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-rwxr-xr-xweb/webqtl/intervalMapping/IntervalMappingPage.py2454
-rwxr-xr-xweb/webqtl/intervalMapping/__init__.py0
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("&nbsp;", width=25), traitRemapTD), border=0, cellspacing=0, cellpadding=0)
-
- ################################################################
- # Outputs goes here
- ################################################################
- #this form is used for opening Locus page or trait page, only available for genetic mapping
- if showLocusForm:
- showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
- name=showLocusForm, submit=HT.Input(type='hidden'))
- hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
- for key in hddn.keys():
- showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
- showLocusForm.append(intImg)
- else:
- showLocusForm = intImg
-
- ################################################################
- # footnote goes here
- ################################################################
- btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
-
- if (self.additiveChecked):
- btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
-
- if self.traitList and self.traitList[0].db and self.traitList[0].db.type == 'Geno':
- btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
-
- TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
-
- if geneTable:
- iaForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=intervalAnalyst"), enctype='multipart/form-data',
- name="iaForm", submit=HT.Input(type='hidden'))
- hddn = {'chromosome':self.genotype[0].name, 'species':self.species,'startMb':self.startMb,'endMb':self.endMb}
- if self.diffCol:
- hddn['s1'] = self.diffCol[0]
- hddn['s2'] = self.diffCol[1]
- for key in hddn.keys():
- iaForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
- iaForm.append(HT.Paragraph("Interval Analyst : Chr %s from %2.6f to %2.6f Mb" % (self.genotype[0].name, self.startMb, self.endMb),
- HT.Input(name='customize', value='Customize', onClick= "formInNewWindow(this.form);", type='button', Class="button"), Class="subtitle"))
- TD_LR.append(HT.Blockquote(iaForm, geneTable))
-
- self.dict['body'] = TD_LR
- self.dict['title'] = "Mapping"
-
- def writeQTL2Text(self, fd, filename):
- if self.multipleInterval:
- return ""
- _dominance = (self.genotype.type == 'intercross')
- _Mb = self.genotype.Mbmap
-
- ###Write to text file
- fpText = open(os.path.join(webqtlConfig.TMPDIR, filename) + '.txt','wb')
-
- fpText.write("Source: WebQTL, The GeneNetwork (%s)\n" % webqtlConfig.PORTADDR)
- #
- fpText.write("Site: %s\n" % webqtlConfig.SITENAME)
- fpText.write("Page: Map Viewer\n")
- fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime()))
- fpText.write("Trait ID: %s\n" % fd.identification)
- fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive)
- fpText.write("Significant LRS = %0.2f\n" % self.significance)
- """
- if fd.traitInfo:
- writeSymbol, writeChromosome, writeMb = string.split(fd.traitInfo)
- else:
- writeSymbol, writeChromosome, writeMb = (" ", " ", " ")
- fpText.write("Gene Symbol: %s\n" % writeSymbol)
- fpText.write("Location: Chr %s @ %s Mb\n" % (writeChromosome, writeMb))
- selectedChr = self.indexToChrName(int(fd.formdata.getvalue('chromosomes', -1)))
- fpText.write("Chromosome: %s\n" % selectedChr)
- fpText.write("Region: %0.6f-%0.6f Mb\n\n" % (self.startMb, self.endMb))
- """
-
- if hasattr(self, 'LRSArray'):
- if _dominance:
- fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\tDominance\n')
- else:
- fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\n')
- else:
- if _dominance:
- fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\tDominance\n')
- else:
- fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\n')
-
- i = 0
- for qtlresult in self.qtlresults[0]:
- if _Mb:
- locusMb = '%2.3f' % qtlresult.locus.Mb
- else:
- locusMb = 'N/A'
-
- if hasattr(self, 'LRSArray'):
- P_value = self.calculatePValue(qtlresult.lrs, self.LRSArray)
-
- if _dominance:
- fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
- qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value, qtlresult.additive, qtlresult.dominance))
- else:
- fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
- qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value, qtlresult.additive))
- else:
- if _dominance:
- fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
- qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive, qtlresult.dominance))
- else:
- fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
- qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive))
-
- i += 1
-
- fpText.close()
- textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='smallsize')
- return textUrl
-
- def plotIntMapping(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
- #calculating margins
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- if self.multipleInterval:
- yTopOffset = max(80, yTopOffset)
- else:
- if self.legendChecked:
- yTopOffset = max(80, yTopOffset)
- else:
- pass
-
- if self.plotScale != 'physic':
- yBottomOffset = max(120, yBottomOffset)
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- xLeftOffset = int(xLeftOffset*fontZoom)
- xRightOffset = int(xRightOffset*fontZoom)
- yBottomOffset = int(yBottomOffset*fontZoom)
-
- cWidth = canvas.size[0]
- cHeight = canvas.size[1]
- plotWidth = cWidth - xLeftOffset - xRightOffset
- plotHeight = cHeight - yTopOffset - yBottomOffset
- startPixelX = xLeftOffset
- endPixelX = (xLeftOffset + plotWidth)
-
- #Drawing Area Height
- drawAreaHeight = plotHeight
- if self.plotScale == 'physic' and self.selectedChr > -1:
- drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
- if self.geneChecked:
- drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
- else:
- if self.selectedChr > -1:
- drawAreaHeight -= 20
- else:
- drawAreaHeight -= 30
-
-## BEGIN HaplotypeAnalyst
- if self.haplotypeAnalystChecked and self.selectedChr > -1:
- drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS+10) * 2 * zoom
-## END HaplotypeAnalyst
-
- #Image map
- gifmap = HT.Map(name='WebQTLImageMap')
-
- newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
- # Draw the alternating-color background first and get plotXScale
- plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-
- #draw bootstap
- if self.bootChecked and not self.multipleInterval:
- self.drawBootStrapResult(canvas, fd.nboot, drawAreaHeight, plotXScale, offset=newoffset)
-
- # Draw clickable region and gene band if selected
- if self.plotScale == 'physic' and self.selectedChr > -1:
- self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
- if self.geneChecked and self.geneCol:
- self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
- if self.SNPChecked:
- self.drawSNPTrackNew(canvas, offset=newoffset, zoom= 2*zoom, startMb=startMb, endMb = endMb)
-## BEGIN HaplotypeAnalyst
- if self.haplotypeAnalystChecked:
- self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-## END HaplotypeAnalyst
- # Draw X axis
- self.drawXAxis(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
- # Draw QTL curve
- self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-
- #draw legend
- if self.multipleInterval:
- self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
- elif self.legendChecked:
- self.drawLegendPanel(fd, canvas, offset=newoffset)
- else:
- pass
-
- #draw position, no need to use a separate function
- if fd.genotype.Mbmap:
- self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset)
-
- return gifmap
-
- def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- bootHeightThresh = drawAreaHeight*3/4
-
- #break bootstrap result into groups
- BootCoord = []
- i = 0
- startX = xLeftOffset
- for j, _chr in enumerate(self.genotype):
- BootCoord.append( [])
- for _locus in _chr:
- if self.plotScale == 'physic':
- Xc = startX + (_locus.Mb-self.startMb)*plotXScale
- else:
- Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
- BootCoord[-1].append([Xc, self.bootResult[i]])
- i += 1
- startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale
-
- #reduce bootResult
- if self.selectedChr > -1:
- maxBootBar = 80.0
- else:
- maxBootBar = 200.0
- stepBootStrap = plotWidth/maxBootBar
- reducedBootCoord = []
- maxBootCount = 0
-
- for BootChrCoord in BootCoord:
- nBoot = len(BootChrCoord)
- bootStartPixX = BootChrCoord[0][0]
- bootCount = BootChrCoord[0][1]
