diff options
Diffstat (limited to 'web/webqtl/intervalMapping')
| -rwxr-xr-x | web/webqtl/intervalMapping/IntervalMappingPage.py | 2454 | ||||
| -rwxr-xr-x | web/webqtl/intervalMapping/__init__.py | 0 |
2 files changed, 0 insertions, 2454 deletions
diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py deleted file mode 100755 index c3ef1cbd..00000000 --- a/web/webqtl/intervalMapping/IntervalMappingPage.py +++ /dev/null @@ -1,2454 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by 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(" ", 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(" ", 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 diff --git a/web/webqtl/intervalMapping/__init__.py b/web/webqtl/intervalMapping/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/intervalMapping/__init__.py +++ /dev/null |