATIVE
+ for k, aPoint in enumerate(AdditiveCoordXY):
+ if k > 0:
+ Xc0, Yc0 = AdditiveCoordXY[k-1]
+ Xc, Yc = aPoint
+ if (Yc0-yZero)*(Yc-yZero) < 0:
+ if Xc == Xc0: #genotype , locus distance is 0
+ Xcm = Xc
+ else:
+ Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+ if Yc0 < yZero:
+ canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ elif (Yc0-yZero)*(Yc-yZero) > 0:
+ if Yc < yZero:
+ canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ minYc = min(Yc-yZero, Yc0-yZero)
+ if minYc < 0:
+ canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
+ plusColor = self.DOMINANCE_COLOR_POSITIVE
+ minusColor = self.DOMINANCE_COLOR_NEGATIVE
+ for k, aPoint in enumerate(DominanceCoordXY):
+ if k > 0:
+ Xc0, Yc0 = DominanceCoordXY[k-1]
+ Xc, Yc = aPoint
+ if (Yc0-yZero)*(Yc-yZero) < 0:
+ if Xc == Xc0: #genotype , locus distance is 0
+ Xcm = Xc
+ else:
+ Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+ if Yc0 < yZero:
+ canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ elif (Yc0-yZero)*(Yc-yZero) > 0:
+ if Yc < yZero:
+ canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ minYc = min(Yc-yZero, Yc0-yZero)
+ if minYc < 0:
+ canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ else:
+ canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
+
+ ###draw additive scale
+ if not self.multipleInterval and self.additiveChecked:
+ additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0)
+ additiveScale = Plot.detScaleOld(0,additiveMax)
+ additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+ additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
+ maxAdd = additiveScale[1]
+ addPlotScale = AdditiveHeightThresh/additiveMax
+
+ additiveAxisList.append(additiveScale[1])
+ for item in additiveAxisList:
+ additiveY = yZero - item*addPlotScale
+ canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+ scaleStr = "%2.3f" % item
+ canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE)
+
+ canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+
+ canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis
+
+
+ def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
+ ##conditions
+ ##multiple Chromosome view
+ ##single Chromosome Physical
+ ##single Chromosome Genetic
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ fontZoom = zoom
+ if zoom == 2:
+ fontZoom = 1.5
+
+ #calculate plot scale
+ if self.plotScale != 'physic':
+ self.ChrLengthDistList = self.ChrLengthCMList
+ drawRegionDistance = self.ChrLengthCMSum
+ else:
+ self.ChrLengthDistList = self.ChrLengthMbList
+ drawRegionDistance = self.ChrLengthMbSum
+
+ if self.selectedChr > -1: #single chromosome view
+ spacingAmt = plotWidth/13.5
+ i = 0
+ for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt):
+ if (i % 2 == 0):
+ theBackColor = self.GRAPH_BACK_DARK_COLOR
+ else:
+ theBackColor = self.GRAPH_BACK_LIGHT_COLOR
+ i += 1
+ canvas.drawRect(startPix, yTopOffset, min(startPix+spacingAmt, xLeftOffset+plotWidth), \
+ yTopOffset+plotHeight, edgeColor=theBackColor, fillColor=theBackColor)
+
+ drawRegionDistance = self.ChrLengthDistList[self.selectedChr]
+ self.ChrLengthDistList = [drawRegionDistance]
+ if self.plotScale == 'physic':
+ plotXScale = plotWidth / (endMb-startMb)
+ else:
+ plotXScale = plotWidth / drawRegionDistance
+
+ else: #multiple chromosome view
+ plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance)
+
+ startPosX = xLeftOffset
+ chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)
+
+ for i, _chr in enumerate(self.genotype):
+ if (i % 2 == 0):
+ theBackColor = self.GRAPH_BACK_DARK_COLOR
+ else:
+ theBackColor = self.GRAPH_BACK_LIGHT_COLOR
+
+ #draw the shaded boxes and the sig/sug thick lines
+ canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
+ yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)
+
+ chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
+ chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
+ chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
+
+ canvas.drawString(_chr.name, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
+ COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
+
+ #add by NL 09-03-2010
+ HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
+ Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+ gifmap.areas.append(Areas)
+ startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
+
+ return plotXScale
+
+ def calculateAllResult(self, fd):
+
+ weightedRegression = fd.formdata.getvalue('applyVarianceSE')
+
+ self.genotype = self.genotype.addinterval()
+ resultSlice = []
+ controlGeno = []
+
+ if self.multipleInterval:
+ self.suggestive = 0
+ self.significance = 0
+ if self.selectedChr > -1:
+ self.genotype.chromosome = [self.genotype[self.selectedChr]]
+ else:
+ #single interval mapping
+ try:
+ self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
+ self.significance = float(fd.formdata.getvalue('permSignificance'))
+ except:
+ self.suggestive = None
+ self.significance = None
+
+ _strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
+
+ if webqtlUtil.ListNotNull(_vars):
+ pass
+ else:
+ weightedRegression = 0
+ _strains, _vals, _vars = self.traitList[0].exportInformative()
+
+ ##locate genotype of control Locus
+ if self.controlLocus:
+ controlGeno2 = []
+ _FIND = 0
+ for _chr in self.genotype:
+ for _locus in _chr:
+ if _locus.name == self.controlLocus:
+ controlGeno2 = _locus.genotype
+ _FIND = 1
+ break
+ if _FIND:
+ break
+ if controlGeno2:
+ _prgy = list(self.genotype.prgy)
+ for _strain in _strains:
+ _idx = _prgy.index(_strain)
+ controlGeno.append(controlGeno2[_idx])
+ else:
+ return "The control marker you selected is not in the genofile."
+
+
+ if self.significance and self.suggestive:
+ pass
+ else:
+ if self.permChecked:
+ if weightedRegression:
+ self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
+ variance = _vars, nperm=fd.nperm)
+ else:
+ self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
+ nperm=fd.nperm)
+ self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)]
+ self.significance = self.LRSArray[int(fd.nperm*0.95-1)]
+
+ else:
+ self.suggestive = 9.2
+ self.significance = 16.1
+
+ #calculating bootstrap
+ #from now on, genotype could only contain a single chromosome
+ #permutation need to be performed genome wide, this is not the case for bootstrap
+
+ #due to the design of qtlreaper, composite regression need to be performed genome wide
+ if not self.controlLocus and self.selectedChr > -1:
+ self.genotype.chromosome = [self.genotype[self.selectedChr]]
+ elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
+ lociPerChr = map(len, self.genotype)
+ resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
+ resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
+ else:
+ pass
+
+ #calculate QTL for each trait
+ self.qtlresults = []
+
+ for thisTrait in self.traitList:
+ _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
+ if self.controlLocus:
+ if weightedRegression:
+ qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
+ variance = _vars, control = self.controlLocus)
+ else:
+ qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
+ control = self.controlLocus)
+ if resultSlice:
+ qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
+ else:
+ if weightedRegression:
+ qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
+ variance = _vars)
+ else:
+ qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
+
+ self.qtlresults.append(qtlresult)
+
+ if not self.multipleInterval:
+ if self.controlLocus and self.selectedChr > -1:
+ self.genotype.chromosome = [self.genotype[self.selectedChr]]
+
+ if self.bootChecked:
+ if controlGeno:
+ self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
+ control = controlGeno, nboot=fd.nboot)
+ elif weightedRegression:
+ self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
+ variance = _vars, nboot=fd.nboot)
+ else:
+ self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
+ nboot=fd.nboot)
+ else:
+ self.bootResult = []
+
+ def calculatePValue (self, query_LRS, permutation_LRS_array):
+ query_index = len(permutation_LRS_array)
+ for i, one_permutation_LRS in enumerate(permutation_LRS_array):