- for i in range(1, nBoot):
- if BootChrCoord[i][0] - bootStartPixX < stepBootStrap:
- bootCount += BootChrCoord[i][1]
- continue
- else:
- if maxBootCount < bootCount:
- maxBootCount = bootCount
- # end if
- reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount])
- bootStartPixX = BootChrCoord[i][0]
- bootCount = BootChrCoord[i][1]
- # end else
- # end for
- #add last piece
- if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap/2.0:
- reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount])
- else:
- reducedBootCoord[-1][2] += bootCount
- reducedBootCoord[-1][1] = BootChrCoord[-1][0]
- # end else
- if maxBootCount < reducedBootCoord[-1][2]:
- maxBootCount = reducedBootCoord[-1][2]
- # end if
- for item in reducedBootCoord:
- if item[2] > 0:
- if item[0] < xLeftOffset:
- item[0] = xLeftOffset
- if item[0] > xLeftOffset+plotWidth:
- item[0] = xLeftOffset+plotWidth
- if item[1] < xLeftOffset:
- item[1] = xLeftOffset
- if item[1] > xLeftOffset+plotWidth:
- item[1] = xLeftOffset+plotWidth
- if item[0] != item[1]:
- canvas.drawRect(item[0], yZero, item[1], yZero - item[2]*bootHeightThresh/maxBootCount,
- fillColor=self.BOOTSTRAP_BOX_COLOR)
-
- ###draw boot scale
- highestPercent = (maxBootCount*100.0)/nboot
- bootScale = Plot.detScale(0, highestPercent)
- bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1]/bootScale[2])
- bootScale = bootScale[:-1] + [highestPercent]
-
- bootOffset = 50*fontZoom
- bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0)
- canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow)
- canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black)
- canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black)
- for item in bootScale:
- if item == 0:
- continue
- bootY = yZero-bootHeightThresh*item/highestPercent
- canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=pid.black)
- canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=pid.black)
-
- if self.legendChecked:
- startPosY = 30
- nCol = 2
- smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
- leftOffset = xLeftOffset+(nCol-1)*200
- canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=pid.yellow)
- canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=pid.black)
-
- def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- if len(self.traitList) != 1:
- return
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- try:
- Chr = self.traitList[0].chr
- Mb = self.traitList[0].mb
- except:
- return
-
- if self.plotScale == 'physic':
- if self.selectedChr > -1:
- if self.genotype[0].name != Chr or Mb < self.startMb or Mb > self.endMb:
- return
- else:
- locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
- else:
- locPixel = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- if _chr.name != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
- else:
- locPixel += Mb*plotXScale
- break
- else:
- if self.selectedChr > -1:
- if self.genotype[0].name != Chr:
- return
- else:
- for i, _locus in enumerate(self.genotype[0]):
- #the trait's position is on the left of the first genotype
- if i==0 and _locus.Mb >= Mb:
- locPixel=-1
- break
-
- #the trait's position is between two traits
- if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
- locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
- break
-
- #the trait's position is on the right of the last genotype
- if i==len(self.genotype[0]) and Mb>=_locus.Mb:
- locPixel = -1
- else:
- locPixel = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- if _chr.name != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
- else:
- locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
- break
- if locPixel >= 0:
- traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
- canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
-
- if self.legendChecked:
- startPosY = 15
- nCol = 2
- smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
- leftOffset = xLeftOffset+(nCol-1)*200
- canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
- canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)
-
-
- def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
- return
-
- SNP_HEIGHT_MODIFIER = 18.0
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- drawSNPLocationY = yTopOffset + plotHeight
- chrName = self.genotype[0].name
-
- stepMb = (endMb-startMb)/plotWidth
- strainId1, strainId2 = self.diffCol
- SNPCounts = []
-
- while startMb<endMb:
- self.cursor.execute("""
- select
- count(*) from BXDSnpPosition
- where
- Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
- StrainId1 = %d AND StrainId2 = %d
- """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2))
- SNPCounts.append(self.cursor.fetchone()[0])
- startMb += stepMb
-
- if (len(SNPCounts) > 0):
- maxCount = max(SNPCounts)
- if maxCount>0:
- for i in range(xLeftOffset, xLeftOffset + plotWidth):
- snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
- canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1)
-
- def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
- nameWidths = []
- yPaddingTop = 10
- colorFont=pid.Font(ttf="trebuc",size=12,bold=1)
- if len(self.qtlresults) >20 and self.selectedChr > -1:
- rightShift = 20
- rightShiftStep = 60
- rectWidth = 10
- else:
- rightShift = 40
- rightShiftStep = 80
- rectWidth = 15
-
- for k, thisTrait in enumerate(self.traitList):
- thisLRSColor = self.colorCollection[k]
- kstep = k % 4
- if k!=0 and kstep==0:
- if nameWidths:
- rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20
- rightShift += rightShiftStep
-
- name = thisTrait.displayName()
- nameWidth = canvas.stringWidth(name,font=colorFont)
- nameWidths.append(nameWidth)
-
- canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor)
- canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black)
- if thisTrait.db:
-
- COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
- HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
- Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
- gifmap.areas.append(Areas)
-
-
- def drawLegendPanel(self, fd, canvas, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
-
- labelFont=pid.Font(ttf="trebuc",size=12, bold=1)
- startPosY = 15
- stepPosY = 12
- canvas.drawLine(xLeftOffset,startPosY,xLeftOffset+32,startPosY,color=self.LRS_COLOR, width=2)
- canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=pid.black)
- startPosY += stepPosY
-
- if self.additiveChecked:
- startPosX = xLeftOffset
- canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.ADDITIVE_COLOR_POSITIVE, width=2)
- canvas.drawLine(startPosX+18,startPosY,startPosX+32,startPosY,color=self.ADDITIVE_COLOR_NEGATIVE, width=2)
- canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=pid.black)
-
- if self.genotype.type == 'intercross' and self.dominanceChecked:
- startPosX = xLeftOffset
- startPosY += stepPosY
- canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.DOMINANCE_COLOR_POSITIVE, width=4)
- canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.DOMINANCE_COLOR_NEGATIVE, width=4)
- canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=pid.black)
-
- if self.haplotypeAnalystChecked:
- startPosY += stepPosY
- startPosX = xLeftOffset
- canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.HAPLOTYPE_POSITIVE, width=4)
- canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.HAPLOTYPE_NEGATIVE, width=4)
- canvas.drawLine(startPosX+36,startPosY,startPosX+53,startPosY,color=self.HAPLOTYPE_HETEROZYGOUS, width=4)
- canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4)
- canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black)
-
- if self.permChecked:
- startPosY += stepPosY
- startPosX = xLeftOffset
- canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
- canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
- lod = 1
- if self.LRS_LOD == 'LOD':
- lod = self.LODFACTOR
- canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significance/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
- canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive/lod),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
-
-
-
- labelFont=pid.Font(ttf="verdana",size=12)
- labelColor = pid.black
- if self.selectedChr == -1:
- string1 = 'Mapping for Dataset: %s, mapping on All Chromosomes' % fd.RISet
- else:
- string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (fd.RISet,self.genotype[0].name)
- if self.controlLocus:
