diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/basicStatistics/BasicStatisticsFunctions.py | 174 | ||||
| -rwxr-xr-x | wqflask/basicStatistics/BasicStatisticsPage_alpha.py | 348 | ||||
| -rwxr-xr-x | wqflask/basicStatistics/__init__.py | 0 | ||||
| -rwxr-xr-x | wqflask/basicStatistics/updatedBasicStatisticsPage.py | 150 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 1898 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/__init__.py | 0 |
6 files changed, 2570 insertions, 0 deletions
diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py new file mode 100755 index 00000000..5cbbb145 --- /dev/null +++ b/wqflask/basicStatistics/BasicStatisticsFunctions.py @@ -0,0 +1,174 @@ +#import string +from math import * +#import piddle as pid +#import os + +#import reaper +from htmlgen import HTMLgen2 as HT + +#from utility import Plot +from utility import webqtlUtil +from base import webqtlConfig +from dbFunction import webqtlDatabaseFunction + +def basicStatsTable(vals, trait_type=None, cellid=None, heritability=None): + + valsOnly = [] + dataXZ = vals[:] + for i in range(len(dataXZ)): + valsOnly.append(dataXZ[i][1]) + + traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(valsOnly) #ZS: Should convert this from reaper to R in the future + + tbl = HT.TableLite(cellpadding=20, cellspacing=0) + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + tbl.append(HT.TR(HT.TD("Statistic",align="left", Class="fs14 fwb ffl b1 cw cbrb", width = 180), + HT.TD("Value", align="right", Class="fs14 fwb ffl b1 cw cbrb", width = 60))) + tbl.append(HT.TR(HT.TD("N of Samples",align="left", Class="fs13 b1 cbw c222"), + HT.TD(N,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Mean",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmean,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Median",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmedian,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + #tbl.append(HT.TR(HT.TD("Variance",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + # HT.TD("%2.3f" % traitvar,nowrap="yes",align="left", Class="fs13 b1 cbw c222"))) + tbl.append(HT.TR(HT.TD("Standard Error (SE)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitsem,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Standard Deviation (SD)", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitstdev,nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Minimum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[0][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD("Maximum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[-1][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + if (trait_type != None and trait_type == 'ProbeSet'): + #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") + #IRQuest.append(HT.BR()) + #IRQuest.append(" (fold difference)") + tbl.append(HT.TR(HT.TD("Range (log2)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + tbl.append(HT.TR(HT.TD(HT.Span(HT.Href(url="/glossary.html#Interquartile", target="_blank", text="Interquartile Range", Class="non_bold")), align="left", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right")) + + #XZ, 04/01/2009: don't try to get H2 value for probe. + if cellid: + pass + else: + if heritability: + tbl.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + else: + pass + # Lei Yan + # 2008/12/19 + + return tbl + +def plotNormalProbability(vals=None, RISet='', title=None, showstrains=0, specialStrains=[None], size=(750,500)): + + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + dataLabel = [] + dataX = map(lambda X: X[1], dataXZ) + + showLabel = showstrains + if len(dataXZ) > 50: + showLabel = 0 + for item in dataXZ: + strainName = webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=item[0]) + dataLabel.append(strainName) + + dataY=Plot.U(len(dataX)) + dataZ=map(Plot.inverseCumul,dataY) + c = pid.PILCanvas(size=(750,500)) + Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel) + + filename= webqtlUtil.genRandStr("nP_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + + img=HT.Image('/image/'+filename+'.gif',border=0) + + return img + +def plotBoxPlot(vals): + + valsOnly = [] + dataXZ = vals[:] + for i in range(len(dataXZ)): + valsOnly.append(dataXZ[i][1]) + + plotHeight = 320 + plotWidth = 220 + xLeftOffset = 60 + xRightOffset = 40 + yTopOffset = 40 + yBottomOffset = 60 + + canvasHeight = plotHeight + yTopOffset + yBottomOffset + canvasWidth = plotWidth + xLeftOffset + xRightOffset + canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) + XXX = [('', valsOnly[:])] + + Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") + filename= webqtlUtil.genRandStr("Box_") + canvas.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) + + plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13")) + + return img, plotLink + +def plotBarGraph(identification='', RISet='', vals=None, type="name"): + + this_identification = "unnamed trait" + if identification: + this_identification = identification + + if type=="rank": + dataXZ = vals[:] + dataXZ.sort(webqtlUtil.cmpOrder) + title='%s' % this_identification + else: + dataXZ = vals[:] + title='%s' % this_identification + + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + nnStrain = len(tnames) + + sLabel = 1 + + ###determine bar width and space width + if nnStrain < 20: + sw = 4 + elif nnStrain < 40: + sw = 3 + else: + sw = 2 + + ### 700 is the default plot width minus Xoffsets for 40 strains + defaultWidth = 650 + if nnStrain > 40: + defaultWidth += (nnStrain-40)*10 + defaultOffset = 100 + bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) + if bw < 10: + bw = 10 + + plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset + plotHeight = 500 + #print [plotWidth, plotHeight, bw, sw, nnStrain] + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) + + return img diff --git a/wqflask/basicStatistics/BasicStatisticsPage_alpha.py b/wqflask/basicStatistics/BasicStatisticsPage_alpha.py new file mode 100755 index 00000000..4ba9d54a --- /dev/null +++ b/wqflask/basicStatistics/BasicStatisticsPage_alpha.py @@ -0,0 +1,348 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by GeneNetwork Core Team 2010/10/20 + +import string +from math import * +import piddle as pid +import os + +from htmlgen import HTMLgen2 as HT +import reaper + +from utility import Plot +from base.webqtlTrait import webqtlTrait +from base.templatePage import templatePage +from utility import webqtlUtil +from base import webqtlConfig +from dbFunction import webqtlDatabaseFunction + + + +class BasicStatisticsPage_alpha(templatePage): + + plotMinInformative = 4 + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not fd.genotype: + fd.readGenotype() + strainlist2 = fd.strainlist + + if fd.allstrainlist: + strainlist2 = fd.allstrainlist + + fd.readData(strainlist2) + + specialStrains = [] + setStrains = [] + for item in strainlist2: + if item not in fd.strainlist and item.find('F1') < 0: + specialStrains.append(item) + else: + setStrains.append(item) + specialStrains.sort() + #So called MDP Panel + if specialStrains: + specialStrains = fd.f1list+fd.parlist+specialStrains + + self.plotType = fd.formdata.getvalue('ptype', '0') + plotStrains = strainlist2 + if specialStrains: + if self.plotType == '1': + plotStrains = setStrains + if self.plotType == '2': + plotStrains = specialStrains + + self.dict['title'] = 'Basic Statistics' + if not self.openMysql(): + return + + self.showstrains = 1 + self.identification = "unnamed trait" + + self.fullname = fd.formdata.getvalue('fullname', '') + if self.fullname: + self.Trait = webqtlTrait(fullname=self.fullname, cursor=self.cursor) + self.Trait.retrieveInfo() + else: + self.Trait = None + + if fd.identification: + self.identification = fd.identification + self.dict['title'] = self.identification + ' / '+self.dict['title'] + TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') + + ##should not display Variance, but cannot convert Variance to SE + #print plotStrains, fd.allTraitData.keys() + if len(fd.allTraitData) > 0: + vals=[] + InformData = [] + for _strain in plotStrains: + if fd.allTraitData.has_key(_strain): + _val, _var = fd.allTraitData[_strain].val, fd.allTraitData[_strain].var + if _val != None: + vals.append([_strain, _val, _var]) + InformData.append(_val) + + if len(vals) >= self.plotMinInformative: + supertable2 = HT.TableLite(border=0, cellspacing=0, cellpadding=5,width="800") + + staIntro1 = HT.Paragraph("The table and plots below list the basic statistical analysis result of trait",HT.Strong(" %s" % self.identification)) + + ##### + #anova + ##### + traitmean, traitmedian, traitvar, traitstdev, traitsem, N = reaper.anova(InformData) + TDStatis = HT.TD(width="360", valign="top") + tbl2 = HT.TableLite(cellpadding=5, cellspacing=0, Class="collap") + dataXZ = vals[:] + dataXZ.sort(self.cmpValue) + tbl2.append(HT.TR(HT.TD("Statistic",align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 200), + HT.TD("Value", align="center", Class="fs14 fwb ffl b1 cw cbrb", width = 140))) + tbl2.append(HT.TR(HT.TD("N of Cases",align="center", Class="fs13 b1 cbw c222"), + HT.TD(N,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Mean",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmean,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Median",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitmedian,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + #tbl2.append(HT.TR(HT.TD("Variance",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + # HT.TD("%2.3f" % traitvar,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("SEM",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitsem,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("SD",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % traitstdev,nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Minimum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[0][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD("Maximum",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%s" % dataXZ[-1][1],nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + if self.Trait and self.Trait.db.type == 'ProbeSet': + #IRQuest = HT.Href(text="Interquartile Range", url=webqtlConfig.glossaryfile +"#Interquartile",target="_blank", Class="fs14") + #IRQuest.append(HT.BR()) + #IRQuest.append(" (fold difference)") + tbl2.append(HT.TR(HT.TD("Range (log2)",align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + tbl2.append(HT.TR(HT.TD(HT.Span("Quartile Range",HT.BR()," (fold difference)"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"), + HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + + # (Lei Yan) + # 2008/12/19 + self.Trait.retrieveData() + #XZ, 04/01/2009: don't try to get H2 value for probe. + if self.Trait.cellid: + pass + else: + self.cursor.execute("SELECT DataId, h2 from ProbeSetXRef WHERE DataId = %d" % self.Trait.mysqlid) + dataid, heritability = self.cursor.fetchone() + if heritability: + tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + else: + tbl2.