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 gentextfile(self, db, text):
#
db.getRISet()
info = self.getinfo(db.name)
#
group = db.riset
species = webqtlDatabaseFunction.retrieveSpecies(self.cursor, group)
type = info[4]
database = db.fullname
#
metadatainfofile = "http://www.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s" % info[1]
originaldata = "http://datafiles.genenetwork.org/download/GN%s/" % info[1]
contactinformation = "%s %s, %s, %s, %s, %s %s %s, Tel. %s, %s" % (info[22], info[23], info[33], info[24], info[25], info[26], info[27], info[28], info[29], info[30])
#
attachment = ""
attachment += ("Data source: GeneNetwork http://www.genenetwork.org/\n")
attachment += ("Citations: http://www.genenetwork.org/reference.html\n")
attachment += ("Species: %s\n" % species)
attachment += ("Group: %s\n" % group)
attachment += ("Type: %s\n" % type)
attachment += ("Database: %s\n" % database)
attachment += ("Metadata info file: %s\n" % metadatainfofile)
attachment += ("Original data: %s\n" % originaldata)
attachment += ("Contact Information: %s\n" % contactinformation)
attachment += ("Date: %s\n" % time.strftime("%B %d, %Y", time.gmtime()))
attachment += ("Time: %s\n" % time.strftime("%H:%M", time.gmtime()))
attachment += "\n"
attachment += ("Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)\n")
attachment += ("PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE\n")
attachment += "\n"
rowindex = 0
for row in text:
if rowindex == 0:
row.insert(0, 'Index')
else:
row.insert(0, rowindex)
rowindex += 1
attachment += string.join(map(lambda cell : str(cell).replace("\r\n", " ").strip(), row), '\t') + "\n"
self.content_type = 'text/plain'
self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
self.attachment = attachment
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
searchResult = fd.formdata.getvalue("searchResult")
if not searchResult:
heading = "Partial Correlation"
detail = ["You need to select at least three traits in order to calculate partial correlation."]
self.error(heading=heading, detail=detail)
return
## Adds the Trait instance for each trait name from the collection
traits = []
for item in searchResult:
traits.append(webqtlTrait(fullname=item, cursor=self.cursor))
RISet = fd.formdata.getvalue("RISet")
species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)
# XZ: HTML part
TD_LR = HT.TD(colspan=2, height=200, width="100%", bgColor="#eeeeee")
TD_LR.append(
"Please select one primary trait, one to three control traits, and at least one target trait.", HT.P()
)
mainFormName = "showDatabase"
mainForm = HT.Form(
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
name=mainFormName,
submit=HT.Input(type="hidden"),
)
# XZ: Add hidden form values
hddn = {
"FormID": "calPartialCorrTrait",
"database": "",
"ProbeSetID": "",
"CellID": "", # XZ: These four parameters are required by javascript function showDatabase2.
"controlTraits": "",
"primaryTrait": "",
"targetTraits": "",
"pcMethod": "",
"RISet": RISet,
}
for key in hddn.keys():
mainForm.append(HT.Input(type="hidden", name=key, value=hddn[key]))
radioNames = []
for thisTrait in traits:
oneRadioName = thisTrait.getName()
radioNames.append(oneRadioName)
radioNamesString = ",".join(radioNames)
# Creates the image href that runs the javascript setting all traits as target or ignored
setAllTarget = HT.Href(
url="#redirect",
onClick="setAllAsTarget(document.getElementsByName('showDatabase')[0], '%s');" % radioNamesString,
)
setAllTargetImg = HT.Image("/images/select_all.gif", alt="Select All", title="Select All", style="border:none;")
setAllTarget.append(setAllTargetImg)
setAllIgnore = HT.Href(
url="#redirect",
onClick="setAllAsIgnore(document.getElementsByName('showDatabase')[0], '%s');" % radioNamesString,
)
setAllIgnoreImg = HT.Image("/images/select_all.gif", alt="Select All", title="Select All", style="border:none;")
setAllIgnore.append(setAllIgnoreImg)
tblobj = {}
tblobj["header"] = self.getCollectionTableHeader()
sortby = self.getSortByValue()
tblobj["body"] = self.getCollectionTableBody(traitList=traits, formName=mainFormName, species=species)
filename = webqtlUtil.genRandStr("Search_")
objfile = open("%s.obj" % (webqtlConfig.TMPDIR + filename), "wb")
cPickle.dump(tblobj, objfile)