- string2 = 'Using %s as control' % self.controlLocus
- else:
- string2 = 'Using Haldane mapping function with no control for other QTLs'
- d = 4+ max(canvas.stringWidth(string1,font=labelFont),canvas.stringWidth(string2,font=labelFont))
- if fd.identification:
- identification = "Trait ID: %s" % fd.identification
- canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20,font=labelFont,color=labelColor)
-
- canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35,font=labelFont,color=labelColor)
- canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50,font=labelFont,color=labelColor)
-
-
- def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
- return
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- yPaddingTop = yTopOffset
-
- displayStartInBases = startMb*self.kONE_MILLION
- displayEndInBases = endMb*self.kONE_MILLION
-
- for gIndex, theGO in enumerate(self.geneCol):
- geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s'
- if self.species == "mouse":
- txStart = theGO["TxStart"]
- txEnd = theGO["TxEnd"]
- geneLength = (txEnd - txStart)*1000.0
- tenPercentLength = geneLength*0.0001
- SNPdensity = theGO["snpCount"]/geneLength
-
- exonStarts = map(float, theGO['exonStarts'].split(",")[:-1])
- exonEnds = map(float, theGO['exonEnds'].split(",")[:-1])
- cdsStart = theGO['cdsStart']
- cdsEnd = theGO['cdsEnd']
- accession = theGO['NM_ID']
- geneId = theGO['GeneID']
- geneSymbol = theGO["GeneSymbol"]
- strand = theGO["Strand"]
- exonCount = theGO["exonCount"]
-
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
-
- if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
- elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
- if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
- elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
-
- #color the gene based on SNP density
-
-
- #found earlier, needs to be recomputed as snps are added
-
- #always apply colors now, even if SNP Track not checked - Zach 11/24/2010
-
- densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
- if SNPdensity < densities[0]:
- myColor = pid.black
- elif SNPdensity < densities[1]:
- myColor = pid.purple
- elif SNPdensity < densities[2]:
- myColor = pid.darkblue
- elif SNPdensity < densities[3]:
- myColor = pid.darkgreen
- elif SNPdensity < densities[4]:
- myColor = pid.gold
- elif SNPdensity < densities[5]:
- myColor = pid.darkorange
- else:
- myColor = pid.darkred
-
- outlineColor = myColor
- fillColor = myColor
-
- TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
- # NL: 06-02-2011 Rob required to change this link for gene related
- HREF=geneNCBILink %geneSymbol
-
- elif self.species == "rat":
- exonStarts = []
- exonEnds = []
- txStart = theGO["TxStart"]
- txEnd = theGO["TxEnd"]
- cdsStart = theGO["TxStart"]
- cdsEnd = theGO["TxEnd"]
- geneId = theGO["GeneID"]
- geneSymbol = theGO["GeneSymbol"]
- strand = theGO["Strand"]
- exonCount = 0
-
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
-
- if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
- elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
- if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
- elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
-
- outlineColor = pid.darkblue
- fillColor = pid.darkblue
- TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
- # NL: 06-02-2011 Rob required to change this link for gene related
- HREF=geneNCBILink %geneSymbol
- else:
- outlineColor = pid.orange
- fillColor = pid.orange
- TITLE = "Gene: %s" % geneSymbol
-
- #Draw Genes
- geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
-
- if 1:#drawClickableRegions:
- geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
- else:
- geneYLocation += self.BAND_SPACING
-
- #draw the detail view
- if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
- utrColor = pid.Color(0.66, 0.66, 0.66)
- arrowColor = pid.Color(0.7, 0.7, 0.7)
-
- #draw the line that runs the entire length of the gene
- #canvas.drawString(str(geneStartPix), 300, 400)
- canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
-
- #draw the arrows
- for xCoord in range(0, geneEndPix-geneStartPix):
-
- if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
- if strand == "+":
- canvas.drawLine(geneStartPix + xCoord, geneYLocation, geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
- canvas.drawLine(geneStartPix + xCoord, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH, geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom, color=arrowColor, width=1)
- else:
- canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation, geneStartPix + xCoord, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
- canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord, geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
-
- #draw the blocks for the exon regions
- for i in range(0, len(exonStarts)):
- exonStartPix = (exonStarts[i]-startMb)*plotXScale + xLeftOffset
- exonEndPix = (exonEnds[i]-startMb)*plotXScale + xLeftOffset
- if (exonStartPix < xLeftOffset):
- exonStartPix = xLeftOffset
- if (exonEndPix < xLeftOffset):
- exonEndPix = xLeftOffset
- if (exonEndPix > xLeftOffset + plotWidth):
- exonEndPix = xLeftOffset + plotWidth
- if (exonStartPix > xLeftOffset + plotWidth):
- exonStartPix = xLeftOffset + plotWidth
- canvas.drawRect(exonStartPix, geneYLocation, exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
-
- #draw gray blocks for 3' and 5' UTR blocks
- if cdsStart and cdsEnd:
-
- utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
- utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
- if (utrStartPix < xLeftOffset):
- utrStartPix = xLeftOffset
- if (utrEndPix < xLeftOffset):
- utrEndPix = xLeftOffset
- if (utrEndPix > xLeftOffset + plotWidth):
- utrEndPix = xLeftOffset + plotWidth
- if (utrStartPix > xLeftOffset + plotWidth):
- utrStartPix = xLeftOffset + plotWidth
- canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
-
- if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
- if strand == "-":
- labelText = "3'"
- else:
- labelText = "5'"
- canvas.drawString(labelText, utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
-
- #the second UTR region
-
- utrStartPix = (cdsEnd-startMb)*plotXScale + xLeftOffset
- utrEndPix = (txEnd-startMb)*plotXScale + xLeftOffset
- if (utrStartPix < xLeftOffset):
- utrStartPix = xLeftOffset
- if (utrEndPix < xLeftOffset):
- utrEndPix = xLeftOffset
- if (utrEndPix > xLeftOffset + plotWidth):
- utrEndPix = xLeftOffset + plotWidth
- if (utrStartPix > xLeftOffset + plotWidth):
- utrStartPix = xLeftOffset + plotWidth
- canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
-
- if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
- if tstrand == "-":
- labelText = "5'"
- else:
- labelText = "3'"
- canvas.drawString(labelText, utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
-
- #draw the genes as rectangles
- else:
- canvas.drawRect(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
-
- COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
- # NL: 06-02-2011 Rob required to display NCBI info in a new window
- gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
-
-## BEGIN HaplotypeAnalyst
- def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
- return
-
-
- fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb')
-
- clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- widthMultiplier = 1
-
- yPaddingTop = yTopOffset
-
- exprdrawn = 0
-
- thisTrait = self.traitList[0]
- _strains, _vals, _vars = thisTrait.exportInformative()
-
- smd=[]
- for ii, _val in enumerate(_vals):
- temp = GeneralObject(name=_strains[ii], value=_val)
- smd.append(temp)
-
- smd.sort(lambda A, B: cmp(A.value, B.value))
-
- bxdlist=list(self.genotype.prgy)
-
- oldgeneEndPix = -1
- #Initializing plotRight, error before
- plotRight = xRightOffset
-
-#### find out PlotRight
- for i, _locus in enumerate(self.genotype[0]):
- txStart = self.genotype[0][i].Mb
- txEnd = self.genotype[0][i].Mb
-
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
-
- drawit = 1
- if (geneStartPix < xLeftOffset):
- drawit = 0;
- if (geneStartPix > xLeftOffset + plotWidth):
- drawit = 0;
-
- if drawit == 1:
-
- if self.genotype[0][i].name != " - " :
-
- plotRight = geneEndPix + 4
-
-
-
-#### end find out PlotRight
-
- firstGene = 1
- lastGene = 0
-
- #Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype"
- #was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped.