+ if one_permutation_LRS >= query_LRS:
+ query_index = i
+ break
+
+ P_value = float(len(permutation_LRS_array) - query_index) / len(permutation_LRS_array)
+
+ return P_value
+
+ def helpButton(self, anchor):
+ return HT.Href(self.HELP_PAGE_REF + '#%s' % anchor, self.qmarkImg, target=self.HELP_WINDOW_NAME)
+
+
+ def traitRemapTD(self, cursor, fd):
+ chrList = HT.Select(name="chromosomes", data=self.ChrList, selected=[self.selectedChr],
+ onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
+
+ physicOnly = HT.Span(' *', Class="cr")
+
+ showSNPCheck = HT.Input(type='checkbox', Class='checkbox', name='showSNP', value='ON', checked=self.SNPChecked)
+ showSNPText = HT.Span('SNP Track ', self.helpButton("snpSeismograph"), Class="fs12 fwn")
+
+ showGenesCheck = HT.Input(type='checkbox', Class='checkbox', name='showGenes', value='ON', checked=self.geneChecked)
+ showGenesText = HT.Span('Gene Track', Class="fs12 fwn")
+
+ showIntervalAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='intervalAnalystCheck', value='ON', checked=self.intervalAnalystChecked)
+ showIntervalAnalystText = HT.Span('Interval Analyst', Class="fs12 fwn")
+## BEGIN HaplotypeAnalyst
+
+ showHaplotypeAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='haplotypeAnalystCheck', value='ON', checked=self.haplotypeAnalystChecked)
+ showHaplotypeAnalystText = HT.Span('Haplotype Analyst', Class="fs12 fwn")
+## END HaplotypeAnalyst
+
+ leftBox = HT.Input(type="text", name="startMb", size=10)
+ rightBox = HT.Input(type="text", name="endMb", size=10)
+ if self.selectedChr > -1 and self.plotScale=='physic':
+ leftBox.value = self.startMb
+ rightBox.value = self.endMb
+
+ scaleBox = HT.Select(name="scale", onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
+ scaleBox.append(("Genetic", "morgan"))
+ if fd.genotype.Mbmap:
+ scaleBox.append(("Physical", "physic"))
+ scaleBox.selected.append(self.plotScale)
+
+ permBox = HT.Input(type="checkbox", name="permCheck", value='ON', checked=self.permChecked, Class="checkbox")
+ permText = HT.Span("Permutation Test ", self.helpButton("Permutation"), Class="fs12 fwn")
+ bootBox = HT.Input(type="checkbox", name="bootCheck", value='ON', checked=self.bootChecked, Class="checkbox")
+ bootText = HT.Span("Bootstrap Test ", self.helpButton("bootstrap"), Class="fs12 fwn")
+ additiveBox = HT.Input(type="checkbox", name="additiveCheck", value='ON', checked=self.additiveChecked, Class="checkbox")
+ additiveText = HT.Span("Allele Effects ", self.helpButton("additive"), Class="fs12 fwn")
+ dominanceBox = HT.Input(type="checkbox", name="dominanceCheck", value='ON', checked=self.dominanceChecked, Class="checkbox")
+ dominanceText = HT.Span("Dominance Effects ", self.helpButton("Dominance"), Class="fs12 fwn")
+
+ lrsRadio = HT.Input(type="radio", name="LRSCheck", value='LRS', checked = (self.LRS_LOD == "LRS"))
+ lodRadio = HT.Input(type="radio", name="LRSCheck", value='LOD', checked = (self.LRS_LOD != "LRS"))
+ lrsMaxBox = HT.Input(type="text", name="lrsMax", value=self.lrsMax, size=3)
+ widthBox = HT.Input(type="text", name="graphWidth", size=5, value=str(self.graphWidth))
+ legendBox = HT.Input(type="checkbox", name="viewLegend", value='ON', checked=self.legendChecked, Class="checkbox")
+ legendText = HT.Span("Legend", Class="fs12 fwn")
+
+ draw2XBox = HT.Input(type="checkbox", name="draw2X", value='ON', Class="checkbox")
+ draw2XText = HT.Span("2X Plot", Class="fs12 fwn")
+
+ regraphButton = HT.Input(type="button", Class="button", onClick="javascript:databaseFunc(this.form,'showIntMap');", value="Remap")
+
+ controlsForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype="multipart/form-data", name="changeViewForm", submit=HT.Input(type='hidden'))
+ controlsTable = HT.TableLite(border=0)
+ innerControlsTable = HT.TableLite(border=0)
+ if self.selectedChr == -1:
+ minimumGraphWidth = self.MULT_GRAPH_MIN_WIDTH
+ else:
+ minimumGraphWidth = self.GRAPH_MIN_WIDTH
+
+ innerControlsTable.append(
+ HT.TR(HT.TD("Chr: ", Class="fs12 fwb ffl"),HT.TD(chrList, scaleBox, regraphButton)),