objfile.close()
div = HT.Div(
webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="1"),
Id="sortable",
)
mainForm.append(div)
# XZ: Add button
radioNamesString = ",".join(radioNames)
jsCommand_1 = "validateTrait(this.form, '" + radioNamesString + "', 0, 1);"
jsCommand_2 = "validateTrait(this.form, '" + radioNamesString + "', 0, 2);"
partialCorrTraitButton_1 = HT.Input(
type="button",
name="submitPartialCorrTrait_1",
value="Pearson's r",
onClick="%s" % jsCommand_1,
Class="button",
)
partialCorrTraitButton_2 = HT.Input(
type="button",
name="submitPartialCorrTrait_2",
value="Spearman's rho",
onClick="%s" % jsCommand_2,
Class="button",
)
mainForm.append(
HT.BR(),
"Compute partial correlation for target selected above:",
HT.BR(),
partialCorrTraitButton_1,
partialCorrTraitButton_2,
HT.BR(),
HT.BR(),
HT.HR(color="gray", size=3),
)
jsCommand = "validateTrait(this.form, '" + radioNamesString + "', 1);"
partialCorrDBButton = HT.Input(
type="button", name="submitPartialCorrDB", value="Calculate", onClick="%s" % jsCommand, Class="button"
)
methodText = HT.Span("Calculate:", Class="ffl fwb fs12")
methodMenu = HT.Select(name="method")
methodMenu.append(("Genetic Correlation, Pearson's r", "1"))
methodMenu.append(("Genetic Correlation, Spearman's rho", "2"))
methodMenu.append(("SGO Literature Correlation", "3"))
methodMenu.append(("Tissue Correlation, Pearson's r", "4"))
methodMenu.append(("Tissue Correlation, Spearman's rho", "5"))
databaseText = HT.Span("Choose Database:", Class="ffl fwb fs12")
databaseMenu = HT.Select(name="database2")
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'
% (RISet, webqtlConfig.PUBLICTHRESH)
)
for item in self.cursor.fetchall():
databaseMenu.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'
% (RISet, webqtlConfig.PUBLICTHRESH)
)
for item in self.cursor.fetchall():
databaseMenu.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, RISet)
)
for item2 in self.cursor.fetchall():
databaseMenuSub.append(item2)
nmenu += 1
databaseMenu.append(databaseMenuSub)
if nmenu:
criteriaText = HT.Span("Return:", Class="ffl fwb fs12")
criteriaMenu = HT.Select(name="criteria", selected="500")
criteriaMenu.append(("top 100", "100"))
criteriaMenu.append(("top 200", "200"))
criteriaMenu.append(("top 500", "500"))
criteriaMenu.append(("top 1000", "1000"))
criteriaMenu.append(("top 2000", "2000"))
criteriaMenu.append(("top 5000", "5000"))
criteriaMenu.append(("top 10000", "10000"))
criteriaMenu.append(("top 15000", "15000"))
criteriaMenu.append(("top 20000", "20000"))
self.MPDCell = HT.TD()
correlationMenus = HT.TableLite(
HT.TR(HT.TD(databaseText, HT.BR(), databaseMenu, colspan=4)),
HT.TR(HT.TD(methodText, HT.BR(), methodMenu), self.MPDCell, HT.TD(criteriaText, HT.BR(), criteriaMenu)),
border=0,
cellspacing=4,
cellpadding=0,
)
else:
correlationMenus = ""
mainForm.append(
HT.Font("or", color="red", size=4),
HT.BR(),
HT.BR(),
"Compute partial correlation for each trait in the database selected below:",
HT.BR(),
)
mainForm.append(partialCorrDBButton, HT.BR(), HT.BR(), correlationMenus)
TD_LR.append(mainForm)
self.dict["body"] = str(TD_LR)
self.dict["js1"] = ""
self.dict["title"] = "Partial Correlation Input"
def __init__(self, fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
fd.readGenotype()
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
self.database = fd.formdata.getfirst('database')
self.ProbeSetID = fd.formdata.getfirst('ProbeSetID')
self.CellID = fd.formdata.getfirst('CellID')
self.db = webqtlDataset(self.database, self.cursor)
thisTrait = webqtlTrait(db= self.db, cursor=self.cursor, name=self.ProbeSetID) #, cellid=CellID)
thisTrait.retrieveInfo()
try:
self.cursor.execute('SELECT ProbeFreeze.Name FROM ProbeFreeze,ProbeSetFreeze WHERE ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Name = "%s"' % self.db.name)
self.probeDatabase = self.cursor.fetchall()[0][0]
self.probeInfoDatabase = 'Probe'
except:
heading = 'Probe Information'
intro = ['Trying to retrieve the probe information for ProbeSet ',HT.Span('%s' % self.ProbeSetID, Class="fwb cdg"),' in Database ',HT.Href(text='%s' % self.db.fullname,url=webqtlConfig.infopagehref % self.database)]
detail = ['The information you just requested is not available at this time.']