- #Now there should always be some value set for "oldgeno" - Zach 12/14/2010
- oldgeno = [None]*len(self.strainlist)
-
- for i, _locus in enumerate(self.genotype[0]):
- txStart = self.genotype[0][i].Mb
- txEnd = self.genotype[0][i].Mb
-
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0
-
- if oldgeneEndPix >= xLeftOffset:
- drawStart = oldgeneEndPix + 4
- else:
- drawStart = xLeftOffset + 3
-
- drawEnd = plotRight - 9
-
- drawit = 1
-
- if (geneStartPix < xLeftOffset):
- if firstGene == 1:
- drawit = 1
- else:
- drawit = 0
-
- elif (geneStartPix > (xLeftOffset + plotWidth - 3)):
- if lastGene == 0:
- drawit = 1
- drawEnd = xLeftOffset + plotWidth - 6
- lastGene = 1
- else:
- break
-
- else:
- firstGene = 0
- drawit = 1
-
- if drawit == 1:
- myColor = pid.darkblue
- outlineColor = myColor
- fillColor = myColor
-
- maxind=0
-
- #Draw Genes
-
- geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
-
- if 1:#drawClickableRegions:
- geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
- else:
- geneYLocation += self.BAND_SPACING
-
- if self.genotype[0][i].name != " - " :
-
- if (firstGene == 1) and (lastGene != 1):
- oldgeneEndPix = drawStart = xLeftOffset
- oldgeno = self.genotype[0][i].genotype
- continue
-
- for j,_geno in enumerate (self.genotype[0][i].genotype):
-
- plotbxd=0
- for item in smd:
- if item.name == bxdlist[j]:
- plotbxd=1
-
- if (plotbxd == 1):
- ind = 0
- counter = 0
- for item in smd:
- counter = counter + 1
- if item.name == bxdlist[j]:
- ind = counter
- maxind=max(ind,maxind)
-
- # lines
- if (oldgeno[j] == -1 and _geno == -1):
- mylineColor = self.HAPLOTYPE_NEGATIVE
- elif (oldgeno[j] == 1 and _geno == 1):
- mylineColor = self.HAPLOTYPE_POSITIVE
- elif (oldgeno[j] == 0 and _geno == 0):
- mylineColor = self.HAPLOTYPE_HETEROZYGOUS
- else:
- mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
-
- canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
-
- fillColor=pid.black
- outlineColor=pid.black
- if lastGene == 0:
- canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
-
-
- COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
- TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (bxdlist[j], self.genotype[0][i].name, float(txStart))
- HREF = ''
- gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
-
- # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
- # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
- if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
- drawEnd = xLeftOffset + plotWidth - 6
- mylineColor = self.HAPLOTYPE_RECOMBINATION
- canvas.drawLine(plotRight, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
-
-
- if lastGene == 0:
- canvas.drawString("%s" % (self.genotype[0][i].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)
-
- oldgeneEndPix = geneEndPix;
- oldgeno = self.genotype[0][i].genotype
- firstGene = 0
- else:
- lastGene = 0
-
- for j,_geno in enumerate (self.genotype[0][1].genotype):
-
- plotbxd=0
- for item in smd:
- if item.name == bxdlist[j]:
- plotbxd=1
-
- if (plotbxd == 1):
-
- ind = 0
- counter = 0
- expr = 0
- for item in smd:
- counter = counter + 1
- if item.name == bxdlist[j]:
- ind = counter
- expr = item.value
-
- # Place where font is hardcoded
- canvas.drawString("%s" % (bxdlist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
- canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
-
- fpText.close()
-
-## END HaplotypeAnalyst
-
- def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- if self.plotScale != 'physic' or self.selectedChr == -1:
- return
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- # only draw this many clickable regions (if you set it higher, you get more precision in clicking,
- # but it makes the HTML huge, and takes forever to render the page in the first place)
- # Draw the bands that you can click on to go to UCSC / Ensembl
- MAX_CLICKABLE_REGION_DIVISIONS = 100
- clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
- pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS))
- # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
-
- numBasesCurrentlyOnScreen = self.kONE_MILLION*abs(startMb - endMb) # Number of bases on screen now
- flankingWidthInBases = int ( min( (float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION) ) )
- webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
- # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
-
- currentChromosome = self.genotype[0].name
- i = 0
- for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
-
- calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
-
- xBrowse1 = pixel
- xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
-
- paddingTop = yTopOffset
- ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
- ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
-
- WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
- bandWidth = xBrowse2 - xBrowse1
- WEBQTL_HREF = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (currentChromosome, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
-
- WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
- gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
- canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
- canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
-
- UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
- if self.species == "mouse":
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, currentChromosome)
- else:
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
- UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
- gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
- canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
- canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
-
- ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
- if self.species == "mouse":
- ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
- else:
- ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
- ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
- gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
- canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
- canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
- # end for
-
- canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.WEBQTL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
- canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.UCSC_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
- canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.ENSEMBL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
-
- #draw the gray text
- chrFont = pid.Font(ttf="verdana", size=26, bold=1)
- traitFont = pid.Font(ttf="verdana", size=14, bold=0)
- chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont)
- canvas.drawString("Chr %s" % currentChromosome, chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
- traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
- # end of drawBrowserClickableRegions
-
- pass
-
- def drawXAxis(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yZero = canvas.size[1] - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- #Parameters
- NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
- X_MAJOR_TICK_THICKNESS = 2
- X_MINOR_TICK_THICKNESS = 1
- X_AXIS_THICKNESS = 1*zoom
-
- # ======= Alex: Draw the X-axis labels (megabase location)
- MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
- xMajorTickHeight = 15 # How high the tick extends below the axis
- xMinorTickHeight = 5*zoom
- xAxisTickMarkColor = pid.black
- xAxisLabelColor = pid.black
- fontHeight = 12*fontZoom # How tall the font that we're using is
- spacingFromLabelToAxis = 20
- spacingFromLineToLabel = 3
-
- if self.plotScale == 'physic':
- strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
- ###Physical single chromosome view
- if self.selectedChr > -1:
- graphMbWidth = endMb - startMb
- XScale = Plot.detScale(startMb, endMb)
- XStart, XEnd, XStep = XScale
- if XStep < 8:
- XStep *= 2
- spacingAmtX = spacingAmt = (XEnd-XStart)/XStep
-
- j = 0
- while abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
- j += 1
- spacingAmtX *= 10
-
- formatStr = '%%2.%df' % j
-
- for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
- if _Mb < startMb or _Mb > endMb:
- continue
- Xc = xLeftOffset + plotXScale*(_Mb - startMb)
- if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
- canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
- labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
- strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
- drawStringXc = (Xc - (strWidth / 2.0))
- canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
- else:
- canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
- # end else
-
- ###Physical genome wide view
- else:
- distScale = 0
- startPosX = xLeftOffset
- for i, distLen in enumerate(self.ChrLengthDistList):
- if distScale == 0: #universal scale in whole genome mapping
- if distLen > 75:
- distScale = 25
- elif distLen > 30:
- distScale = 10
- else:
- distScale = 5
- for tickdists in range(distScale, ceil(distLen), distScale):
- canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
- canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
- megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
- canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
- strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
- pass
- else:
- ChrAInfo = []
- preLpos = -1
- distinctCount = 0.0
- if len(self.genotype) > 1:
- for i, _chr in enumerate(self.genotype):
- thisChr = []
- Locus0CM = _chr[0].cM
- nLoci = len(_chr)
- if nLoci <= 8:
- for _locus in _chr:
- if _locus.name != ' - ':
- if _locus.cM != preLpos:
- distinctCount += 1
- preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM-Locus0CM])
- else:
- for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1):
- while _chr[j].name == ' - ':
- j += 1
- if _chr[j].cM != preLpos:
- distinctCount += 1
- preLpos = _chr[j].cM
- thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM])
- ChrAInfo.append(thisChr)
- else:
- for i, _chr in enumerate(self.genotype):
- thisChr = []
- Locus0CM = _chr[0].cM
- for _locus in _chr:
- if _locus.name != ' - ':
- if _locus.cM != preLpos:
- distinctCount += 1
- preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM-Locus0CM])
- ChrAInfo.append(thisChr)
-
- stepA = (plotWidth+0.0)/distinctCount
-
- LRectWidth = 10
- LRectHeight = 3
- offsetA = -stepA
- lineColor = pid.lightblue
- startPosX = xLeftOffset
- for j, ChrInfo in enumerate(ChrAInfo):
- preLpos = -1
- for i, item in enumerate(ChrInfo):
- Lname,Lpos = item
- if Lpos != preLpos:
- offsetA += stepA
- differ = 1
- else:
- differ = 0
- preLpos = Lpos
- Lpos *= plotXScale
- if self.selectedChr > -1:
- Zorder = i % 5
- else:
- Zorder = 0
- if differ:
- canvas.drawLine(startPosX+Lpos,yZero,xLeftOffset+offsetA,\
- yZero+25, color=lineColor)
- canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
- yZero+40+Zorder*(LRectWidth+3),color=lineColor)
- rectColor = pid.orange
- else:
- canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
- xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
- rectColor = pid.deeppink
- canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\
- edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
- COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
- HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
- Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
- gifmap.areas.append(Areas)
- ##piddle bug
- if j == 0:
- canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
- startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-
- canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself
-
-
- def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- INTERCROSS = (self.genotype.type=="intercross")
-
- LRSHeightThresh = drawAreaHeight
- AdditiveHeightThresh = drawAreaHeight/2
- DominanceHeightThresh = drawAreaHeight/2
-
- #draw the LRS scale
- #We first determine whether or not we are using a sliding scale.