+ HT.TR(HT.TD("View: ", Class="fs12 fwb ffl"),HT.TD(leftBox, " to ", rightBox, "Mb", physicOnly, NOWRAP="on")),
+ HT.TR(HT.TD("Units: ", Class="fs12 fwb ffl"), HT.TD(lrsRadio, "LRS ", lodRadio, "LOD ", self.helpButton("LOD"))),
+ HT.TR(HT.TD(" ", Class="fs12 fwb ffl"), HT.TD(lrsMaxBox, "units on Y-axis (0 for default)", Class="fs11 fwn")),
+ HT.TR(HT.TD("Width: ", Class="fs12 fwb ffl"), HT.TD(widthBox, "pixels (minimum=%d)" % minimumGraphWidth, Class="fs11 fwn "))
+ )
+ #whether SNP
+ cursor.execute("Select Species.Id from SnpAll, Species where SnpAll.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
+ SNPorNot = cursor.fetchall()
+ #Whether Gene
+ cursor.execute("Select Species.Id from GeneList, Species where GeneList.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
+ GeneorNot = cursor.fetchall()
+
+ if self.multipleInterval:
+ optionPanel = HT.TD(valign="top", NOWRAP="on")
+ else:
+ optionPanel = HT.TD(permBox, permText, HT.BR(), bootBox, bootText, HT.BR(), additiveBox, additiveText, HT.BR(), valign="top", NOWRAP="on")
+ #whether dominance
+ if self.genotype.type == 'intercross':
+ optionPanel.append(dominanceBox, dominanceText, HT.BR())
+ if SNPorNot:
+ optionPanel.append(showSNPCheck, showSNPText, physicOnly, HT.BR())
+ if GeneorNot:
+ optionPanel.append(showGenesCheck, showGenesText, physicOnly, HT.BR(),
+ showIntervalAnalystCheck, showIntervalAnalystText, physicOnly, HT.BR())
+## BEGIN HaplotypeAnalyst
+ optionPanel.append(showHaplotypeAnalystCheck, showHaplotypeAnalystText, physicOnly, HT.BR())
+## END HaplotypeAnalyst
+ optionPanel.append(legendBox, legendText, HT.BR(),draw2XBox, draw2XText)
+ controlsTable.append(
+ HT.TR(HT.TD(innerControlsTable, valign="top"),
+ HT.TD("&nbsp;", width=15), optionPanel),
+ HT.TR(HT.TD(physicOnly, " only apply to single chromosome physical mapping", align="Center", colspan=3, Class="fs11 fwn"))
+ )
+ controlsForm.append(controlsTable)
+
+ controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden"))
+ controlsForm.append(HT.Input(name="permSignificance", value=self.significance, type="hidden"))
+
+## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below
+## END HaplotypeAnalyst
+
+ for key in fd.formdata.keys():
+ if key == "searchResult" and type([]) == type(fd.formdata.getvalue(key)):
+ controlsForm.append(HT.Input(name=key, value=string.join(fd.formdata.getvalue(key), "\t"), type="hidden"))
+ elif key not in ("endMb", "startMb", "chromosomes", "scale", "permCheck", "bootCheck", "additiveCheck", "dominanceCheck",
+ "LRSCheck", "intervalAnalystCheck", "haplotypeAnalystCheck", "lrsMax", "graphWidth", "viewLegend", 'showGenes', 'showSNP', 'draw2X',
+ 'permSuggestive', "permSignificance"):
+ controlsForm.append(HT.Input(name=key, value=fd.formdata.getvalue(key), type="hidden"))
+ else:
+ pass
+
+ # updated by NL, move function changeView(i) to webqtl.js and change it to function changeView(i, Chr_Mb_list)
+ # move function chrLength(a, b, c) to webqtl.js and change it to function chrLength(a, b, c, Chr_Mb_list)
+ self.dict['js1'] = ''
+
+ return HT.TD(controlsForm, Class="doubleBorder", width=400)
+
+ def traitInfoTD(self, fd):
+ if self.selectedChr == -1:
+ intMapHeading = HT.Paragraph('Map Viewer: Whole Genome', Class="title")
+ else:
+ intMapHeading = HT.Paragraph('Map Viewer: Chr %s' % self.genotype[0].name, Class="title")
+
+ heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (self.species.title(), fd.RISet) , HT.BR())
+ #Trait is from an database
+ if self.traitList and self.traitList[0] and self.traitList[0].db:
+ #single trait
+ if len(self.traitList) == 1:
+ thisTrait = self.traitList[0]
+ trait_url = HT.Href(text=thisTrait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \
+ "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (thisTrait.db.name, thisTrait.name), \
+ target='_blank', Class="normalsize")
+ heading2.append(HT.Strong("Database: "), HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name ,\
+ target='_blank',Class="normalsize"),HT.BR())
+ if thisTrait.db.type == 'ProbeSet':
+ heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(),