self.error(heading=heading,intro=intro,detail=detail)
return
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'}
if fd.RISet == 'BXD':
hddn['parentsf1']='ON'
for key in hddn.keys():
form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
#Buttons on search page
linkinfo ="%s/probeInfo.html" % webqtlConfig.PORTADDR
mintmap = ""
probeinfo = HT.Input(type='button' ,name='mintmap',value='Info', onClick="openNewWin('%s');" % linkinfo, Class="button")
cormatrix = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');")
cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
cormatrix.append(cormatrix_img)
heatmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');")
heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='mintmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
heatmap.append(heatmap_img)
if self.ProbeSetID[-2:] in ('_A', '_B'):
thisProbeSetID = self.ProbeSetID[:-2]
else:
thisProbeSetID = self.ProbeSetID
thisurl = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' % thisProbeSetID
verifyButton = HT.Input(type="button",value="Verify Ensembl",onClick= "openNewWin('%s')" % thisurl, Class="button")
addselect = HT.Input(type='button' ,name='addselect',value='Add to Collection', onClick="addRmvSelection('%s', this.form, 'addToSelection');" % fd.RISet,Class="button")
selectall = HT.Input(type='button' ,name='selectall',value='Select All', onClick="checkAll(this.form);",Class="button")
selectpm = HT.Input(type='button' ,name='selectall',value='Select PM', onClick="checkPM(this.form);",Class="button")
selectmm = HT.Input(type='button' ,name='selectall',value='Select MM', onClick="checkMM(this.form);",Class="button")
selectinvert = HT.Input(type='button' ,name='selectinvert',value='Select Invert', onClick="checkInvert(this.form);",Class="button")
reset = HT.Input(type='reset',name='',value='Select None',Class="button")
chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')
probedata = HT.Input(type='hidden',name='probedata',value='all')
url_rudi_track = self.getProbeTrackURL(self.probeDatabase, self.ProbeSetID)
if url_rudi_track:
rudi_track = HT.Input(type='button', name='ruditrack', value='Probe Track', onClick="openNewWin('%s')"%url_rudi_track, Class="button")
else: rudi_track = None
pinfopage = "/probeInfo.html"
#updated by NL: 07-22-2011 get chosenStrains
_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[fd.RISet]
chosenStrains="%s,%s"%(_mat,_pat)
tblobj = {}
tblobj['header']=[]
tblobj['header'].append([
THCell(HT.TD("", Class="cbrb cw fwb fs13 b1", rowspan=2,nowrap='ON'), sort=0),
THCell(HT.TD(HT.Href(target="_PROBEINFO", url=pinfopage+"#probe", text=HT.Span('Probe', Class="cw fwb fs13")), HT.Sup(HT.Italic('1')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="probe", idx=1),
THCell(HT.TD(HT.Href(text=HT.Span('Sequence', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Sequence"),HT.Sup(HT.Italic('2')), Class="cbrb cw fwb fs13 b1", align='center',rowspan=2,nowrap='ON'), text="seq", idx=2),
THCell(HT.TD(HT.Href(text=HT.Span('bl2seq', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#bl2seq"),HT.Sup(HT.Italic('3')), Class="cbrb cw fwb fs13 b1", align='center',rowspan=2,nowrap='ON'), sort=0),
THCell(HT.TD(HT.Href(text=HT.Span('Exons', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Exon"),HT.Sup(HT.Italic('4')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), sort=0),
THCell(HT.TD(HT.Href(text=HT.Span('Tm °C', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Tm"),HT.Sup(HT.Italic('5')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="tm", idx=5),
THCell(HT.TD(HT.Href(text=HT.Span('Stacking Energy K', HT.Sub('B'),'T', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#KBT"),HT.Sup(HT.Italic('6')), Class="cbrb cw fwb fs13 b1",align='center',colspan=2,NOWRAP="yes",nowrap='ON'), sort=0),
THCell(HT.TD(HT.Href(text=HT.Span('Mean', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Mean"),HT.Sup(HT.Italic('7')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="mean", idx=8),