- #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax.
- #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
- #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.
-
- if self.LRS_LOD == 'LOD':
- lodm = self.LODFACTOR
- else:
- lodm = 1.0
-
- if self.lrsMax <= 0: #sliding scale
- LRSMax = max(map(max, self.qtlresults)).lrs
- #genotype trait will give infinite LRS
- LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
- if self.permChecked and not self.multipleInterval:
- self.significance = min(self.significance, webqtlConfig.MAXLRS)
- self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
- LRSMax = max(self.significance, LRSMax)
- else:
- LRSMax = self.lrsMax*lodm
-
- if LRSMax/lodm > 100:
- LRSScale = 20.0
- elif LRSMax/lodm > 20:
- LRSScale = 5.0
- elif LRSMax/lodm > 7.5:
- LRSScale = 2.5
- else:
- LRSScale = 1.0
-
- LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale)
- #make sure the user's value appears on the y-axis
- #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460
- LRSAxisList.append(round(LRSMax/lodm))
-
- #draw the "LRS" or "LOD" string to the left of the axis
- LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
- LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
- yZero = yTopOffset + plotHeight
-
-
- canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \
- yZero - 150, font=LRSLODFont, color=pid.black, angle=90)
-
- for item in LRSAxisList:
- yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh
- canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom)
- scaleStr = "%2.1f" % item
- canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
-
-
- #"Significant" and "Suggestive" Drawing Routine
- # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
- if self.permChecked and not self.multipleInterval:
- significantY = yZero - self.significance*LRSHeightThresh/LRSMax
- suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax
- startPosX = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
- canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
- width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
- canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
- width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
- sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
- sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2)
- if self.LRS_LOD == 'LRS':
- sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
- sig_title = "Significant LRS = %0.2f" % self.significance
- else:
- sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
- sig_title = "Significant LOD = %0.2f" % (self.significance/4.61)
- Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
- Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
- gifmap.areas.append(Areas1)
- gifmap.areas.append(Areas2)
-
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
-
- if self.multipleInterval:
- lrsEdgeWidth = 1
- else:
- additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
- if INTERCROSS:
- dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
- else:
- dominanceMax = -1
- lrsEdgeWidth = 2
- for i, qtlresult in enumerate(self.qtlresults):
- m = 0
- startPosX = xLeftOffset
- thisLRSColor = self.colorCollection[i]
- for j, _chr in enumerate(self.genotype):
- LRSCoordXY = []
- AdditiveCoordXY = []
- DominanceCoordXY = []
- for k, _locus in enumerate(_chr):
- if self.plotScale == 'physic':
- Xc = startPosX + (_locus.Mb-startMb)*plotXScale
- else:
- Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
- # updated by NL 06-18-2011:
- # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
- # for any lrs is over than 460(LRS max in this system), it will be reset to 460
- if qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf':
- Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
- else:
- Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax
-
- LRSCoordXY.append((Xc, Yc))
- if not self.multipleInterval and self.additiveChecked:
- Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
- AdditiveCoordXY.append((Xc, Yc))
- if not self.multipleInterval and INTERCROSS and self.additiveChecked:
- Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
- DominanceCoordXY.append((Xc, Yc))
- m += 1
- canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- if not self.multipleInterval and self.additiveChecked:
- plusColor = self.ADDITIVE_COLOR_POSITIVE
- minusColor = self.ADDITIVE_COLOR_NEGATIVE
- for k, aPoint in enumerate(AdditiveCoordXY):
- if k > 0:
- Xc0, Yc0 = AdditiveCoordXY[k-1]
- Xc, Yc = aPoint
- if (Yc0-yZero)*(Yc-yZero) < 0:
- if Xc == Xc0: #genotype , locus distance is 0
- Xcm = Xc
- else:
- Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
- if Yc0 < yZero:
- canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- elif (Yc0-yZero)*(Yc-yZero) > 0:
- if Yc < yZero:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- minYc = min(Yc-yZero, Yc0-yZero)
- if minYc < 0:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
- plusColor = self.DOMINANCE_COLOR_POSITIVE
- minusColor = self.DOMINANCE_COLOR_NEGATIVE
- for k, aPoint in enumerate(DominanceCoordXY):
- if k > 0:
- Xc0, Yc0 = DominanceCoordXY[k-1]
- Xc, Yc = aPoint
- if (Yc0-yZero)*(Yc-yZero) < 0:
- if Xc == Xc0: #genotype , locus distance is 0
- Xcm = Xc
- else:
- Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
- if Yc0 < yZero:
- canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- elif (Yc0-yZero)*(Yc-yZero) > 0:
- if Yc < yZero:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- minYc = min(Yc-yZero, Yc0-yZero)
- if minYc < 0:
- canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- else:
- canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-
- ###draw additive scale
- if not self.multipleInterval and self.additiveChecked:
- additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0)
- additiveScale = Plot.detScaleOld(0,additiveMax)
- additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
- additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
- maxAdd = additiveScale[1]
- addPlotScale = AdditiveHeightThresh/additiveMax
-
- additiveAxisList.append(additiveScale[1])
- for item in additiveAxisList:
- additiveY = yZero - item*addPlotScale
- canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
- scaleStr = "%2.3f" % item
- canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE)
-
- canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
-
- canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis
-
-
- def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
- ##conditions
- ##multiple Chromosome view
- ##single Chromosome Physical
- ##single Chromosome Genetic
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- fontZoom = zoom
- if zoom == 2:
- fontZoom = 1.5
-
- #calculate plot scale
- if self.plotScale != 'physic':
- self.ChrLengthDistList = self.ChrLengthCMList
- drawRegionDistance = self.ChrLengthCMSum
- else:
- self.ChrLengthDistList = self.ChrLengthMbList
- drawRegionDistance = self.ChrLengthMbSum
-
- if self.selectedChr > -1: #single chromosome view
- spacingAmt = plotWidth/13.5
- i = 0
- for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt):
- if (i % 2 == 0):
- theBackColor = self.GRAPH_BACK_DARK_COLOR
- else:
- theBackColor = self.GRAPH_BACK_LIGHT_COLOR
- i += 1
- canvas.drawRect(startPix, yTopOffset, min(startPix+spacingAmt, xLeftOffset+plotWidth), \
- yTopOffset+plotHeight, edgeColor=theBackColor, fillColor=theBackColor)
-
- drawRegionDistance = self.ChrLengthDistList[self.selectedChr]
- self.ChrLengthDistList = [drawRegionDistance]
- if self.plotScale == 'physic':