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("NaN", nowrap="yes",align="center", Class="fs13 b1 cbw c222"))) + + # Lei Yan + # 2008/12/19 + + TDStatis.append(tbl2) + + plotHeight = 220 + plotWidth = 120 + xLeftOffset = 60 + xRightOffset = 25 + yTopOffset = 20 + yBottomOffset = 53 + + canvasHeight = plotHeight + yTopOffset + yBottomOffset + canvasWidth = plotWidth + xLeftOffset + xRightOffset + canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight)) + XXX = [('', InformData[:])] + + Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait") + filename= webqtlUtil.genRandStr("Box_") + canvas.save(webqtlConfig.IMGDIR+filename, format='gif') + img=HT.Image('/image/'+filename+'.gif',border=0) + + #supertable2.append(HT.TR(HT.TD(staIntro1, colspan=3 ))) + tb = HT.TableLite(border=0, cellspacing=0, cellpadding=0) + tb.append(HT.TR(HT.TD(img, align="left", style="border: 1px solid #999999; padding:0px;"))) + supertable2.append(HT.TR(TDStatis, HT.TD(tb))) + + dataXZ = vals[:] + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + nnStrain = len(tnames) + + sLabel = 1 + + ###determine bar width and space width + if nnStrain < 20: + sw = 4 + elif nnStrain < 40: + sw = 3 + else: + sw = 2 + + ### 700 is the default plot width minus Xoffsets for 40 strains + defaultWidth = 650 + if nnStrain > 40: + defaultWidth += (nnStrain-40)*10 + defaultOffset = 100 + bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain) + if bw < 10: + bw = 10 + + plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset + plotHeight = 500 + #print [plotWidth, plotHeight, bw, sw, nnStrain] + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (sorted by name)' % self.identification, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img0=HT.Image('/image/'+filename+'.gif',border=0) + + dataXZ = vals[:] + dataXZ.sort(self.cmpValue) + tvals = [] + tnames = [] + tvars = [] + for i in range(len(dataXZ)): + tvals.append(dataXZ[i][1]) + tnames.append(webqtlUtil.genShortStrainName(fd, dataXZ[i][0])) + tvars.append(dataXZ[i][2]) + + c = pid.PILCanvas(size=(plotWidth,plotHeight)) + Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title='%s by Case (ranked)' % self.identification, sLabel = sLabel, barSpace = sw) + + filename= webqtlUtil.genRandStr("Bar_") + c.save(webqtlConfig.IMGDIR+filename, format='gif') + img1=HT.Image('/image/'+filename+'.gif',border=0) + + # Lei Yan + # 05/18/2009 + # report + + title = HT.Paragraph('REPORT on the variation of Shh (or PCA Composite Trait XXXX) (sonic hedgehog) in the (insert Data set name) of (insert Species informal name, e.g., Mouse, Rat, Human, Barley, Arabidopsis)', Class="title") + header = HT.Paragraph('''This report was generated by GeneNetwork on May 11, 2009, at 11.20 AM using the Basic Statistics module (v 1.0) and data from the Hippocampus Consortium M430v2 (Jun06) PDNN data set. For more details and updates on this data set please link to URL:get Basic Statistics''') + hr = HT.HR() + p1 = HT.Paragraph('''Trait values for Shh were taken from the (insert Database name, Hippocampus Consortium M430v2 (Jun06) PDNN). GeneNetwork contains data for NN (e.g., 99) cases. In general, data are averages for each case. A summary of mean, median, and the range of these data are provided in Table 1 and in the box plot (Figure 1). Data for individual cases are provided in Figure 2A and 2B, often with error bars (SEM). ''') + p2 = HT.Paragraph('''Trait values for Shh range 5.1-fold: from a low of 8.2 (please round value) in 129S1/SvImJ to a high of 10.6 (please round value) in BXD9. The interquartile range (the difference between values closest to the 25% and 75% levels) is a more modest 1.8-fold. The mean value is XX. ''') + t1 = HT.Paragraph('''Table 1. Summary of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + f1 = HT.Paragraph('''Figure 1. ''') + f1.append(HT.Href(text="Box plot", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs14")) + f1.append(HT.Text(''' of Shh data from the Hippocampus Consortium M430v2 (june06) PDNN data set''')) + f2A = HT.Paragraph('''Figure 2A: Bar chart of Shh data ordered by case from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + f2B = HT.Paragraph('''Figure 2B: Bar chart of Shh values ordered by from the Hippocampus Consortium M430v2 (june06) PDNN data set''') + TD_LR.append(HT.Blockquote(title, HT.P(), header, hr, p1, HT.P(), p2, HT.P(), supertable2, t1, f1, HT.P(), img0, f2A, HT.P(), img1, f2B)) + self.dict['body'] = str(TD_LR) + else: + heading = "Basic Statistics" + detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] + self.error(heading=heading,detail=detail) + return + else: + heading = "Basic Statistics" + detail = ['Empty data set, please check your data.'] + self.error(heading=heading,detail=detail) + return + + def traitInfo(self, fd, specialStrains = None): + species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (species.title(), fd.RISet) , HT.BR()) + if self.Trait: + trait_url = HT.Href(text=self.Trait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \ + "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (self.Trait.db.name, self.Trait.name), \ + target='_blank', Class="fs13 fwn") + heading2.append(HT.Strong("Database: "), + HT.Href(text=self.Trait.db.fullname, url = webqtlConfig.INFOPAGEHREF % self.Trait.db.name , + target='_blank',Class="fs13 fwn"),HT.BR()) + if self.Trait.db.type == 'ProbeSet': + heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(), + HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.symbol,id="green"),HT.BR()) + if self.Trait.chr and self.Trait.mb: + heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) + elif self.Trait.db.type == 'Geno': + heading2.append(HT.Strong('Locus : '), trait_url, HT.BR()) + #heading2.append(HT.Strong("Gene Symbol: "), HT.Italic('%s' % self.Trait.Symbol,id="green"),HT.BR()) + if self.Trait.chr and self.Trait.mb: + heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (self.Trait.chr, self.Trait.mb)) + elif self.Trait.db.type == 'Publish': + heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR()) + heading2.append(HT.Strong('Phenotype: '), self.Trait.phenotype, HT.BR()) + heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) + elif self.Trait.db.type == 'Temp': + heading2.append(HT.Strong('Description: '), self.Trait.description, HT.BR()) + #heading2.append(HT.Strong('Author: '), self.Trait.authors, HT.BR()) + else: + pass + else: + heading2.append(HT.Strong("Trait Name: "), fd.identification) + + if specialStrains: + mdpform = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='MDP_Form',submit=HT.Input(type='hidden')) + mdphddn = {'FormID':'dataEditing', 'submitID':'basicStatistics','RISet':fd.RISet, "allstrainlist":string.join(fd.allstrainlist, " "), "ptype":self.plotType, 'identification':fd.identification, "incparentsf1":1} + if self.fullname: mdphddn['fullname'] = self.fullname + webqtlUtil.exportData(mdphddn, fd.allTraitData) + for key in mdphddn.keys(): + mdpform.append(HT.Input(name=key, value=mdphddn[key], type='hidden')) + btn0 = HT.Input(type='button' ,name='',value='All Cases',onClick="this.form.ptype.value=0;submit();", Class="button") + btn1 = HT.Input(type='button' ,name='',value='%s Only' % fd.RISet,onClick="this.form.ptype.value=1;submit();", Class="button") + btn2 = HT.Input(type='button' ,name='',value='MDP Only', onClick="this.form.ptype.value=2;submit();", Class="button") + mdpform.append(btn0) + mdpform.append(btn1) + mdpform.append(btn2) + heading2.append(HT.P(), mdpform) + + return HT.Span(heading2) + + def calSD(self,var): + try: + return sqrt(abs(var)) + except: + return None + + + def cmpValue(self,A,B): + try: + if A[1] < B[1]: + return -1 + elif A[1] == B[1]: + return 0 + else: + return 1 + except: + return 0 + + + + diff --git a/wqflask/basicStatistics/__init__.py b/wqflask/basicStatistics/__init__.py new file mode 100755 index 00000000..e69de29b --- /dev/null +++ b/wqflask/basicStatistics/__init__.py diff --git a/wqflask/basicStatistics/updatedBasicStatisticsPage.py b/wqflask/basicStatistics/updatedBasicStatisticsPage.py new file mode 100755 index 00000000..ab7ed07d --- /dev/null +++ b/wqflask/basicStatistics/updatedBasicStatisticsPage.py @@ -0,0 +1,150 @@ +from htmlgen import HTMLgen2 as HT + +from base.templatePage import templatePage +from dbFunction import webqtlDatabaseFunction +import BasicStatisticsFunctions + +#Window generated from the Trait Data and Analysis page (DataEditingPage.py) with updated stats figures; takes the page's values that can bed edited by the user +class updatedBasicStatisticsPage(templatePage): + + plotMinInformative = 4 + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not fd.genotype: + fd.readGenotype() + this_strainlist = fd.strainlist + + if fd.allstrainlist: + this_strainlist = fd.allstrainlist + + fd.readData(this_strainlist) + + specialStrains = [] #This appears to be the "other/non-RISet strainlist" without parents/f1 strains; not sure what to name it + setStrains = [] + for item in this_strainlist: + if item not in fd.strainlist and item.find('F1') < 0: + specialStrains.append(item) + else: + continue + + specialStrains.sort() + if specialStrains: + specialStrains = fd.f1list+fd.parlist+specialStrains + + self.dict['title'] = 'Basic Statistics' + TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") + + stats_row = HT.TR() + stats_cell = HT.TD() + stats_script = HT.Script(language="Javascript") + + #Get strain names, values, and variances + strain_names = fd.formdata.getvalue('strainNames').split(',') + strain_vals = fd.formdata.getvalue('strainVals').split(',') + strain_vars = fd.formdata.getvalue('strainVars').split(',') + + vals = [] + if (len(strain_names) > 0): + if (len(strain_names) > 3): + #Need to create "vals" object + for i in range(len(strain_names)): + try: + this_strain_val = float(strain_vals[i]) + except: + continue + try: + this_strain_var = float(strain_vars[i]) + except: + this_strain_var = None + + thisValFull = [strain_names[i], this_strain_val, this_strain_var] + vals.append(thisValFull) + + stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"), + HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), + HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")] + stats_tabs = HT.List(stats_tab_list) + + stats_container = HT.Div(id="stats_tabs", Class="ui-tabs") + stats_container.append(stats_tabs) + + stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs + + table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;") + table_container = HT.Paragraph() + + statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + this_trait_type = fd.formdata.getvalue('trait_type', None) + this_cellid = fd.formdata.getvalue('cellid', None) + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait_type, cellid=this_cellid) + statsTable.append(HT.TR(HT.TD(statsTableCell))) + + table_container.append(statsTable) + table_div.append(table_container) + stats_container.append(table_div) + + normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;") + normalplot_container = HT.Paragraph() + normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + plotTitle = fd.formdata.getvalue("normalPlotTitle","") + normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + normalplot.append(HT.TR(HT.TD(normalplot_img))) + normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + normalplot_container.append(normalplot) + normalplot_div.append(normalplot_container) + stats_container.append(normalplot_div) + + barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;") + barName_container = HT.Paragraph() + barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") + barName.append(HT.TR(HT.TD(barName_img))) + barName_container.append(barName) + barName_div.append(barName_container) + stats_container.append(barName_div) + + barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;") + barRank_container = HT.Paragraph() + barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") + barRank.append(HT.TR(HT.TD(barRank_img))) + barRank_container.append(barRank) + barRank_div.append(barRank_container) + stats_container.append(barRank_div) + + boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;") + boxplot_container = HT.Paragraph() + boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + boxplot_container.append(boxplot) + boxplot_div.append(boxplot_container) + stats_container.append(boxplot_div) + + stats_cell.append(stats_container) + stats_script.append(stats_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + stats_row.append(stats_cell) + + submitTable.append(stats_row) + submitTable.append(stats_script) + + TD_LR.append(submitTable) + self.dict['body'] = str(TD_LR) + else: + heading = "Basic Statistics" + detail = ['Fewer than %d case data were entered for %s data set. No statitical analysis has been attempted.' % (self.plotMinInformative, fd.RISet)] + self.error(heading=heading,detail=detail) + return + else: + heading = "Basic Statistics" + detail = ['Empty data set, please check your data.'] + self.error(heading=heading,detail=detail) + return
\ No newline at end of file diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py new file mode 100755 index 00000000..c2e1c37f --- /dev/null +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -0,0 +1,1898 @@ +import string +import os +import cPickle +#import pyXLWriter as xl + +from htmlgen import HTMLgen2 as HT + +from base import webqtlConfig +from utility import webqtlUtil #, Plot +from base.webqtlTrait import webqtlTrait +from dbFunction import webqtlDatabaseFunction +from base.templatePage import templatePage +from basicStatistics import BasicStatisticsFunctions + + +######################################### +# DataEditingPage +######################################### +class DataEditingPage(templatePage): + + def __init__(self, fd, thisTrait=None): + + templatePage.__init__(self, fd) + + self.dict['title'] = 'Data Editing' + TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") + + if not self.openMysql(): + return + if not fd.genotype: + fd.readData(incf1=1) + + ############################# + # determine data editing page format + ############################# + varianceDataPage = 0 + if fd.formID == 'varianceChoice': + varianceDataPage = 1 + + if varianceDataPage: + fmID='dataEditing' + nCols = 6 + else: + if fd.enablevariance: + fmID='pre_dataEditing' + nCols = 4 + else: + fmID='dataEditing' + nCols = 4 + + ############################# + ## titles, etc. + ############################# + + titleTop = HT.Div() + + title1 = HT.Paragraph(" Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader") + title1Body = HT.Paragraph(Id="sectionbody1") + + if fd.enablevariance and not varianceDataPage: + title2 = HT.Paragraph(" Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader") + else: + title2 = HT.Paragraph(" Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader") + title2Body = HT.Paragraph(Id="sectionbody2") + + title3 = HT.Paragraph(" Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader") + title3Body = HT.Paragraph(Id="sectionbody3") + + title4 = HT.Paragraph(" Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader") + title4Body = HT.Paragraph(Id="sectionbody4") + + title5 = HT.Paragraph(" Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader") + title5Body = HT.Paragraph(Id="sectionbody5") + + ############################# + ## Hidden field + ############################# + + # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery + hddn = {'FormID':fmID, 'RISet':fd.RISet, 'submitID':'', 'scale':'physic', 'additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'method':None,\ + 'parentsf14regression':'OFF', 'stats_method':'1', 'chromosomes':'-1', 'topten':'', 'viewLegend':'ON', 'intervalAnalystCheck':'ON', 'valsHidden':'OFF',\ + 'database':'', 'criteria':None, 'MDPChoice':None, 'bootCheck':None, 'permCheck':None, 'applyVarianceSE':None, 'strainNames':'_', 'strainVals':'_',\ + 'strainVars':'_', 'otherStrainNames':'_', 'otherStrainVals':'_', 'otherStrainVars':'_', 'extra_attributes':'_', 'other_extra_attributes':'_'} + + if fd.enablevariance: + hddn['enablevariance']='ON' + if fd.incparentsf1: + hddn['incparentsf1']='ON' + + if thisTrait: + hddn['fullname'] = str(thisTrait) + try: + hddn['normalPlotTitle'] = thisTrait.symbol + hddn['normalPlotTitle'] += ": " + hddn['normalPlotTitle'] += thisTrait.name + except: + hddn['normalPlotTitle'] = str(thisTrait.name) + hddn['fromDataEditingPage'] = 1 + if thisTrait.db and thisTrait.db.type and thisTrait.db.type == 'ProbeSet': + hddn['trait_type'] = thisTrait.db.type + if thisTrait.cellid: + hddn['cellid'] = thisTrait.cellid + else: + self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % thisTrait.mysqlid) + heritability = self.cursor.fetchone() + hddn['heritability'] = heritability + + hddn['attribute_names'] = "" + + hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet) + + ############################# + ## Display Trait Information + ############################# + + headSpan = self.dispHeader(fd,thisTrait) #Draw header + + titleTop.append(headSpan) + + if fd.identification: + hddn['identification'] = fd.identification + + else: + hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named + + self.dispTraitInformation(fd, title1Body, hddn, thisTrait) #Display trait information + function buttons + + ############################# + ## Generate form and buttons + ############################# + + mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), + name='dataInput', submit=HT.Input(type='hidden')) + + next=HT.Input(type='submit', name='submit',value='Next',Class="button") + reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") + correlationMenus = [] + + if thisTrait == None: + thisTrait = webqtlTrait(data=fd.allTraitData, db=None) + + # Variance submit page only + if fd.enablevariance and not varianceDataPage: + title2Body.append("Click the next button to go to the variance submission form.", + HT.Center(next,reset)) + else: + self.dispBasicStatistics(fd, title2Body, thisTrait) + self.dispCorrelationTools(fd, title3Body, thisTrait) + self.dispMappingTools(fd, title4Body, thisTrait) + + ############################# + ## Trait Value Table + ############################# + + self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait) + + if fd.allstrainlist: + hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') + for key in hddn.keys(): + mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) + + if fd.enablevariance and not varianceDataPage: + #pre dataediting page, need to submit variance + mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) + else: + mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) + TD_LR.append(HT.Paragraph(mainForm)) + self.dict['body'] = str(TD_LR) + + ########################################## + ## Function to display header + ########################################## + def dispHeader(self, fd, thisTrait): + headSpan = HT.Div(style="font-size:14px;") + + #If trait, use trait name; otherwise, use identification value + if thisTrait: + if thisTrait.cellid: + headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', thisTrait.cellid) + else: + headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', thisTrait.name) + else: + if fd.identification: + headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification) + else: + headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;')) + + return headSpan + + ########################################## + ## Function to display trait infos + ########################################## + def dispTraitInformation(self, fd, title1Body, hddn, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") + + reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") + + #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object. + addSelectionButton = "" + verifyButton = "" + rnaseqButton = "" + geneWikiButton = "" + probeButton = "" + similarButton = "" + snpBrowserButton = "" + updateButton = "" + + addSelectionText = "" + verifyText = "" + rnaseqText = "" + geneWikiText = "" + probeText = "" + similarText = "" + snpBrowserText = "" + updateText = "" + + if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: + + if thisTrait==None or thisTrait.db.type=='Temp': + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + elif thisTrait.db.type != 'Temp': + if thisTrait.db.type == 'Publish' and thisTrait.confidential: #XZ: confidential phenotype trait + if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + else: + updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") + updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") + updateButton.append(updateButton_img) + updateText = "Edit" + else: + pass + + self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.RISet) + if thisTrait: + addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, 'dataInput')) + addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") + addSelectionButton.append(addSelectionButton_img) + addSelectionText = "Add" + elif self.cursor.fetchall(): + addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) + addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") + addSelectionButton.append(addSelectionButton_img) + addSelectionText = "Add" + else: + pass + + + # Microarray database information to display + if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': #before, this line was only reached if thisTrait != 0, but now we need to check + try: + hddn['GeneId'] = int(string.strip(thisTrait.geneid)) + except: + pass + + Info2Disp = HT.Paragraph() + + #XZ: Gene Symbol + if thisTrait.symbol: + #XZ: Show SNP Browser only for mouse + if _Species == 'mouse': + self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", thisTrait.symbol) + geneName = self.cursor.fetchone() + if geneName: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] + else: + if thisTrait.chr and thisTrait.mb: + snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \ + "&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002) + else: + snpurl = "" + + if snpurl: + snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) + snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") + snpBrowserButton.append(snpBrowserButton_img) + snpBrowserText = "SNPs" + + #XZ: Show GeneWiki for all species + geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol)) + geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") + geneWikiButton.append(geneWikiButton_img) + geneWikiText = 'GeneWiki' + + #XZ: display similar traits in other selected datasets + if thisTrait and thisTrait.db and thisTrait.db.type=="ProbeSet" and thisTrait.symbol: + if _Species in ("mouse", "rat", "human"): + similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species) + similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) + similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") + similarButton.append(similarButton_img) + similarText = "Find" + else: + pass + tbl.append(HT.TR( + HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740) + )) + else: + tbl.append(HT.TR( + HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top") + )) + + #XZ: Gene Alias + if thisTrait.alias: + alias = string.replace(thisTrait.alias, ";", " ") + alias = string.join(string.split(alias), ", ") + tbl.append(HT.TR( + HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top") + )) + + #XZ: Description + if thisTrait.description: + tSpan = HT.Span(thisTrait.description, Class="fs13") + if thisTrait.probe_target_description: + tSpan.append('; ', thisTrait.probe_target_description) + else: + tSpan = HT.Span('Not available', Class="fs13") + tbl.append(HT.TR( + HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + #XZ: Location + + #XZ: deal with Chr and Mb + if thisTrait.chr and thisTrait.mb: + tSpan = HT.Span('Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb),Class="fs13") + elif (thisTrait.chr): + tSpan = HT.Span('Chr %s @ Unknown position' % (thisTrait.chr), Class="fs13") + else: + tSpan = HT.Span('Not available', Class="fs13") + + #XZ: deal with direction + if thisTrait.strand_probe == '+': + tSpan.append(' on the plus strand ') + elif thisTrait.strand_probe == '-': + tSpan.append(' on the minus strand ') + else: + pass + + tbl.append(HT.TR( + HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + ##display Verify Location button + try: + blatsequence = thisTrait.blatseq + if not blatsequence: + #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + self.cursor.execute("""SELECT Probe.Sequence, Probe.Name + FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' AND + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) + seqs = self.cursor.fetchall() + if not seqs: + raise ValueError + else: + blatsequence = '' + for seqt in seqs: + if int(seqt[1][-1]) % 2 == 1: + blatsequence += string.strip(seqt[0]) + + #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe + blatsequence = '%3E'+thisTrait.name+'%0A'+blatsequence+'%0A' + #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. + self.cursor.execute("""SELECT Probe.Sequence, Probe.Name + FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' AND + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) ) + + seqs = self.cursor.fetchall() + for seqt in seqs: + if int(seqt[1][-1]) %2 == 1: + blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' + #-------- + #XZ, 07/16/2009: targetsequence is not used, so I comment out this block + #targetsequence = thisTrait.targetseq + #if targetsequence==None: + # targetsequence = "" + + #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. + if _Species == "rat": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + UTHSC_BLAT_URL = "" + elif _Species == "mouse": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) + elif _Species == "human": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + UTHSC_BLAT_URL = "" + else: + UCSC_BLAT_URL = "" + UTHSC_BLAT_URL = "" + + if UCSC_BLAT_URL: + verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", + title=" Check probe locations at UCSC ", style="border:none;") + verifyButton.append(verifyButtonImg) + verifyText = 'Verify' + if UTHSC_BLAT_URL: + rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", + title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton.append(rnaseqButtonImg) + rnaseqText = 'RNA-seq' + tSpan.append(HT.BR()) + except: + pass + + #Display probe information (if any) + if thisTrait.db.name.find('Liver') >= 0 and thisTrait.db.name.find('F2') < 0: + pass + else: + #query database for number of probes associated with trait; if count > 0, set probe tool button and text + self.cursor.execute("""SELECT count(*) + FROM Probe, ProbeSet + WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (thisTrait.name)) + + probeResult = self.cursor.fetchone() + if probeResult[0] > 0: + probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \ + % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet) + probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) + probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") + probeButton.append(probeButton_img) + probeText = "Probes" + + tSpan = HT.Span(Class="fs13") + + #XZ: deal with blat score and blat specificity. + if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score: + if thisTrait.probe_set_specificity: + tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3) + if thisTrait.probe_set_blat_score: + tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2) + + onClick="openNewWin('/blatInfo.html')" + + tbl.append(HT.TR( + HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + tSpan = HT.Span(Class="fs13") + tSpan.append(str(_Species).capitalize(), ", ", fd.RISet) + + tbl.append(HT.TR( + HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + if thisTrait.cellid: + self.cursor.execute(""" + select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze + where + ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Id = %d""" % thisTrait.db.id) + probeDBName = self.cursor.fetchone()[0] + tbl.append(HT.TR( + HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top") + )) + else: + tbl.append(HT.TR( + HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name, + target='_blank', Class="fs13 fwn non_bold"), valign="top") + )) + + #XZ: ID links + if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid: + idStyle = "background:#dddddd;padding:2" + tSpan = HT.Span(Class="fs13") + if thisTrait.geneid: + gurl = HT.Href(text= 'Gene', target='_blank',\ + url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.omim: + gurl = HT.Href(text= 'OMIM', target='_blank', \ + url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.unigeneid: + try: + gurl = HT.Href(text= 'UniGene',target='_blank',\ + url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + except: + pass + if thisTrait.genbankid: + thisTrait.genbankid = '|'.join(thisTrait.genbankid.split('|')[0:10]) + if thisTrait.genbankid[-1]=='|': + thisTrait.genbankid=thisTrait.genbankid[0:-1] + gurl = HT.Href(text= 'GenBank', target='_blank', \ + url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes") + tSpan.append(HT.Span(gurl, style=idStyle), " "*2) + if thisTrait.homologeneid: + hurl = HT.Href(text= 'HomoloGene', target='_blank',\ + url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species") + tSpan.append(HT.Span(hurl, style=idStyle), " "*2) + + tbl.append( + HT.TR(HT.TD(colspan=3,height=6)), + HT.TR( + HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top") + )) + + #XZ: Resource Links: + if thisTrait.symbol: + linkStyle = "background:#dddddd;padding:2" + tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px") + + #XZ,12/26/2008: Gene symbol may contain single quotation mark. + #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) + #I debug this by using double quotation marks. + if _Species == "rat": + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #symatlas_species = "Rattus norvegicus" + + #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % thisTrait.symbol) + self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % thisTrait.symbol) + try: + kgId, chr, txst, txen = self.cursor.fetchall()[0] + if chr and txst and txen and kgId: + txst = int(txst*1000000) + txen = int(txen*1000000) + tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ + title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle) + , " "*2) + except: + pass + if _Species == "mouse": + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #symatlas_species = "Mus musculus" + + #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % thisTrait.symbol) + self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % thisTrait.symbol) + try: + chr, txst, txen = self.cursor.fetchall()[0] + if chr and txst and txen and thisTrait.refseq_transcriptid : + txst = int(txst*1000000) + txen = int(txen*1000000) + tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ + title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',thisTrait.refseq_transcriptid,chr,txst,txen), + Class="fs14 fwn"), style=linkStyle) + , " "*2) + except: + pass + + #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more + #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ + # url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \ + # % (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \ + # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) + if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): + tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\ + url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \ + % (_Species, thisTrait.geneid),Class="fs14 fwn", \ + title="Expression across many tissues and cell types"), style=linkStyle), " "*2) + tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\ + url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ + % thisTrait.symbol,Class="fs14 fwn", \ + title="Protein interactions: known and inferred"), style=linkStyle), " "*2) + if thisTrait.symbol: + #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input + #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users + if _Species == "mouse": + species_scientific = "Mus%20musculus" + elif _Species == "rat": + species_scientific = "Rattus%20norvegicus" + elif _Species == "human": + species_scientific = "Homo%20sapiens" + elif _Species == "drosophila": + species_scientific = "Drosophila%20melanogaster" + else: + species_scientific = "all" + + species_scientific + tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ + url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ + % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \ + title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) + else: + pass + #tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\ + # url="http://bind.ca/?textquery=%s" \ + # % thisTrait.symbol,Class="fs14 fwn", \ + # title="Protein interactions"), style=linkStyle), " "*2) + if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"): + tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\ + url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \ + % thisTrait.geneid, Class="fs14 fwn", \ + title="Meta-analysis of gene expression data"), style=linkStyle), " "*2) + tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\ + url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \ + % thisTrait.symbol, Class="fs14 fwn", \ + title="Brain synapse database"), style=linkStyle), " "*2) + if _Species == "mouse": + tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + url="http://mouse.brain-map.org/brain/%s.html" \ + % thisTrait.symbol, Class="fs14 fwn", \ + title="Allen Brain Atlas"), style=linkStyle), " "*2) + + if thisTrait.geneid: + #if _Species == "mouse": + # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + # url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \ + # % thisTrait.geneid, Class="fs14 fwn", \ + # title="Allen Brain Atlas"), style=linkStyle), " "*2) + if _Species == "human": + tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ + url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \ + % thisTrait.geneid, Class="fs14 fwn", \ + title="Allen Brain Atlas"), style=linkStyle), " "*2) + tbl.append( + HT.TR(HT.TD(colspan=3,height=6)), + HT.TR( + HT.TD(' '), + HT.TD(width=10, valign="top"), + HT.TD(tSpan, valign="top"))) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + + #for zhou mi's cliques, need to be removed + #if self.database[:6] == 'BXDMic' and self.ProbeSetID in cliqueID: + # Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\ + # url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \ + # % self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR()) + + #linkTable.append(HT.TR(linkTD)) + #Info2Disp.append(linkTable) + title1Body.append(tbl, HT.BR(), menuTable) + + elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype + + if thisTrait.confidential: + tbl.append(HT.TR( + HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740) + )) + if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users): + tbl.append(HT.TR( + HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740) + )) + else: + tbl.append(HT.TR( + HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Authors: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.authors, Class="fs13"), + valign="top", width=740) + )) + tbl.append(HT.TR( + HT.TD('Title: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(thisTrait.title, Class="fs13"), + valign="top", width=740) + )) + if thisTrait.journal: + journal = thisTrait.journal + if thisTrait.year: + journal = thisTrait.journal + " (%s)" % thisTrait.year + + tbl.append(HT.TR( + HT.TD('Journal: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(journal, Class="fs13"), + valign="top", width=740) + )) + PubMedLink = "" + if thisTrait.pubmed_id: + PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id + if PubMedLink: + tbl.append(HT.TR( + HT.TD('Link: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"), + style = "background:#cddcff;padding:2"), valign="top", width=740) + )) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype + + GenoInfo = HT.Paragraph() + if thisTrait.chr and thisTrait.mb: + location = ' Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb) + else: + location = "not available" + + if thisTrait.sequence and len(thisTrait.sequence) > 100: + if _Species == "rat": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', thisTrait.sequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', thisTrait.sequence) + elif _Species == "mouse": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', thisTrait.sequence) + elif _Species == "human": + UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', thisTrait.sequence) + else: + UCSC_BLAT_URL = "" + UTHSC_BLAT_URL = "" + if UCSC_BLAT_URL: + #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) + verifyButton = HT.Href(url="#") + verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") + verifyButton.append(verifyButtonImg) + verifyText = "Verify" + rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) + rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") + rnaseqButton.append(rnaseqButtonImg) + rnaseqText = "RNA-seq" + + tbl.append(HT.TR( + HT.TD('Location: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740) + ), + HT.TR( + HT.TD('SNP Search: ', Class="fs13 fwb", + valign="top", nowrap="on", width=90), + HT.TD(width=10, valign="top"), + HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"), + valign="top", width=740) + )) + + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1") + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) + + TempInfo = HT.Paragraph() + if thisTrait != None: + if thisTrait.description: + tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15)) + else: + tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15)) + + if (updateText == "Edit"): + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") + else: + menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1") + + menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;") ) + menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) + + title1Body.append(tbl, HT.BR(), menuTable) + + else: + pass + + + ########################################## + ## Function to display analysis tools + ########################################## + def dispBasicStatistics(self, fd, title2Body, thisTrait): + + #XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later. + stats_row = HT.TR() + stats_cell = HT.TD() + + if fd.genotype.type == "riset": + strainlist = fd.f1list + fd.strainlist + else: + strainlist = fd.f1list + fd.parlist + fd.strainlist + + other_strains = [] #XZ: strain that is not of primary group + specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains. + all_strains = [] + primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS + + MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp') + + for strain in thisTrait.data.keys(): + strainName = strain.replace("_2nd_", "") + if strain not in strainlist: + if (thisTrait.data[strainName].val != None): + if strain.find('F1') < 0: + specialStrains.append(strain) + if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group + else: + if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)): + primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD) + + if len(other_strains) > 3: + other_strains.sort(key=webqtlUtil.natsort_key) + primary_strains.sort(key=webqtlUtil.natsort_key) + primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added. + all_strains = primary_strains + other_strains + other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #XZ: note that fd.f1list and fd.parlist are added. + MDP_menu.append(('All Cases','0')) + MDP_menu.append(('%s Only' % fd.RISet,'1')) + MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) + stats_row.append("Include: ", MDP_menu, HT.BR(), HT.BR()) + else: + if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3): + MDP_menu.append(('All Cases','0')) + MDP_menu.append(('%s Only' % fd.RISet,'1')) + MDP_menu.append(('Non-%s Only' % fd.RISet,'2')) + stats_row.append("Include: ", MDP_menu, " "*3) + all_strains = primary_strains + all_strains.sort(key=webqtlUtil.natsort_key) + all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains + primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains + else: + all_strains = strainlist + + other_strains.sort(key=webqtlUtil.natsort_key) + all_strains = all_strains + other_strains + pass + + update_button = HT.Input(type='button',value=' Update Figures ', Class="button update") #This is used to reload the page and update the Basic Statistics figures with user-edited data + stats_row.append(update_button, HT.BR(), HT.BR()) + + if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4): + #One set of vals for all, selected strain only, and non-selected only + vals1 = [] + vals2 = [] + vals3 = [] + + #Using all strains/cases for values + for i, strainNameOrig in enumerate(all_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals1.append(thisValFull) + + #Using just the RISet strain + for i, strainNameOrig in enumerate(primary_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals2.append(thisValFull) + + #Using all non-RISet strains only + for i, strainNameOrig in enumerate(other_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals3.append(thisValFull) + + vals_set = [vals1,vals2,vals3] + + else: + vals = [] + + #Using all strains/cases for values + for i, strainNameOrig in enumerate(all_strains): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals.append(thisValFull) + + vals_set = [vals] + + stats_script = HT.Script(language="Javascript") #script needed for tabs + + for i, vals in enumerate(vals_set): + if i == 0 and len(vals) < 4: + stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element + stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted."))) + stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" + stats_cell.append(stats_container) + break + elif (i == 1 and len(primary_strains) < 4): + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) + elif (i == 2 and len(other_strains) < 4): + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted."))) + stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" + else: + stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs") + stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});""" + if len(vals) > 4: + stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), + HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), + HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")] + stats_tabs = HT.List(stats_tab_list) + stats_container.append(stats_tabs) + + table_div = HT.Div(id="statstabs-1") + table_container = HT.Paragraph() + + statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + + if thisTrait.db: + if thisTrait.cellid: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type, cellid=thisTrait.cellid) + else: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type) + else: + statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals) + + statsTable.append(HT.TR(HT.TD(statsTableCell))) + + table_container.append(statsTable) + table_div.append(table_container) + stats_container.append(table_div) + + normalplot_div = HT.Div(id="statstabs-5") + normalplot_container = HT.Paragraph() + normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + + try: + plotTitle = thisTrait.symbol + plotTitle += ": " + plotTitle += thisTrait.name + except: + plotTitle = str(thisTrait.name) + + normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + normalplot.append(HT.TR(HT.TD(normalplot_img))) + normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + normalplot_container.append(normalplot) + normalplot_div.append(normalplot_container) + stats_container.append(normalplot_div) + + boxplot_div = HT.Div(id="statstabs-2") + boxplot_container = HT.Paragraph() + boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + boxplot_container.append(boxplot) + boxplot_div.append(boxplot_container) + stats_container.append(boxplot_div) + + + barName_div = HT.Div(id="statstabs-3") + barName_container = HT.Paragraph() + barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") + barName.append(HT.TR(HT.TD(barName_img))) + barName_container.append(barName) + barName_div.append(barName_container) + stats_container.append(barName_div) + + barRank_div = HT.Div(id="statstabs-4") + barRank_container = HT.Paragraph() + barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") + barRank.append(HT.TR(HT.TD(barRank_img))) + barRank_container.append(barRank) + barRank_div.append(barRank_container) + stats_container.append(barRank_div) + + stats_cell.append(stats_container) + + stats_script.append(stats_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") + stats_row.append(stats_cell) + + submitTable.append(stats_row) + submitTable.append(stats_script) + + title2Body.append(submitTable) + + + def dispCorrelationTools(self, fd, title3Body, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + RISetgp = fd.RISet + if RISetgp[:3] == 'BXD': + RISetgp = 'BXD' + + if RISetgp: + sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr") + lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr") + tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr") + methodText = HT.Span("Calculate:", Class="ffl fwb fs12") + + databaseText = HT.Span("Database:", Class="ffl fwb fs12") + databaseMenu1 = HT.Select(name='database1') + databaseMenu2 = HT.Select(name='database2') + databaseMenu3 = HT.Select(name='database3') + + nmenu = 0 + self.cursor.execute('SELECT PublishFreeze.FullName,PublishFreeze.Name FROM \ + PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id \ + and InbredSet.Name = "%s" and PublishFreeze.public > %d' % \ + (RISetgp,webqtlConfig.PUBLICTHRESH)) + for item in self.cursor.fetchall(): + databaseMenu1.append(item) + databaseMenu2.append(item) + databaseMenu3.append(item) + nmenu += 1 + self.cursor.execute('SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,\ + InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = \ + "%s" and GenoFreeze.public > %d' % (RISetgp,webqtlConfig.PUBLICTHRESH)) + for item in self.cursor.fetchall(): + databaseMenu1.append(item) + databaseMenu2.append(item) + databaseMenu3.append(item) + nmenu += 1 + #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob. + self.cursor.execute('SELECT Id, Name FROM Tissue order by Name') + for item in self.cursor.fetchall(): + TId, TName = item + databaseMenuSub = HT.Optgroup(label = '%s ------' % TName) + self.cursor.execute('SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, \ + InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and \ + ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like "%s%%" \ + order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ' % (TId,webqtlConfig.PUBLICTHRESH, RISetgp)) + for item2 in self.cursor.fetchall(): + databaseMenuSub.append(item2) + nmenu += 1 + databaseMenu1.append(databaseMenuSub) + databaseMenu2.append(databaseMenuSub) + databaseMenu3.append(databaseMenuSub) + if nmenu: + if thisTrait and thisTrait.db != None: + databaseMenu1.selected.append(thisTrait.db.fullname) + databaseMenu2.selected.append(thisTrait.db.fullname) + databaseMenu3.selected.append(thisTrait.db.fullname) + + criteriaText = HT.Span("Return:", Class="ffl fwb fs12") + + criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu1.append(('top 100','100')) + criteriaMenu1.append(('top 200','200')) + criteriaMenu1.append(('top 500','500')) + criteriaMenu1.append(('top 1000','1000')) + criteriaMenu1.append(('top 2000','2000')) + criteriaMenu1.append(('top 5000','5000')) + criteriaMenu1.append(('top 10000','10000')) + criteriaMenu1.append(('top 15000','15000')) + criteriaMenu1.append(('top 20000','20000')) + + criteriaMenu2 = HT.Select(name='criteria2', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu2.append(('top 100','100')) + criteriaMenu2.append(('top 200','200')) + criteriaMenu2.append(('top 500','500')) + criteriaMenu2.append(('top 1000','1000')) + criteriaMenu2.append(('top 2000','2000')) + criteriaMenu2.append(('top 5000','5000')) + criteriaMenu2.append(('top 10000','10000')) + criteriaMenu2.append(('top 15000','15000')) + criteriaMenu2.append(('top 20000','20000')) + + criteriaMenu3 = HT.Select(name='criteria3', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") + criteriaMenu3.append(('top 100','100')) + criteriaMenu3.append(('top 200','200')) + criteriaMenu3.append(('top 500','500')) + criteriaMenu3.append(('top 1000','1000')) + criteriaMenu3.append(('top 2000','2000')) + criteriaMenu3.append(('top 5000','5000')) + criteriaMenu3.append(('top 10000','10000')) + criteriaMenu3.append(('top 15000','15000')) + criteriaMenu3.append(('top 20000','20000')) + + + self.MDPRow1 = HT.TR(Class='mdp1') + self.MDPRow2 = HT.TR(Class='mdp2') + self.MDPRow3 = HT.TR(Class='mdp3') + + correlationMenus1 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)), + self.MDPRow1, cellspacing=0, width="619px", cellpadding=2) + correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden')) # to replace the orderBy menu + correlationMenus2 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)), + self.MDPRow2, cellspacing=0, width="619px", cellpadding=2) + correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden')) + correlationMenus3 = HT.TableLite( + HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")), + HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)), + self.MDPRow3, cellspacing=0, width="619px", cellpadding=2) + correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden')) + + else: + correlationMenus = "" + + + corr_row = HT.TR() + corr_container = HT.Div(id="corr_tabs", Class="ui-tabs") + + if (thisTrait.db != None and thisTrait.db.type =='ProbeSet'): + corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), HT.Href(text='Literature r', url="#corrtabs-2"), HT.Href(text='Tissue r', url="#corrtabs-3")] + else: + corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")] + + corr_tabs = HT.List(corr_tab_list) + corr_container.append(corr_tabs) + + if correlationMenus1 or correlationMenus2 or correlationMenus3: + sample_div = HT.Div(id="corrtabs-1") + sample_container = HT.Span() + + sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked") + sample_type2 = HT.Input(type="radio", name="sample_method", value="2") + + sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + sampleTD = HT.TD(correlationMenus1, HT.BR(), + "Pearson", sample_type, " "*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(), + sample_correlation, HT.BR(), HT.BR()) + + sampleTD.append(HT.Span("The ",HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank", text="Sample Correlation")," is computed between trait data and", + " any ",HT.BR()," other traits in the sample database selected above. Use ", + HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"), + HT.BR(),"when the sample size is small (<20) or when there are influential \ + outliers.", HT.BR(),Class="fs12")) + + sampleTable.append(sampleTD) + + sample_container.append(sampleTable) + sample_div.append(sample_container) + corr_container.append(sample_div) + + literature_div = HT.Div(id="corrtabs-2") + literature_container = HT.Span() + + literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR()) + literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(), + "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"), + " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \ + but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(), + HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12")) + literatureTable.append(literatureTD) + + literature_container.append(literatureTable) + literature_div.append(literature_container) + + if thisTrait.db != None: + if (thisTrait.db.type =='ProbeSet'): + corr_container.append(literature_div) + + tissue_div = HT.Div(id="corrtabs-3") + tissue_container = HT.Span() + + tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked") + tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5") + + tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + tissueTD = HT.TD(correlationMenus3,HT.BR(), + "Pearson", tissue_type, " "*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(), + tissue_correlation, HT.BR(), HT.BR()) + tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"), + " (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \ + transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \ + Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \ + single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \ + of genes",HT.BR()," using data from mouse samples.", + HT.BR(), Class="fs12")) + tissueTable.append(tissueTD) + + tissue_container.append(tissueTable) + tissue_div.append(tissue_container) + if thisTrait.db != None: + if (thisTrait.db.type =='ProbeSet'): + corr_container.append(tissue_div) + + corr_row.append(HT.TD(corr_container)) + + corr_script = HT.Script(language="Javascript") + corr_script_text = """$(function() { $("#corr_tabs").tabs(); });""" + corr_script.append(corr_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4") + submitTable.append(corr_row) + submitTable.append(corr_script) + + title3Body.append(submitTable) + + + def dispMappingTools(self, fd, title4Body, thisTrait): + + _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) + + RISetgp = fd.RISet + if RISetgp[:3] == 'BXD': + RISetgp = 'BXD' + + #check boxes - one for regular interval mapping, the other for composite + permCheck1= HT.Input(type='checkbox', Class='checkbox', name='permCheck1',checked="on") + bootCheck1= HT.Input(type='checkbox', Class='checkbox', name='bootCheck1',checked=0) + permCheck2= HT.Input(type='checkbox', Class='checkbox', name='permCheck2',checked="on") + bootCheck2= HT.Input(type='checkbox', Class='checkbox', name='bootCheck2',checked=0) + optionbox1 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression1',checked=0) + optionbox2 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression2',checked=0) + optionbox3 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression3',checked=0) + applyVariance1 = HT.Input(name='applyVarianceSE1',type='checkbox', Class='checkbox') + applyVariance2 = HT.Input(name='applyVarianceSE2',type='checkbox', Class='checkbox') + + IntervalMappingButton=HT.Input(type='button' ,name='interval',value=' Compute ', Class="button") + CompositeMappingButton=HT.Input(type='button' ,name='composite',value=' Compute ', Class="button") + MarkerRegressionButton=HT.Input(type='button',name='marker', value=' Compute ', Class="button") + + chrText = HT.Span("Chromosome:", Class="ffl fwb fs12") + + # updated by NL 5-28-2010 + # Interval Mapping + chrMenu = HT.Select(name='chromosomes1') + chrMenu.append(tuple(["All",-1])) + for i in range(len(fd.genotype)): + if len(fd.genotype[i]) > 1: + chrMenu.append(tuple([fd.genotype[i].name,i])) + + #Menu for Composite Interval Mapping + chrMenu2 = HT.Select(name='chromosomes2') + chrMenu2.append(tuple(["All",-1])) + for i in range(len(fd.genotype)): + if len(fd.genotype[i]) > 1: + chrMenu2.append(tuple([fd.genotype[i].name,i])) + + if fd.genotype.Mbmap: + scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") + scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)") + scaleMenu1.append(("Megabase",'physic')) + scaleMenu1.append(("Centimorgan",'morgan')) + scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)") + scaleMenu2.append(("Megabase",'physic')) + scaleMenu2.append(("Centimorgan",'morgan')) + + controlText = HT.Span("Control Locus:", Class="ffl fwb fs12") + controlMenu = HT.Input(type="text", name="controlLocus", Class="controlLocus") + + if fd.genotype.Mbmap: + intMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), + HT.TR(HT.TD(scaleText), HT.TD(scaleMenu1)), + cellspacing=0, width="263px", cellpadding=2) + compMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), + HT.TR(HT.TD(scaleText), HT.TD(scaleMenu2)), + HT.TR(HT.TD(controlText), HT.TD(controlMenu)), + cellspacing=0, width="325px", cellpadding=2) + else: + intMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")), + cellspacing=0, width="263px", cellpadding=2) + compMappingMenu = HT.TableLite( + HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")), + HT.TR(HT.TD(controlText), HT.TD(controlMenu)), + cellspacing=0, width="325px", cellpadding=2) + + directPlotButton = "" + directPlotButton = HT.Input(type='button',name='', value=' Compute ',\ + onClick="dataEditingFunc(this.form,'directPlot');",Class="button") + directPlotSortText = HT.Span(HT.Bold("Sort by: "), Class="ffl fwb fs12") + directPlotSortMenu = HT.Select(name='graphSort') + directPlotSortMenu.append(('LRS Full',0)) + directPlotSortMenu.append(('LRS Interact',1)) + directPlotPermuText = HT.Span("Permutation Test (n=500)", Class="ffl fs12") + directPlotPermu = HT.Input(type='checkbox', Class='checkbox',name='directPermuCheckbox', checked="on") + pairScanReturnText = HT.Span(HT.Bold("Return: "), Class="ffl fwb fs12") + pairScanReturnMenu = HT.Select(name='pairScanReturn') + pairScanReturnMenu.append(('top 50','50')) + pairScanReturnMenu.append(('top 100','100')) + pairScanReturnMenu.append(('top 200','200')) + pairScanReturnMenu.append(('top 500','500')) + + pairScanMenus = HT.TableLite( + HT.TR(HT.TD(directPlotSortText), HT.TD(directPlotSortMenu)), + HT.TR(HT.TD(pairScanReturnText), HT.TD(pairScanReturnMenu)), + cellspacing=0, width="232px", cellpadding=2) + + markerSuggestiveText = HT.Span(HT.Bold("Display LRS greater than:"), Class="ffl fwb fs12") + markerSuggestive = HT.Input(name='suggestive', size=5, maxlength=8) + displayAllText = HT.Span(" Display all LRS ", Class="ffl fs12") + displayAll = HT.Input(name='displayAllLRS', type="checkbox", Class='checkbox') + useParentsText = HT.Span(" Use Parents ", Class="ffl fs12") + useParents = optionbox2 + applyVarianceText = HT.Span(" Use Weighted ", Class="ffl fs12") + + markerMenu = HT.TableLite( + HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive)), + HT.TR(HT.TD(displayAll,displayAllText)), + HT.TR(HT.TD(useParents,useParentsText)), + HT.TR(HT.TD(applyVariance2,applyVarianceText)), + cellspacing=0, width="263px", cellpadding=2) + + + mapping_row = HT.TR() + mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") + + mapping_tab_list = [HT.Href(text="Interval", url="#mappingtabs-1"), HT.Href(text="Marker Regression", url="#mappingtabs-2"), HT.Href(text="Composite", url="#mappingtabs-3"), HT.Href(text="Pair-Scan", url="#mappingtabs-4")] + mapping_tabs = HT.List(mapping_tab_list) + mapping_container.append(mapping_tabs) + + interval_div = HT.Div(id="mappingtabs-1") + interval_container = HT.Span() + + intervalTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + intTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + intTD.append(intMappingMenu,HT.BR()) + + intTD.append(permCheck1,'Permutation Test (n=2000)',HT.BR(), + bootCheck1,'Bootstrap Test (n=2000)', HT.BR(), optionbox1, 'Use Parents', HT.BR(), + applyVariance1,'Use Weighted', HT.BR(), HT.BR(),IntervalMappingButton, HT.BR(), HT.BR()) + intervalTable.append(HT.TR(intTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#intmap', target='_blank', text='Interval Mapping'), + ' computes linkage maps for the entire genome or single',HT.BR(),' chromosomes.', + ' The ',HT.Href(url='/glossary.html#permutation', target='_blank', text='Permutation Test'),' estimates suggestive and significant ',HT.BR(),' linkage scores. \ + The ',HT.Href(url='/glossary.html#bootstrap', target='_blank', text='Bootstrap Test'), ' estimates the precision of the QTL location.' + ,Class="fs12"), HT.BR(), valign="top"))) + + interval_container.append(intervalTable) + interval_div.append(interval_container) + mapping_container.append(interval_div) + + # Marker Regression + + marker_div = HT.Div(id="mappingtabs-2") + marker_container = HT.Span() + + markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + markerTD.append(markerMenu,HT.BR()) + + markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) + + markerTable.append(HT.TR(markerTD),HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#',target='_blank',text='Marker regression'), + ' computes and displays LRS values for individual markers.',HT.BR(), + 'This function also lists additive effects (phenotype units per allele) and', HT.BR(), + 'dominance deviations for some datasets.', HT.BR(),Class="fs12"), HT.BR(), valign="top"))) + + marker_container.append(markerTable) + marker_div.append(marker_container) + mapping_container.append(marker_div) + + # Composite interval mapping + composite_div = HT.Div(id="mappingtabs-3") + composite_container = HT.Span() + + compositeTable = HT.TableLite(cellspacing=0, cellpadding=3, width="100%") + compTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + compTD.append(compMappingMenu,HT.BR()) + + compTD.append(permCheck2, 'Permutation Test (n=2000)',HT.BR(), + bootCheck2,'Bootstrap Test (n=2000)', HT.BR(), + optionbox3, 'Use Parents', HT.BR(), HT.BR(), CompositeMappingButton, HT.BR(), HT.BR()) + compositeTable.append(HT.TR(compTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Composite',target='_blank',text='Composite Interval Mapping'), + " allows you to control for a single marker as",HT.BR()," a cofactor. ", + "To find a control marker, run the ",HT.Bold("Marker Regression")," function."), + HT.BR(), valign="top"))) + + composite_container.append(compositeTable) + composite_div.append(composite_container) + mapping_container.append(composite_div) + + # Pair Scan + + pairscan_div = HT.Div(id="mappingtabs-4") + pairscan_container = HT.Span() + + pairScanTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + pairScanTD = HT.TD(NOWRAP='ON', Class="fs12 fwn") + pairScanTD.append(pairScanMenus,HT.BR()) + pairScanTD.append(directPlotPermu, directPlotPermuText, HT.BR(), HT.BR(), + directPlotButton,HT.BR(),HT.BR()) + pairScanTable.append(HT.TR(pairScanTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Pair_Scan', target="_blank", text='Pair-Scan'), + ' searches for pairs of chromosomal regions that are',HT.BR(), + 'involved in two-locus epistatic interactions.'), HT.BR(), valign="top"))) + + pairscan_container.append(pairScanTable) + pairscan_div.append(pairscan_container) + mapping_container.append(pairscan_div) + + mapping_row.append(HT.TD(mapping_container)) + + # Treat Interval Mapping and Marker Regression and Pair Scan as a group for displaying + #disable Interval Mapping and Marker Regression and Pair Scan for human and the dataset doesn't have genotype file + mappingMethodId = webqtlDatabaseFunction.getMappingMethod(cursor=self.cursor, groupName=RISetgp) + + mapping_script = HT.Script(language="Javascript") + mapping_script_text = """$(function() { $("#mapping_tabs").tabs(); });""" + mapping_script.append(mapping_script_text) + + submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") + + if mappingMethodId != None: + if int(mappingMethodId) == 1: + submitTable.append(mapping_row) + submitTable.append(mapping_script) + elif int(mappingMethodId) == 4: + # NL; 09-26-2011 testing for Human Genome Association function + mapping_row=HT.TR() + mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs") + + mapping_tab_list = [HT.Href(text="Genome Association", url="#mappingtabs-1")] + mapping_tabs = HT.List(mapping_tab_list) + mapping_container.append(mapping_tabs) + + # Genome Association + markerSuggestiveText = HT.Span(HT.Bold("P Value:"), Class="ffl fwb fs12") + + markerSuggestive = HT.Input(name='pValue', value='0.001', size=10, maxlength=20,onClick="this.value='';",onBlur="if(this.value==''){this.value='0.001'};") + markerMenu = HT.TableLite(HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive),HT.TD(HT.Italic(' (e.g. 0.001 or 1e-3 or 1E-3 or 3)'))),cellspacing=0, width="400px", cellpadding=2) + MarkerRegressionButton=HT.Input(type='button',name='computePlink', value=' Compute Using PLINK ', onClick= "validatePvalue(this.form);", Class="button") + + marker_div = HT.Div(id="mappingtabs-1") + marker_container = HT.Span() + markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn") + markerTD.append(markerMenu,HT.BR()) + markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR()) + markerTable.append(HT.TR(markerTD)) + + marker_container.append(markerTable) + marker_div.append(marker_container) + + mapping_container.append(marker_div) + mapping_row.append(HT.TD(mapping_container)) + submitTable.append(mapping_row) + submitTable.append(mapping_script) + else: + submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("mappingMethodId %s has not been implemented for this dataset yet." % mappingMethodId), id="mapping_tabs", Class="ui-tabs")))) + submitTable.append(mapping_script) + + else: + submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("Mapping options are disabled for data not matched with genotypes."), id="mapping_tabs", Class="ui-tabs")))) + submitTable.append(mapping_script) + + title4Body.append(submitTable) + + + def natural_sort(strain_list): + + sorted = [] + for strain in strain_list: + try: + strain = int(strain) + try: sorted[-1] = sorted[-1] * 10 + strain + except: sorted.append(strain) + except: + sorted.append(strain) + return sorted + + ########################################## + ## Function to display trait tables + ########################################## + def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait): + traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;") + resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button") + blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField") + blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button") + showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button') + blockMenuSpan = HT.Span(Id="blockMenuSpan") + blockMenu = HT.Select(name='block_method') + + if fd.genotype.type == "riset": + allstrainlist_neworder = fd.f1list + fd.strainlist + else: + allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist + + attribute_ids = [] + attribute_names = [] + try: + #ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create + self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id))) + + exclude_menu = HT.Select(name="exclude_menu") + dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) + + for attribute in self.cursor.fetchall(): + attribute_ids.append(attribute[0]) + attribute_names.append(attribute[1]) + for this_attr_name in attribute_names: + exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) + self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttribute.Name = '%s' AND + CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) + try: + distinct_values = self.cursor.fetchall() + attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus + attr_value_menu = HT.Select(name=this_attr_name) + attr_value_menu.append(("None", "show_all")) + for value in distinct_values: + attr_value_menu.append((str(value[0]), value[0])) + attr_value_menu_div.append(attr_value_menu) + dropdown_menus.append(attr_value_menu_div) + except: + pass + except: + pass + + other_strains = [] + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + other_strains.append(strain) + + if other_strains: + blockMenu.append(('%s Only' % fd.RISet,'1')) + blockMenu.append(('Non-%s Only' % fd.RISet,'0')) + blockMenuSpan.append(blockMenu) + else: + pass + + showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button') + showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;") + if other_strains: + showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockMenuSpan, " ", blockSamplesButton, HT.BR()) + else: + showHideMenuOptions.append(HT.Bold(" Block samples by index: "), blockSamplesField, " ", blockSamplesButton, HT.BR()) + + exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button') + if len(attribute_names) > 0: + excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button') + showHideMenuOptions.append(HT.Bold(" Block samples by group:"), " "*5, exclude_menu, " "*5) + for menu in dropdown_menus: + showHideMenuOptions.append(menu) + showHideMenuOptions.append(" "*5, excludeButton, HT.BR()) + showHideMenuOptions.append(HT.Bold(" Options:"), " "*5, showHideNoValue, " "*5, showHideOutliers, " "*5, resetButton, " "*5, exportButton) + + traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR()) + traitTableOptions.append(HT.Span(" Outliers highlighted in ", HT.Bold(" yellow ", style="background-color:yellow;"), " can be hidden using the ", + HT.Strong(" Hide Outliers "), " button,",HT.BR()," and samples with no value (x) can be hidden by clicking ", + HT.Strong(" Hide No Value "), "."), HT.BR()) + + + dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;") + + table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work + container = HT.Div() #This will contain everything and be put into a cell of the table defined above + + container.append(dispintro, traitTableOptions, HT.BR()) + + primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter") + primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object + + other_strainsExist = False + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + other_strainsExist = True + break + + primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary') + + primary_table.append(primary_header) + for i in range(len(primary_body)): + primary_table.append(primary_body[i]) + + other_strains = [] + for strain in thisTrait.data.keys(): + if strain not in allstrainlist_neworder: + allstrainlist_neworder.append(strain) + other_strains.append(strain) + + if other_strains: + other_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable2", Class="tablesorter") #Table object with other (for example, non-BXD / MDP) traits + other_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for other table object; same function is used as the one used for the primary table, since the header is the same + other_strains.sort() #Sort other strains + other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #Append F1 and parent strains to the beginning of the sorted list of other strains + + MDPText = HT.Span("Samples:", Class="ffl fwb fs12") + MDPMenu1 = HT.Select(name='MDPChoice1') + MDPMenu2 = HT.Select(name='MDPChoice2') + MDPMenu3 = HT.Select(name='MDPChoice3') + MDPMenu1.append(('%s Only' % fd.RISet,'1')) + MDPMenu2.append(('%s Only' % fd.RISet,'1')) + MDPMenu3.append(('%s Only' % fd.RISet,'1')) + MDPMenu1.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu2.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu3.append(('Non-%s Only' % fd.RISet,'2')) + MDPMenu1.append(('All Cases','0')) + MDPMenu2.append(('All Cases','0')) + MDPMenu3.append(('All Cases','0')) + self.MDPRow1.append(HT.TD(MDPText),HT.TD(MDPMenu1)) + self.MDPRow2.append(HT.TD(MDPText),HT.TD(MDPMenu2)) + self.MDPRow3.append(HT.TD(MDPText),HT.TD(MDPMenu3)) + + other_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='other') + + other_table.append(other_header) + for i in range(len(other_body)): + other_table.append(other_body[i]) + else: + pass + + if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \ + or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])): + fd.allstrainlist = allstrainlist_neworder + + if nCols == 6 and fd.varianceDispName != 'Variance': + mainForm.append(HT.Input(name='isSE', value="yes", type='hidden')) + + primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values + container.append(primary_div) + + if other_strains: + other_div = HT.Div(other_table, Id="other") #Container for table with other (for example, Non-BXD/MDP) strain values + container.append(HT.Div(' ', height=30)) + container.append(other_div) + + table.append(HT.TR(HT.TD(container))) + title5Body.append(table) + + def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'): + #XZ, Aug 23, 2010: I commented the code related to the display of animal case + #strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo + + table_body = [] + vals = [] + + for i, strainNameOrig in enumerate(strainlist): + strainName = strainNameOrig.replace("_2nd_", "") + + try: + thisval = thisTrait.data[strainName].val + thisvar = thisTrait.data[strainName].var + thisValFull = [strainName,thisval,thisvar] + except: + continue + + vals.append(thisValFull) + + upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. + + for i, strainNameOrig in enumerate(strainlist): + + trId = strainNameOrig + selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)") + + strainName = strainNameOrig.replace("_2nd_", "") + strainNameAdd = '' + if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'): + strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") + + try: + thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N + if thisNP: + mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden')) + else: + pass + except: + thisval = thisvar = 'x' + + try: + traitVal = thisval + dispVal = "%2.3f" % thisval + except: + traitVal = '' + dispVal = 'x' + + strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl') + + if varianceDataPage: + try: + traitVar = thisvar + dispVar = "%2.3f" % thisvar + except: + traitVar = '' + dispVar = 'x' + + if thisval == 'x': + traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing" + + className = 'fs13 b1 c222 ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = 'novalue ' + else: + if (thisval >= upperBound) or (thisval <= lowerBound): + className = 'fs13 b1 c222 outlier ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = 'outlier' + else: + className = 'fs13 b1 c222 ' + valueClassName = 'fs13 b1 c222 valueField ' + rowClassName = ' ' + + if varianceDataPage: + varClassName = valueClassName + str(traitVar) + valueClassName += str(traitVal) + + if strainNameOrig == strainName: + if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list): + ######################################################################################################################################################## + # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user + # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. + ######################################################################################################################################################### + + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, + onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + else: + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName) + else: + valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, + onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName) + if varianceDataPage: + seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, + onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName) + + if (strains == 'primary'): + table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName) + else: + table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName) + + if varianceDataPage: + table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + table_row.append(HT.TD("±", width=20, align='center', Class=className)) + table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className)) + else: + table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className)) + table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className)) + table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className)) + + if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet': + if len(attribute_ids) > 0: + + #ZS: Get StrainId value for the next query + self.cursor.execute("""SELECT Strain.Id + FROM Strain, StrainXRef, InbredSet + WHERE Strain.Name = '%s' and + StrainXRef.StrainId = Strain.Id and + InbredSet.Id = StrainXRef.InbredSetId and + InbredSet.Name = '%s'""" % (strainName, fd.RISet)) + + strain_id = self.cursor.fetchone()[0] + + attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). + for attribute_id in attribute_ids: + + #ZS: Add extra case attribute values (if any) + self.cursor.execute("""SELECT Value + FROM CaseAttributeXRef + WHERE ProbeSetFreezeId = '%s' AND + StrainId = '%s' AND + CaseAttributeId = '%s' + group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id))) + + attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any + + #ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints) + try: + attributeValue = int(attributeValue) + except: + pass + + span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1) + attr_container = HT.Span(attributeValue, Id=span_Id) + attr_className = str(attributeValue) + " " + className + table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) + attr_counter += 1 + + table_body.append(table_row) + return table_body + + def getTableHeader(self, fd, thisTrait, nCols, attribute_names): + + table_header = HT.TR() + + col_class = "fs13 fwb ff1 b1 cw cbrb" + + if nCols == 6: + try: + if fd.varianceDispName: + pass + except: + fd.varianceDispName = 'Variance' + + table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), + HT.TH('Sample', align='right', width=100, Class=col_class), + HT.TH('Value', align='right', width=70, Class=col_class), + HT.TH(' ', width=20, Class=col_class), + HT.TH(fd.varianceDispName, align='right', width=80, Class=col_class)) + + elif nCols == 4: + table_header.append(HT.TH('Index', align='right', width=60, Class=col_class), + HT.TH('Sample', align='right', width=100, Class=col_class), + HT.TH('Value', align='right', width=70, Class=col_class)) + + else: + pass + + if len(attribute_names) > 0: + i=0 + for attribute in attribute_names: + char_count = len(attribute) + cell_width = char_count * 14 + table_header.append(HT.TH(attribute, align='right', width=cell_width, Class="attribute_name " + col_class)) + i+=1 + + return table_header + + + def getSortByValue(self): + + sortby = ("", "") + + return sortby diff --git a/wqflask/wqflask/show_trait/__init__.py b/wqflask/wqflask/show_trait/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/wqflask/show_trait/__init__.py |