THCell(HT.TD(HT.Href(text=HT.Span('Stdev', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#Stdev"),HT.Sup(HT.Italic('8')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,nowrap='ON'), text="std", idx=9),
THCell(HT.TD(HT.Href(text=HT.Span('Probe h2', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#h2"),HT.Sup(HT.Italic('9')), Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes"), text="h2", idx=10),
THCell(HT.TD(HT.Href(text=HT.Span('Probe Location', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#location"), HT.Sup(HT.Italic('10')),Class="cbrb cw fwb fs13 b1",align='center',colspan=3)),
THCell(HT.TD(HT.Href(text=HT.Span('SNPs', HT.BR(), '(Across all strains)', Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#snps"), HT.Sup(HT.Italic('11')),Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes")),
THCell(HT.TD(HT.Href(text=HT.Span('SNPs', HT.BR(),'(Different alleles only between %s and %s)'%(_mat,_pat), Class="cw fwb fs13"), target="_PROBEINFO", url=pinfopage+"#snps"), HT.Sup(HT.Italic('11')),Class="cbrb cw fwb fs13 b1",align='center',rowspan=2,NOWRAP="yes"))
])
tblobj['header'].append([
THCell(HT.TD(HT.Span('GSB', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",), text="gsb", idx=6),
THCell(HT.TD(HT.Span('NSB', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",), text="nsb", idx=7),
THCell(HT.TD(HT.Span('Chr', Class="cw fwb fs13"), align='center', Class="cbrb ffl2 fwb fs13 b1",)),
THCell(HT.TD(HT.Span('Start', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",)),
THCell(HT.TD(HT.Span('End', Class="cw fwb fs13"),align='center', Class="cbrb ffl fwb fs13 b1",)),
])
tblobj['body'] = []
blatbutton = ''
fetchField = ['Probe.Name','Probe.Sequence','Probe.ExonNo','Probe.Tm', 'Probe.E_GSB','Probe.E_NSB', 'ProbeH2.h2', 'ProbeH2.weight']
query = "SELECT %s FROM (Probe, ProbeSet, ProbeFreeze) left join ProbeH2 on ProbeH2.ProbeId = Probe.Id and ProbeH2.ProbeFreezeId = ProbeFreeze.Id WHERE ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeFreeze.Name = '%s' order by Probe.SerialOrder" % (string.join(fetchField,','), self.ProbeSetID, self.probeDatabase)
self.cursor.execute(query)
results = self.cursor.fetchall()
blatsequence = ""
# add by NL: get strains' name in SnpPattern database table
strainsInSnpPatternDBtable=self.getStrainNameIndexPair() # after snpBrowserPage.py change to MVC, this function can be removed in this class and called from other class;
allStrainNameList=[v[0] for v in strainsInSnpPatternDBtable]
speciesid = webqtlDatabaseFunction.retrieveSpeciesId(cursor=self.cursor,RISet=fd.RISet)
for result in results:
"""
ProbeId, CellID,Sequence,ExonNo,Tm, E_GSB,E_NSB = map(self.nullRecord,result)
h2 = ''
query = "SELECT h2 FROM ProbeH2 WHERE ProbeFreezeId = '%s' and ProbeId=%s" % (self.probeDatabase, ProbeId)
self.cursor.execute(query)
results = self.cursor.fetchall()
"""
CellID,Sequence,ExonNo,Tm, E_GSB,E_NSB,h2, weight = map(self.nullRecord,result)
Average = ''
STDEV = ''
mean = -10000.0
stdev = -10000.0
try:
thisTrait.cellid = CellID
thisTrait.retrieveData()
mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1])
if mean:
Average = '%2.2f' % mean
if stdev:
STDEV = '%2.2f' % stdev
except:
pass
if CellID == self.CellID:
bkColor = "cbrdull fs11 b1"
else:
bkColor = "fs11 b1"
seqcolor= ''
if thisTrait.blatseq:
blatsequence = thisTrait.blatseq
if int(CellID[-1]) % 2 == 1:
seqcolor= 'cdg'
else:
if int(CellID[-1]) % 2 == 1:
seqcolor= 'cdg'
blatsequence += string.strip(Sequence)
if thisTrait.genbankid and (int(CellID[-1]) % 2 == 1):
probeurl = 'http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi?one=%s&sseq=%s' % (thisTrait.genbankid, Sequence)
probefy1 = HT.Input(type="button",value="Blast",onClick= "openNewWin('%s')" % probeurl, Class="buttonsmaller")
else:
probefy1 = ''
traitName = str(thisTrait)
#XZ, Aug 08, 2011: Note that probesets on some affy chips are not name as "xxx_at" (i.e., Affy Mouse Gene 1.0 ST (GPL6246)).