- plotXScale = plotWidth / (endMb-startMb)
- else:
- plotXScale = plotWidth / drawRegionDistance
-
- else: #multiple chromosome view
- plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance)
-
- startPosX = xLeftOffset
- chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)
-
- for i, _chr in enumerate(self.genotype):
- if (i % 2 == 0):
- theBackColor = self.GRAPH_BACK_DARK_COLOR
- else:
- theBackColor = self.GRAPH_BACK_LIGHT_COLOR
-
- #draw the shaded boxes and the sig/sug thick lines
- canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
- yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)
-
- chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
- chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
- chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
-
- canvas.drawString(_chr.name, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
- COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
-
- #add by NL 09-03-2010
- HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
- Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
- gifmap.areas.append(Areas)
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
- return plotXScale
-
- def calculateAllResult(self, fd):
-
- weightedRegression = fd.formdata.getvalue('applyVarianceSE')
-
- self.genotype = self.genotype.addinterval()
- resultSlice = []
- controlGeno = []
-
- if self.multipleInterval:
- self.suggestive = 0
- self.significance = 0
- if self.selectedChr > -1:
- self.genotype.chromosome = [self.genotype[self.selectedChr]]
- else:
- #single interval mapping
- try:
- self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
- self.significance = float(fd.formdata.getvalue('permSignificance'))
- except:
- self.suggestive = None
- self.significance = None
-
- _strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
-
- if webqtlUtil.ListNotNull(_vars):
- pass
- else:
- weightedRegression = 0
- _strains, _vals, _vars = self.traitList[0].exportInformative()
-
- ##locate genotype of control Locus
- if self.controlLocus:
- controlGeno2 = []
- _FIND = 0
- for _chr in self.genotype:
- for _locus in _chr:
- if _locus.name == self.controlLocus:
- controlGeno2 = _locus.genotype
- _FIND = 1
- break
- if _FIND:
- break
- if controlGeno2:
- _prgy = list(self.genotype.prgy)
- for _strain in _strains:
- _idx = _prgy.index(_strain)
- controlGeno.append(controlGeno2[_idx])
- else:
- return "The control marker you selected is not in the genofile."
-
-
- if self.significance and self.suggestive:
- pass
- else:
- if self.permChecked:
- if weightedRegression:
- self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
- variance = _vars, nperm=fd.nperm)
- else:
- self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
- nperm=fd.nperm)
- self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)]
- self.significance = self.LRSArray[int(fd.nperm*0.95-1)]
-
- else:
- self.suggestive = 9.2
- self.significance = 16.1
-
- #calculating bootstrap
- #from now on, genotype could only contain a single chromosome
- #permutation need to be performed genome wide, this is not the case for bootstrap
-
- #due to the design of qtlreaper, composite regression need to be performed genome wide
- if not self.controlLocus and self.selectedChr > -1:
- self.genotype.chromosome = [self.genotype[self.selectedChr]]
- elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
- lociPerChr = map(len, self.genotype)
- resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
- resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
- else:
- pass
-
- #calculate QTL for each trait
- self.qtlresults = []
-
- for thisTrait in self.traitList:
- _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
- if self.controlLocus:
- if weightedRegression:
- qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- variance = _vars, control = self.controlLocus)
- else:
- qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- control = self.controlLocus)
- if resultSlice:
- qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
- else:
- if weightedRegression:
- qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- variance = _vars)
- else:
- qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
-
- self.qtlresults.append(qtlresult)
-
- if not self.multipleInterval:
- if self.controlLocus and self.selectedChr > -1:
- self.genotype.chromosome = [self.genotype[self.selectedChr]]
-
- if self.bootChecked:
- if controlGeno:
- self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- control = controlGeno, nboot=fd.nboot)
- elif weightedRegression:
- self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- variance = _vars, nboot=fd.nboot)
- else:
- self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- nboot=fd.nboot)
- else:
- self.bootResult = []
-
- def calculatePValue (self, query_LRS, permutation_LRS_array):
- query_index = len(permutation_LRS_array)
- for i, one_permutation_LRS in enumerate(permutation_LRS_array):
- if one_permutation_LRS >= query_LRS:
- query_index = i
- break
-
- P_value = float(len(permutation_LRS_array) - query_index) / len(permutation_LRS_array)
-
- return P_value
-
- def helpButton(self, anchor):
- return HT.Href(self.HELP_PAGE_REF + '#%s' % anchor, self.qmarkImg, target=self.HELP_WINDOW_NAME)
-
-
- def traitRemapTD(self, cursor, fd):
- chrList = HT.Select(name="chromosomes", data=self.ChrList, selected=[self.selectedChr],
- onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
-
- physicOnly = HT.Span(' *', Class="cr")
-
- showSNPCheck = HT.Input(type='checkbox', Class='checkbox', name='showSNP', value='ON', checked=self.SNPChecked)
- showSNPText = HT.Span('SNP Track ', self.helpButton("snpSeismograph"), Class="fs12 fwn")
-
- showGenesCheck = HT.Input(type='checkbox', Class='checkbox', name='showGenes', value='ON', checked=self.geneChecked)
- showGenesText = HT.Span('Gene Track', Class="fs12 fwn")
-
- showIntervalAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='intervalAnalystCheck', value='ON', checked=self.intervalAnalystChecked)
- showIntervalAnalystText = HT.Span('Interval Analyst', Class="fs12 fwn")
-## BEGIN HaplotypeAnalyst
-
- showHaplotypeAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='haplotypeAnalystCheck', value='ON', checked=self.haplotypeAnalystChecked)
- showHaplotypeAnalystText = HT.Span('Haplotype Analyst', Class="fs12 fwn")
-## END HaplotypeAnalyst
-
- leftBox = HT.Input(type="text", name="startMb", size=10)
- rightBox = HT.Input(type="text", name="endMb", size=10)
- if self.selectedChr > -1 and self.plotScale=='physic':
- leftBox.value = self.startMb
- rightBox.value = self.endMb
-
- scaleBox = HT.Select(name="scale", onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
- scaleBox.append(("Genetic", "morgan"))
- if fd.genotype.Mbmap:
- scaleBox.append(("Physical", "physic"))
- scaleBox.selected.append(self.plotScale)
-
- permBox = HT.Input(type="checkbox", name="permCheck", value='ON', checked=self.permChecked, Class="checkbox")
- permText = HT.Span("Permutation Test ", self.helpButton("Permutation"), Class="fs12 fwn")
- bootBox = HT.Input(type="checkbox", name="bootCheck", value='ON', checked=self.bootChecked, Class="checkbox")
- bootText = HT.Span("Bootstrap Test ", self.helpButton("bootstrap"), Class="fs12 fwn")
- additiveBox = HT.Input(type="checkbox", name="additiveCheck", value='ON', checked=self.additiveChecked, Class="checkbox")
- additiveText = HT.Span("Allele Effects ", self.helpButton("additive"), Class="fs12 fwn")
- dominanceBox = HT.Input(type="checkbox", name="dominanceCheck", value='ON', checked=self.dominanceChecked, Class="checkbox")