+ HT.Strong("Gene Symbol: "), HT.Italic('%s' % thisTrait.symbol,id="green"),HT.BR())
+ if thisTrait.chr and thisTrait.mb:
+ heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
+ elif thisTrait.db.type == 'Geno':
+ heading2.append(HT.Strong('Locus : '), trait_url, HT.BR())
+ if thisTrait.chr and thisTrait.mb:
+ heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
+ elif thisTrait.db.type == 'Publish':
+ heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR())
+ else:
+ pass
+ else:
+ heading2.append(HT.Strong("Traits: "), "Multiple Traits")
+ else:
+ heading2.append(HT.Strong("Trait Name: "), fd.identification)
+ return HT.TD(intMapHeading, heading2, valign="top")
+
+ def geneTables(self, geneCol, refGene=None):
+ SNPLink = 0
+ tableIterationsCnt = 0
+ if self.species == "mouse":
+ geneTableMain = HT.TableLite(border=0, width=1280, cellpadding=0, cellspacing=0, Class="collap")
+ columns = HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
+ HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
+ HT.TD('Mb Start (mm9)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD("SNP Count", Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD("SNP Density (SNP/Kb)", Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
+ HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1))
+
+ # http://compbio.uthsc.edu/miRSNP/
+
+ td_pd = HT.TD(Class="fs14 fwb ffl b1 cw cbrb")
+ td_pd.append(HT.Text("PolymiRTS"))
+ td_pd.append(HT.BR())
+ td_pd.append(HT.Text("Database"))
+ td_pd.append(HT.BR())
+ td_pd.append(HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"))
+
+ if refGene:
+ columns.append(HT.TD('Literature Correlation', Class="fs14 fwb ffl b1 cw cbrb", width=1))
+ columns.append(HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb"))
+ columns.append(td_pd)
+ geneTableMain.append(columns)
+
+ # polymiRTS
+ # http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125
+ #XZ: We can NOT assume their web service is always on. We must put this block of code in try except.
+ try:
+ conn = httplib.HTTPConnection("lily.uthsc.edu:8080")
+ conn.request("GET", "/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=%s&chrom_from=%s&chrom_to=%s" % (self.genotype[0].name, self.startMb, self.endMb))
+ response = conn.getresponse()
+ data = response.read()
+ data = data.split()
+ conn.close()
+ dic = {}
+ index = 0
+ for i in data:
+ if index%3==0:
+ dic[data[index]] = HT.Href(url=data[index+2], text=data[index+1], target="_blank", Class="normalsize")
+ index = index+1
+ except Exception:
+ dic={}
+
+
+ for gIndex, theGO in enumerate(geneCol):
+ geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
+ tenPercentLength = geneLength*0.0001
+ txStart = theGO["TxStart"]
+ txEnd = theGO["TxEnd"]
+ theGO["snpDensity"] = theGO["snpCount"]/geneLength
+ if (self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST and geneTableMain):
+ #accessionString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=gene&term=%s' % theGO["NM_ID"]
+ geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
+
+ allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"])
+ if theGO["snpCount"]:
+ snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'),
+ theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]),
+ text=theGO["snpCount"], target="_blank", Class="normalsize")
+ else:
+ snpString = 0
+
+ mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit"
+
+ if theGO['humanGene']:
+ huGO = theGO['humanGene']
+ if huGO["TxStart"] == '':
+ humanStartDisplay = ""
+ else:
+ humanStartDisplay = "%0.6f" % huGO["TxStart"]
+ humanChr = huGO["Chromosome"]
+ if humanChr.find("q") > -1:
+ humanChr = humanChr[:humanChr.find("q")]
+ if humanChr.find("p") > -1:
+ humanChr = humanChr[:humanChr.find("p")]
+ humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000*huGO["TxStart"]), int(1000000*huGO["TxEnd"]))
+ else:
+ humanStartString = humanChr = humanStartDisplay = ""
+
+ geneDescription = theGO["GeneDescription"]
+ if len(geneDescription) > 26:
+ geneDescription = geneDescription[:26]+"..."