#EnsemblProbeSetID = self.ProbeSetID[0:self.ProbeSetID.index('_at')+3]
EnsemblProbeSetID = self.ProbeSetID
if '_at' in self.ProbeSetID:
EnsemblProbeSetID = self.ProbeSetID[0:self.ProbeSetID.index('_at')+3]
self.cursor.execute('''
SELECT EnsemblProbeLocation.*
FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze
WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
ProbeFreeze.Name=%s group by Chr, Start, End'''
,(CellID, EnsemblProbeSetID, self.probeDatabase))
LocationFields = self.cursor.fetchall()
Chr=''
Start=''
End=''
if (len(LocationFields)>=1):
Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0])
Start /= 1000000.0
End /= 1000000.0
if (len(LocationFields)>1):
self.cursor.execute('''
SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze
WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeFreeze.Name=%s'''
,(self.ProbeSetID, self.probeDatabase))
ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0])
self.cursor.execute('''
SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb
FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze
WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
EnsemblProbeLocation.Chr=%s and ProbeFreeze.Name=%s order by Mb limit 1'''
,(ProbeSetMb, CellID, EnsemblProbeSetID, ProbeSetChr, self.probeDatabase))
NewLocationFields = self.cursor.fetchall()
if (len(NewLocationFields)>0):
Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0])
Start /= 1000000.0
End /= 1000000.0
snp_collection = []
snpDiff_collection=[]
startIndex=3
if Chr != '' and Start != '' and End != '' and speciesid != None:
self.cursor.execute('''
SELECT a.SnpName, a.Id, b.* FROM SnpAll a, SnpPattern b
WHERE a.Chromosome=%s and a.Position>=%s and a.Position<=%s
and a.SpeciesId=%s and a.Id=b.SnpId'''
,(Chr, Start, End, speciesid)) #chr,Start, End, 1))
snpresults = self.cursor.fetchall()
index1=allStrainNameList.index(_mat) #_mat index in results
index2=allStrainNameList.index(_pat) #_pat index in results
for v in snpresults:
#updated by NL: 07-22-2011 check 'limit to' to get snpBrowser snpresults
snp_collection.append(HT.Href(text=v[0], url=os.path.join(webqtlConfig.CGIDIR,
"main.py?FormID=SnpBrowserResultPage&submitStatus=1&customStrain=1")+ "&geneName=%s" % v[0], Class="fs12 fwn", target="_blank"))
snp_collection.append(HT.BR())
#updated by NL: 07-27-2011 link snp info for different allele only
strain1_allele=v[startIndex+index1]
strain2_allele=v[startIndex+index2]
if strain1_allele!=strain2_allele:
snpDiff_collection.append(HT.Href(text=v[0], url=os.path.join(webqtlConfig.CGIDIR,
"main.py?FormID=SnpBrowserResultPage&submitStatus=1&customStrain=1&diffAlleles=1&chosenStrains=%s"%chosenStrains)+ "&geneName=%s" % v[0], Class="fs12 fwn", target="_blank"))
snpDiff_collection.append(HT.BR())
tr = []
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class='checkbox', name="searchResult",value=traitName, onClick="highlight(this)"), align="right", Class=bkColor, nowrap="on"), text=traitName))
tr.append(TDCell(HT.TD(HT.Href(text=CellID, url = "javascript:showDatabase2('%s','%s','%s');" % (self.database,self.ProbeSetID,CellID),Class="fs12 fwn"),Class=bkColor), traitName, traitName.upper()))
tr.append(TDCell(HT.TD(Sequence, Class=bkColor + " %s ffmono fs14" % seqcolor),Sequence,Sequence.upper()))
tr.append(TDCell(HT.TD(probefy1,align='center',Class=bkColor)))
tr.append(TDCell(HT.TD(ExonNo,align='center',Class=bkColor)))
try:
TmValue = float(Tm)