- dominanceText = HT.Span("Dominance Effects ", self.helpButton("Dominance"), Class="fs12 fwn")
-
- lrsRadio = HT.Input(type="radio", name="LRSCheck", value='LRS', checked = (self.LRS_LOD == "LRS"))
- lodRadio = HT.Input(type="radio", name="LRSCheck", value='LOD', checked = (self.LRS_LOD != "LRS"))
- lrsMaxBox = HT.Input(type="text", name="lrsMax", value=self.lrsMax, size=3)
- widthBox = HT.Input(type="text", name="graphWidth", size=5, value=str(self.graphWidth))
- legendBox = HT.Input(type="checkbox", name="viewLegend", value='ON', checked=self.legendChecked, Class="checkbox")
- legendText = HT.Span("Legend", Class="fs12 fwn")
-
- draw2XBox = HT.Input(type="checkbox", name="draw2X", value='ON', Class="checkbox")
- draw2XText = HT.Span("2X Plot", Class="fs12 fwn")
-
- regraphButton = HT.Input(type="button", Class="button", onClick="javascript:databaseFunc(this.form,'showIntMap');", value="Remap")
-
- controlsForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype="multipart/form-data", name="changeViewForm", submit=HT.Input(type='hidden'))
- controlsTable = HT.TableLite(border=0)
- innerControlsTable = HT.TableLite(border=0)
- if self.selectedChr == -1:
- minimumGraphWidth = self.MULT_GRAPH_MIN_WIDTH
- else:
- minimumGraphWidth = self.GRAPH_MIN_WIDTH
-
- innerControlsTable.append(
- HT.TR(HT.TD("Chr: ", Class="fs12 fwb ffl"),HT.TD(chrList, scaleBox, regraphButton)),
- HT.TR(HT.TD("View: ", Class="fs12 fwb ffl"),HT.TD(leftBox, " to ", rightBox, "Mb", physicOnly, NOWRAP="on")),
- HT.TR(HT.TD("Units: ", Class="fs12 fwb ffl"), HT.TD(lrsRadio, "LRS ", lodRadio, "LOD ", self.helpButton("LOD"))),
- HT.TR(HT.TD(" ", Class="fs12 fwb ffl"), HT.TD(lrsMaxBox, "units on Y-axis (0 for default)", Class="fs11 fwn")),
- HT.TR(HT.TD("Width: ", Class="fs12 fwb ffl"), HT.TD(widthBox, "pixels (minimum=%d)" % minimumGraphWidth, Class="fs11 fwn "))
- )
- #whether SNP
- cursor.execute("Select Species.Id from SnpAll, Species where SnpAll.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
- SNPorNot = cursor.fetchall()
- #Whether Gene
- cursor.execute("Select Species.Id from GeneList, Species where GeneList.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
- GeneorNot = cursor.fetchall()
-
- if self.multipleInterval:
- optionPanel = HT.TD(valign="top", NOWRAP="on")
- else:
- optionPanel = HT.TD(permBox, permText, HT.BR(), bootBox, bootText, HT.BR(), additiveBox, additiveText, HT.BR(), valign="top", NOWRAP="on")
- #whether dominance
- if self.genotype.type == 'intercross':
- optionPanel.append(dominanceBox, dominanceText, HT.BR())
- if SNPorNot:
- optionPanel.append(showSNPCheck, showSNPText, physicOnly, HT.BR())
- if GeneorNot:
- optionPanel.append(showGenesCheck, showGenesText, physicOnly, HT.BR(),
- showIntervalAnalystCheck, showIntervalAnalystText, physicOnly, HT.BR())
-## BEGIN HaplotypeAnalyst
- optionPanel.append(showHaplotypeAnalystCheck, showHaplotypeAnalystText, physicOnly, HT.BR())
-## END HaplotypeAnalyst
- optionPanel.append(legendBox, legendText, HT.BR(),draw2XBox, draw2XText)
- controlsTable.append(
- HT.TR(HT.TD(innerControlsTable, valign="top"),
- HT.TD("&nbsp;", width=15), optionPanel),
- HT.TR(HT.TD(physicOnly, " only apply to single chromosome physical mapping", align="Center", colspan=3, Class="fs11 fwn"))
- )
- controlsForm.append(controlsTable)
-
- controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden"))
- controlsForm.append(HT.Input(name="permSignificance", value=self.significance, type="hidden"))
-
-## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below
-## END HaplotypeAnalyst
-
- for key in fd.formdata.keys():
- if key == "searchResult" and type([]) == type(fd.formdata.getvalue(key)):
- controlsForm.append(HT.Input(name=key, value=string.join(fd.formdata.getvalue(key), "\t"), type="hidden"))
- elif key not in ("endMb", "startMb", "chromosomes", "scale", "permCheck", "bootCheck", "additiveCheck", "dominanceCheck",
- "LRSCheck", "intervalAnalystCheck", "haplotypeAnalystCheck", "lrsMax", "graphWidth", "viewLegend", 'showGenes', 'showSNP', 'draw2X',
- 'permSuggestive', "permSignificance"):
- controlsForm.append(HT.Input(name=key, value=fd.formdata.getvalue(key), type="hidden"))
- else:
- pass
-
- # updated by NL, move function changeView(i) to webqtl.js and change it to function changeView(i, Chr_Mb_list)
- # move function chrLength(a, b, c) to webqtl.js and change it to function chrLength(a, b, c, Chr_Mb_list)
- self.dict['js1'] = ''
-
- return HT.TD(controlsForm, Class="doubleBorder", width=400)
-
- def traitInfoTD(self, fd):
- if self.selectedChr == -1:
- intMapHeading = HT.Paragraph('Map Viewer: Whole Genome', Class="title")
- else:
- intMapHeading = HT.Paragraph('Map Viewer: Chr %s' % self.genotype[0].name, Class="title")
-
- heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (self.species.title(), fd.RISet) , HT.BR())
- #Trait is from an database
- if self.traitList and self.traitList[0] and self.traitList[0].db:
- #single trait
- if len(self.traitList) == 1:
- thisTrait = self.traitList[0]
- trait_url = HT.Href(text=thisTrait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \
- "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (thisTrait.db.name, thisTrait.name), \
- target='_blank', Class="normalsize")
- heading2.append(HT.Strong("Database: "), HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name ,\
- target='_blank',Class="normalsize"),HT.BR())
- if thisTrait.db.type == 'ProbeSet':
- heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(),
- HT.Strong("Gene Symbol: "), HT.Italic('%s' % thisTrait.symbol,id="green"),HT.BR())
- if thisTrait.chr and thisTrait.mb:
- heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
- elif thisTrait.db.type == 'Geno':
- heading2.append(HT.Strong('Locus : '), trait_url, HT.BR())
- if thisTrait.chr and thisTrait.mb:
- heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
- elif thisTrait.db.type == 'Publish':
- heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR())
- else:
- pass
- else:
- heading2.append(HT.Strong("Traits: "), "Multiple Traits")
- else:
- heading2.append(HT.Strong("Trait Name: "), fd.identification)
- return HT.TD(intMapHeading, heading2, valign="top")
-
- def geneTables(self, geneCol, refGene=None):
- SNPLink = 0
- tableIterationsCnt = 0
- if self.species == "mouse":
- geneTableMain = HT.TableLite(border=0, width=1280, cellpadding=0, cellspacing=0, Class="collap")
- columns = HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
- HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
- HT.TD('Mb Start (mm9)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD("SNP Count", Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD("SNP Density (SNP/Kb)", Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
- HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1))
-
- # http://compbio.uthsc.edu/miRSNP/
-
- td_pd = HT.TD(Class="fs14 fwb ffl b1 cw cbrb")
- td_pd.append(HT.Text("PolymiRTS"))
- td_pd.append(HT.BR())
- td_pd.append(HT.Text("Database"))
- td_pd.append(HT.BR())
- td_pd.append(HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"))
-
- if refGene:
- columns.append(HT.TD('Literature Correlation', Class="fs14 fwb ffl b1 cw cbrb", width=1))
- columns.append(HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb"))
- columns.append(td_pd)
- geneTableMain.append(columns)
-
- # polymiRTS
- # http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125
- #XZ: We can NOT assume their web service is always on. We must put this block of code in try except.