+ probeSetSearch = HT.Href(allProbeString, HT.Image("/images/webqtl_search.gif", border=0), target="_blank")
+
+ if theGO["snpDensity"] < 0.000001:
+ snpDensityStr = "0"
+ else:
+ snpDensityStr = "%0.6f" % theGO["snpDensity"]
+
+ avgExpr = []#theGO["avgExprVal")
+ if avgExpr in ([], None):
+ avgExpr = ""
+ else:
+ avgExpr = "%0.6f" % avgExpr
+
+ tableIterationsCnt = tableIterationsCnt + 1
+
+ # polymiRTS
+ polymiRTS = ' '
+ if dic.has_key(theGO["GeneID"]):
+ polymiRTS = dic[theGO["GeneID"]]
+
+ # If we have a referenceGene then we will show the Literature Correlation
+ if refGene:
+ literatureCorrelation = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+ geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
+ HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
+ HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+ HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+ HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
+ HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
+ HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
+ HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(literatureCorrelation, align='left',Class="fs13 b1 cbw c222"),
+ HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
+ HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
+
+ else:
+ geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
+ HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
+ HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+ HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+ HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
+ HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
+ HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
+ HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
+ HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
+
+ return geneTableMain
+ elif self.species == "rat":
+ geneTableMain = HT.TableLite(border=0, width=1050, cellpadding=0, cellspacing=0, Class="collap")
+ geneTableMain.append(HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
+ HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
+ HT.TD('Mb Start (rn3)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
+ HT.TD('Mouse Chr', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Mb Start (mm9)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+ HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb")))
+
+ for gIndex, theGO in enumerate(geneCol):
+ geneDesc = theGO["GeneDescription"]
+ if geneDesc == "---":
+ geneDesc = ""
+ 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))
+
+ #the chromosomes for human 1 are 1qXX.XX
+ if theGO['humanGene']:
+ humanChr = theGO['humanGene']["Chromosome"]
+ if 'q' in humanChr:
+ humanChr = humanChr[:humanChr.find("q")]
+ if 'p' in humanChr:
+ humanChr = humanChr[:humanChr.find("p")]
+ humanTxStart = theGO['humanGene']["TxStart"]
+ else:
+ humanChr = humanTxStart = ""
+
+ #Mouse Gene
+ if theGO['mouseGene']:
+ mouseChr = theGO['mouseGene']["Chromosome"]
+ mouseTxStart = theGO['mouseGene']["TxStart"]
+ else:
+ mouseChr = mouseTxStart = ""
+
+ if theGO["GeneID"] != "":
+ geneSymbolURL = 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")
+ else:
+ geneSymbolURL = theGO["GeneSymbol"]
+
+ if len(geneDesc) > 34:
+ geneDesc = geneDesc[:32] + "..."
+
+ avgExprVal = [] #theGO["avgExprVal"]
+ if avgExprVal != "" and avgExprVal:
+ avgExprVal = "%0.5f" % float(avgExprVal)
+ else:
+ avgExprVal = ""
+
+ geneTableMain.append(HT.TR(HT.TD(gIndex+1, align="right", Class="fs13 b1 cbw c222"),
+ HT.TD(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"), Class="fs13 bt1 bb1 cbw c222"),
+ HT.TD(geneSymbolURL, Class="fs13 bt1 bb1 cbw c222"),
+ HT.TD(theGO["TxStart"], Class="fs13 b1 cbw c222"),
+ HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0), Class="normalsize"), Class="fs13 b1 cbw c222"),
+ HT.TD(avgExprVal, Class="fs13 b1 cbw c222"),
+ HT.TD(mouseChr, Class="fs13 b1 cbw c222"),
+ HT.TD(mouseTxStart, Class="fs13 b1 cbw c222"),
+ HT.TD(humanChr, Class="fs13 b1 cbw c222"),
+ HT.TD(humanTxStart, Class="fs13 b1 cbw c222"),
+ HT.TD(geneDesc, Class="fs13 b1 cbw c222")))
+ return geneTableMain
+ else:
+ return ""
+
+ def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None):
+ if not geneId1 or not geneId2:
+ return None
+ if geneId1 == geneId2:
+ return 1.0
+ geneId1 = str(geneId1)
+ geneId2 = str(geneId2)
+ lCorr = None
+ try:
+ query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
+ for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
+ cursor.execute(query,(x,y))
+ lCorr = cursor.fetchone()
+ if lCorr:
+ lCorr = lCorr[0]
+ break
+ except: raise #lCorr = None
+ return lCorr