except:
TmValue = 0.0
tr.append(TDCell(HT.TD(Tm,align='center',Class=bkColor), Tm, TmValue))
try:
E_GSBValue = float(E_GSB)
except:
E_GSBValue = -10000.0
tr.append(TDCell(HT.TD(E_GSB,align='center',Class=bkColor), E_GSB, E_GSBValue))
try:
E_NSBValue = float(E_NSB)
except:
E_NSBValue = -10000.0
tr.append(TDCell(HT.TD(E_NSB,align='center',Class=bkColor), E_NSB, E_NSBValue))
tr.append(TDCell(HT.TD(Average,align='center',Class=bkColor), Average, mean))
tr.append(TDCell(HT.TD(STDEV,align='center',Class=bkColor), STDEV, stdev))
try:
h2Value = float(h2)
except:
h2Value = -10000.0
tr.append(TDCell(HT.TD(h2,align='center',Class=bkColor), h2, h2Value))
tr.append(TDCell(HT.TD(Chr,align='left',Class=bkColor)))
tr.append(TDCell(HT.TD(Start,align='left',Class=bkColor)))
tr.append(TDCell(HT.TD(End,align='left',Class=bkColor)))
snp_td = HT.TD(align='left',Class=bkColor)
for one_snp_href in snp_collection:
snp_td.append(one_snp_href)
tr.append(TDCell(snp_td))
#07-27-2011:add by NL: show SNP results for different allele only
snpDiff_td= HT.TD(align='left', valign='top', Class=bkColor)
for one_snpDiff_href in snpDiff_collection:
snpDiff_td.append(one_snpDiff_href)
tr.append(TDCell(snpDiff_td))
tblobj['body'].append(tr)
# import cPickle
filename = webqtlUtil.genRandStr("Probe_")
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
cPickle.dump(tblobj, objfile)
objfile.close()
# NL, 07/27/2010. genTableObj function has been moved from templatePage.py to webqtlUtil.py;
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=("", ""), tableID = "sortable", addIndex = "1"), Id="sortable")
#UCSC
_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
if _Species == "rat":
thisurl = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
elif _Species == "mouse":
thisurl = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence)
else:
thisurl = ""
if thisurl:
blatbutton = HT.Input(type='button' ,name='blatPM',value='Verify UCSC', onClick="window.open('%s','_blank')" % thisurl,Class="button")
else:
blatbutton = ""
#GenBank
genbankSeq = ""
if thisTrait.genbankid:
self.cursor.execute("SELECT Sequence FROM Genbank WHERE Id = '%s'" % thisTrait.genbankid )
genbankSeq = self.cursor.fetchone()
if genbankSeq:
genbankSeq = genbankSeq[0]
if genbankSeq:
if _Species == "rat":
thisurl2 = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', genbankSeq)
if _Species == "mouse":
thisurl2 = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', genbankSeq)
else:
thisurl2 = ''
if thisurl2:
blatbutton2 = HT.Input(type='button' ,name='blatPM',value='Verify GenBank', onClick="window.open('%s','_blank')" % thisurl2,Class="button")
else:
blatbutton2 = ""
#Snp
snpBrowser = ""
if thisTrait.symbol and _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=snpBrowser") + "&geneName=%s" % geneName[0]
else:
if thisTrait.chr and thisTrait.mb:
snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=snpBrowser") + \
"&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002)
else:
snpurl = ""
if snpurl:
snpBrowser = HT.Input(type="button",value="SNP Browser",onClick= \
"openNewWin('%s')" % snpurl, Class="button")
else:
snpBrowser = ""
#end if
heading = HT.Paragraph('Probe Information', Class="title")
intro = HT.Paragraph('The table below lists information of all probes of probe set ',HT.Span(self.ProbeSetID, Class="fwb fs13"),' from database ', HT.Span(self.probeDatabase, Class="fwb fs13"), ".")