- try:
- conn = httplib.HTTPConnection("lily.uthsc.edu:8080")
- conn.request("GET", "/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=%s&chrom_from=%s&chrom_to=%s" % (self.genotype[0].name, self.startMb, self.endMb))
- response = conn.getresponse()
- data = response.read()
- data = data.split()
- conn.close()
- dic = {}
- index = 0
- for i in data:
- if index%3==0:
- dic[data[index]] = HT.Href(url=data[index+2], text=data[index+1], target="_blank", Class="normalsize")
- index = index+1
- except Exception:
- dic={}
-
-
- for gIndex, theGO in enumerate(geneCol):
- geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
- tenPercentLength = geneLength*0.0001
- txStart = theGO["TxStart"]
- txEnd = theGO["TxEnd"]
- theGO["snpDensity"] = theGO["snpCount"]/geneLength
- if (self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST and geneTableMain):
- #accessionString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=gene&term=%s' % theGO["NM_ID"]
- geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
-
- allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"])
- if theGO["snpCount"]:
- snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'),
- theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]),
- text=theGO["snpCount"], target="_blank", Class="normalsize")
- else:
- snpString = 0
-
- mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit"
-
- if theGO['humanGene']:
- huGO = theGO['humanGene']
- if huGO["TxStart"] == '':
- humanStartDisplay = ""
- else:
- humanStartDisplay = "%0.6f" % huGO["TxStart"]
- humanChr = huGO["Chromosome"]
- if humanChr.find("q") > -1:
- humanChr = humanChr[:humanChr.find("q")]
- if humanChr.find("p") > -1:
- humanChr = humanChr[:humanChr.find("p")]
- humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000*huGO["TxStart"]), int(1000000*huGO["TxEnd"]))
- else:
- humanStartString = humanChr = humanStartDisplay = ""
-
- geneDescription = theGO["GeneDescription"]
- if len(geneDescription) > 26:
- geneDescription = geneDescription[:26]+"..."
- probeSetSearch = HT.Href(allProbeString, HT.Image("/images/webqtl_search.gif", border=0), target="_blank")
-
- if theGO["snpDensity"] < 0.000001:
- snpDensityStr = "0"
- else:
- snpDensityStr = "%0.6f" % theGO["snpDensity"]
-
- avgExpr = []#theGO["avgExprVal")
- if avgExpr in ([], None):
- avgExpr = ""
- else:
- avgExpr = "%0.6f" % avgExpr
-
- tableIterationsCnt = tableIterationsCnt + 1
-
- # polymiRTS
- polymiRTS = ' '
- if dic.has_key(theGO["GeneID"]):
- polymiRTS = dic[theGO["GeneID"]]
-
- # If we have a referenceGene then we will show the Literature Correlation
- if refGene:
- literatureCorrelation = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
- geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
- HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
- HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
- HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
- HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
- HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
- HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
- HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
- HT.TD(literatureCorrelation, align='left',Class="fs13 b1 cbw c222"),
- HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
- HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
-
- else:
- geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
- HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
- HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
- HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
- HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
- HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
- HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
- HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
- HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
- HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
-
- return geneTableMain
- elif self.species == "rat":
- geneTableMain = HT.TableLite(border=0, width=1050, cellpadding=0, cellspacing=0, Class="collap")
- geneTableMain.append(HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
- HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
- HT.TD('Mb Start (rn3)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
- HT.TD('Mouse Chr', Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Mb Start (mm9)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
- HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb")))
-
- for gIndex, theGO in enumerate(geneCol):
- geneDesc = theGO["GeneDescription"]
- if geneDesc == "---":
- geneDesc = ""
- geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
- geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
-
- #the chromosomes for human 1 are 1qXX.XX
- if theGO['humanGene']:
- humanChr = theGO['humanGene']["Chromosome"]
- if 'q' in humanChr:
- humanChr = humanChr[:humanChr.find("q")]
- if 'p' in humanChr:
- humanChr = humanChr[:humanChr.find("p")]
- humanTxStart = theGO['humanGene']["TxStart"]
- else:
- humanChr = humanTxStart = ""
-
- #Mouse Gene
- if theGO['mouseGene']:
- mouseChr = theGO['mouseGene']["Chromosome"]
- mouseTxStart = theGO['mouseGene']["TxStart"]
- else:
- mouseChr = mouseTxStart = ""
-
- if theGO["GeneID"] != "":
- geneSymbolURL = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blanK")
- else:
- geneSymbolURL = theGO["GeneSymbol"]
-
- if len(geneDesc) > 34:
- geneDesc = geneDesc[:32] + "..."
-
- avgExprVal = [] #theGO["avgExprVal"]
- if avgExprVal != "" and avgExprVal:
- avgExprVal = "%0.5f" % float(avgExprVal)
- else:
- avgExprVal = ""
-
- geneTableMain.append(HT.TR(HT.TD(gIndex+1, align="right", Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], HT.Image("/images/webqtl_search.gif", border=0), target="_blank"), Class="fs13 bt1 bb1 cbw c222"),
- HT.TD(geneSymbolURL, Class="fs13 bt1 bb1 cbw c222"),
- HT.TD(theGO["TxStart"], Class="fs13 b1 cbw c222"),
- HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0), Class="normalsize"), Class="fs13 b1 cbw c222"),
- HT.TD(avgExprVal, Class="fs13 b1 cbw c222"),
- HT.TD(mouseChr, Class="fs13 b1 cbw c222"),
- HT.TD(mouseTxStart, Class="fs13 b1 cbw c222"),
- HT.TD(humanChr, Class="fs13 b1 cbw c222"),
- HT.TD(humanTxStart, Class="fs13 b1 cbw c222"),
- HT.TD(geneDesc, Class="fs13 b1 cbw c222")))
- return geneTableMain
- else:
- return ""
-
- def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None):
- if not geneId1 or not geneId2:
- return None
- if geneId1 == geneId2:
- return 1.0
- geneId1 = str(geneId1)
- geneId2 = str(geneId2)
- lCorr = None
- try:
- query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
- for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
- cursor.execute(query,(x,y))
- lCorr = cursor.fetchone()
- if lCorr:
- lCorr = lCorr[0]
- break
- except: raise #lCorr = None
- return lCorr
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