buttons = HT.Paragraph(probedata,probeinfo,heatmap,cormatrix,blatbutton,blatbutton2,verifyButton,snpBrowser, HT.P(),selectall,selectpm,selectmm,selectinvert,reset,addselect)
if rudi_track:
buttons.append(rudi_track)
form.append(buttons,div,HT.P())
TD_LR.append(heading,intro,form, HT.P())
self.dict['basehref'] = ''
self.dict['body'] = str(TD_LR)
self.dict['title'] = self.db.shortname + ' : ' + self.ProbeSetID +' / Probe Information'
# updated by NL, javascript function xmlhttpPost(strURL, div, querystring) and function updatepage(Id, str)
# have been moved to dhtml.js
self.dict['js1'] = ''
def writeHTML(self,fd):
TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top")
pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left")
seq = 1
SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}")
mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
mintmap.append(mintmap_img)
mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}")
mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;")
mcorr.append(mcorr_img)
cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}")
cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
cormatrix.append(cormatrix_img)
networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}")
networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;")
networkGraph.append(networkGraph_img)
heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}")
heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
heatmap.append(heatmap_img)
partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}")
partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
partialCorr.append(partialCorr_img)
BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}")
networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;")
BN.append(networkGraph_img)
removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet)
removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;")
removeselect.append(removeselect_img)
selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);")
selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
selectall.append(selectall_img)
reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);")
reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
reset.append(reset_img)
exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');")
exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;")
exportSelect.append(exportSelect_img)
selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);")
selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
selectinvert.append(selectinvert_img)
chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')
importFile = HT.Input(type='file', name='importfile', size=15)
importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button")
exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button")
importMenu = HT.Select(name='importmethod')
importMenu.append(('append','append'))
importMenu.append(('replace','replace'))
GeneWeaver = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');")
GeneWeaver_img = HT.Image("/images/ODE_logo_final.jpg", name="GeneWeaver", alt="GeneWeaver", title="GeneWeaver", style="border:none")
GeneWeaver.append(GeneWeaver_img)
GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');")
GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
GCATButton.append(GCATButton_img)
GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');")
GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
GeneSet.append(GeneSet_img)
BNW = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'BNW');")
BNW_img = HT.Image("/images/bnw.jpg", name="BNW", alt="Bayesian Network Webserver", title="Bayesian Network Webserver", style="border:none; width:57px; height:55px;")
BNW.append(BNW_img)
#need to be refined
if fd.genotype.Mbmap:
scale = HT.Input(name="scale", value="physic", type="hidden")
else:
scale = ""
formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
#XZ, July 22, 2011: I add parameters for interval mapping
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None}
for key in hddn.keys():
formMain.append(HT.Input(name=key, value=hddn[key], type='hidden'))
if not self.searchResult:
SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton)
TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain))
self.dict['body'] = str(TD_LR)
self.dict['title'] = "%s Trait Collection" % fd.RISet
return
#########################################
# Creating table object for AJAX table #
#########################################
tblobj = {}
mainfmName = 'showDatabase'
# NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py;
species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
if species == 'human':
chrMenu = scale = mintmap = heatmap = ""
tblobj['header'] = self.getCollectionTableHeader()
sortby = self.getSortByValue()
thisRISet = fd.RISet
tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species)
filename= webqtlUtil.genRandStr("Search_")
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
cPickle.dump(tblobj, objfile)
objfile.close()
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable")
containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0, width="640", border=0, align="Left")
optionsTable.append(HT.TR(
HT.TD(selectall, width="77", style="text-align:center"),
HT.TD(reset, width="77", style="text-align:center"),
HT.TD(selectinvert, width="77", style="text-align:center"),
HT.TD(removeselect, width="77", style="text-align:center"),
HT.TD(exportSelect, width="77", style="text-align:center"),
HT.TD(" ", width="8"),
HT.TD(GeneWeaver, width="77", style="text-align:center"),
HT.TD(GCATButton, width="77", style="text-align:center"),
HT.TD(GeneSet, width="77", style="text-align:center"),
HT.TD(BNW, width="77", style="text-align:center")))
optionsTable.append(HT.TR(
HT.TD("Select", style="text-align:center"),
HT.TD("Deselect", style="text-align:center"),
HT.TD("Invert", style="text-align:center"),
HT.TD("Remove", style="text-align:center"),
HT.TD("Export", style="text-align:center"),
HT.TD(" "),
HT.TD("Gene", HT.BR(), "Weaver", style="text-align:center"),
HT.TD("GCAT", style="text-align:center"),
HT.TD("Gene Set", style="text-align:center"),
HT.TD("BNW", style="text-align:center")))
postContainerTable.append(HT.TR(HT.TD(optionsTable)))
containerTable.append(HT.TR(HT.TD(optionsTable)))
functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left")
functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap))
if species == "human":
labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
else:
labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
functionTable.append(functionRow, labelRow)
postContainerTable.append(HT.TR(HT.TD(functionTable)))
containerTable.append(HT.TR(HT.TD(functionTable)))
containerTable.append(HT.TR(HT.TD(" ")))
pageTable.append(HT.TR(HT.TD(containerTable)))
chrMenu = scale = ""
pageTable.append(HT.TR(HT.TD(div)))
pageTable.append(HT.TR(HT.TD(" ")))
if len(self.theseTraits) > 20:
pageTable.append(HT.TR(HT.TD(postContainerTable)))
pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton)))
#Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010
formMain.append(chrMenu,scale,pageTable)
#Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js
self.dict['js1'] = ''
TD_LR.append(SelectionHeading,formMain)
self.dict['body'] = str(TD_LR)
self.dict['js2'] = 'onLoad="pageOffset()"'
self.dict['layer'] = self.generateWarningLayer()
self.dict['title'] = "%s Trait Collection" % thisRISet
def __init__(self,fd):
self.theseTraits = []
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
templatePage.__init__(self, fd)
if not self.openMysql():
return
self.searchResult = fd.formdata.getvalue('searchResult', [])
if type("1") == type(self.searchResult):
self.searchResult = [self.searchResult]
#XZ, self.theseTraits holds the "ProbeSet" traits.
for item in self.searchResult:
try:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo(QTL=1)
if thisTrait.db.type == "ProbeSet":
self.theseTraits.append(thisTrait)
except:
pass
if self.theseTraits:
pass
else:
templatePage.__init__(self, fd)
heading = 'WebGestalt'
detail = ['You need to select at least one microarray trait to submit.']
self.error(heading=heading,detail=detail)
return
chipName = self.testChip(fd)
#XZ, 8/24/2009: the name of arraylist is misleading. It holds the name of traits.
arraylist, geneIdList = self.genGeneIdList(fd)
target_url = "http://bioinfo.vanderbilt.edu/webgestalt/webgestalt.php"
formWebGestalt = HT.Form(cgi=target_url, enctype='multipart/form-data', name='WebGestalt', submit = HT.Input(type='hidden'))
id_type = chipName
hddnWebGestalt = {'id_list':string.join(arraylist, ","),
'id_type':id_type}
hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
hddnWebGestalt['analysis_type'] = 'GO'
hddnWebGestalt['significancelevel'] = '.05'
hddnWebGestalt['stat'] = 'Hypergeometric'
hddnWebGestalt['mtc'] = 'BH'
hddnWebGestalt['min'] = '2'
hddnWebGestalt['id_value'] = fd.formdata.getvalue('correlation')
species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
if species == 'rat':
hddnWebGestalt['org'] = 'Rattus norvegicus'
elif species == 'human':
hddnWebGestalt['org'] = 'H**o sapiens'
elif species == 'mouse':
hddnWebGestalt['org'] = 'Mus musculus'
else:
hddnWebGestalt['org'] = ''
hddnWebGestalt['org'] = hddnWebGestalt['org'].replace(' ','_')
for key in hddnWebGestalt.keys():
formWebGestalt.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
TD_LR.append(formWebGestalt)
TD_LR.append(HT.Paragraph("Your selection of %d traits is being submitted to GO Tree" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
# updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
# moved unknownChipError() to webqtl.js and change it to unknownChipError(chipName)
if chipName == 'mixed':
methodName = "WebGestalt"
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout("mixedChipError('%s')" ,1000);
</SCRIPT>
""" % methodName
elif chipName.find('_NA') > 0:
chipName = chipName[0:-3]
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout("unknownChipError('%s')",1000);
</SCRIPT>
""" % chipName
else:
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout('document.WebGestalt.submit()',1000);
</SCRIPT>
"""
self.dict['body'] = TD_LR
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
#XZ, self.theseTraits holds the "ProbeSet" traits.
self.theseTraits = []
self.searchResult = fd.formdata.getvalue('searchResult', [])
if type("1") == type(self.searchResult):
self.searchResult = [self.searchResult]
for item in self.searchResult:
try:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo(QTL=1)
if thisTrait.db.type == "ProbeSet":
self.theseTraits.append(thisTrait)
except:
pass
if self.theseTraits:
pass
else:
heading = 'ODE'
detail = ['You need to select at least one microarray trait to submit.']
self.error(heading=heading,detail=detail)
return
chipName = self.getChipName(fd)
species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
if species == 'rat':
species = 'Rattus norvegicus'
elif species == 'human':
species = 'H**o sapiens'
elif species == 'mouse':
species = 'Mus musculus'
else:
species = ''
probesetNameList = self.getProbesetNameList(fd)
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
formODE = HT.Form(cgi="http://ontologicaldiscovery.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))
hddnODE = {}
hddnODE['client'] = 'genenetwork'
hddnODE['species'] = species
hddnODE['idtype'] = chipName
hddnODE['list'] = string.join(probesetNameList, ",")
for key in hddnODE.keys():
formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))
TD_LR.append(formODE)
TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
# updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
if chipName == 'mixed':
methodName = "ODE"
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout("mixedChipError('%s')",1000);
</SCRIPT>
""" % methodName
else:
self.dict['js1'] = """
<SCRIPT LANGUAGE="JavaScript">
setTimeout('document.formODE.submit()',1000);
</SCRIPT>
"""
self.dict['body'] = TD_LR