def retrieveMarkerNameForGroupByRange(cursor, InbredSetName, Chr, MbStart, MbEnd): MarkerName = [] SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName) MbStartClause = '' MbEndClause = '' try: MbStartClause = 'and Mb >= %s ' % float(MbStart) except: pass try: MbEndClause = 'and Mb <= %s' % float(MbEnd) except: pass cmd = "SELECT Geno.Name FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Chr='%s' " % (SpeciesId, Chr) + MbStartClause + MbEndClause + " and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id and GenoXRef.Used_for_mapping='Y' order by Mb" % (GenoFreezeId) cursor.execute(cmd) results = cursor.fetchall() for one_result in results: MarkerName.append( one_result[0] ) return MarkerName
def addGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd): SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) Name = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Name' ) Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ) Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' ) Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' ) Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' ) chr_num = get_chr_num (cursor, Chr, SpeciesId) cmd = "INSERT INTO Geno (Id, SpeciesId, Name, Marker_Name, Chr, Mb, Sequence, Source, chr_num) VALUES (%s, %s, '%s', '%s', '%s', %s, '%s', '%s', %s )" % (GenoId, SpeciesId, Name, Name, Chr, Mb, Sequence, Source, chr_num) cursor.execute(cmd)
def updateGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd): SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ) cmd = "UPDATE Geno SET Chr='%s' WHERE Id=%s" % (Chr, GenoId) cursor.execute(cmd) chr_num = get_chr_num (cursor, Chr, SpeciesId) cmd = "UPDATE Geno SET chr_num=%s WHERE Id=%s" % (chr_num, GenoId) cursor.execute(cmd) Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' ) cmd = "UPDATE Geno SET Mb=%s WHERE Id=%s" % (Mb, GenoId) cursor.execute(cmd) Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' ) cmd = "UPDATE Geno SET Sequence='%s' WHERE Id=%s" % (Sequence, GenoId) cursor.execute(cmd) Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' ) cmd = "UPDATE Geno SET Source='%s' WHERE Id=%s" % (Source, GenoId) cursor.execute(cmd)
def retrieveMarkerInfoForGroup(cursor, MarkerName, InbredSetName): """ @type cursor: MySQLdb.connect.cursor @type MarkerName: string @rtype: list @return: the Marker's Id, Name, Chr, cM, Mb, Sequence, Source """ SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName) cmd = ','.join( MarkerInfoField ) cmd = "SELECT Geno.Id," + cmd + " FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Geno.Name='%s' and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id" % (SpeciesId, MarkerName, GenoFreezeId) cursor.execute(cmd) result = cursor.fetchone() if result: return result else: return None
def getCollectionTableBody(self, traitList=None, formName=None, species=""):
tblobj_body = []
className = "fs12 fwn b1 c222"
for thisTrait in traitList:
tr = []
if not thisTrait.haveinfo:
thisTrait.retrieveInfo(QTL=1)
trId = str(thisTrait)
oneRadioName = thisTrait.getName()
tr.append(TDCell(HT.TD(" ", align="center", valign="center", Class=className)))
tr.append(
TDCell(
HT.TD(
HT.Input(type="radio", name=oneRadioName, value="primary"),
align="center",
valign="center",
Class=className,
)
)
)
tr.append(
TDCell(
HT.TD(
HT.Input(type="radio", name=oneRadioName, value="control"),
align="center",
valign="center",
Class=className,
)
)
)
tr.append(
TDCell(
HT.TD(
HT.Input(type="radio", name=oneRadioName, value="target", checked="true"),
align="center",
valign="center",
Class=className,
)
)
)
tr.append(
TDCell(
HT.TD(
HT.Input(type="radio", name=oneRadioName, value="ignored"),
align="center",
valign="center",
Class=className,
)
)
)
tr.append(
TDCell(
HT.TD(thisTrait.db.displayname, Class="fs12 fwn b1 c222"),
thisTrait.db.displayname,
thisTrait.db.displayname.upper(),
)
)
tr.append(
TDCell(
HT.TD(
HT.Href(
text=thisTrait.name,
url="javascript:showDatabase3('%s','%s','%s','')"
% (formName, thisTrait.db.name, thisTrait.name),
Class="fs12 fwn",
),
nowrap="yes",
align="left",
Class=className,
),
str(thisTrait.name),
thisTrait.name,
)
)
# description column
if thisTrait.db.type == "Publish":
PhenotypeString = thisTrait.post_publication_description
if thisTrait.confidential:
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users
):
PhenotypeString = thisTrait.pre_publication_description
tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))
elif thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp":
description_string = str(thisTrait.description).strip()
if thisTrait.db.type == "ProbeSet":
target_string = str(thisTrait.probe_target_description).strip()
description_display = ""
if len(description_string) > 1 and description_string != "None":
description_display = description_string
else:
description_display = thisTrait.symbol
if (
len(description_display) > 1
and description_display != "N/A"
and len(target_string) > 1
and target_string != "None"
):
description_display = description_display + "; " + target_string.strip()
description_string = description_display
tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
# location column
if thisTrait.db.type == "Publish":
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
else:
# ZS: trait_location_value is used for sorting
trait_location_repr = "N/A"
trait_location_value = 1000000
if hasattr(thisTrait, "chr") and hasattr(thisTrait, "mb") and thisTrait.chr and thisTrait.mb:
try:
trait_location_value = int(thisTrait.chr) * 1000 + thisTrait.mb
except:
if thisTrait.chr.upper() == "X":
trait_location_value = 20 * 1000 + thisTrait.mb
else:
trait_location_value = ord(str(thisTrait.chr).upper()[0]) * 1000 + thisTrait.mb
trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb))
tr.append(
TDCell(
HT.TD(trait_location_repr, nowrap="yes", Class=className),
trait_location_repr,
trait_location_value,
)
)
if thisTrait.db.type == "ProbeSet":
self.cursor.execute(
"""
select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %d and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
ProbeSet.Name = '%s'
"""
% (thisTrait.db.id, thisTrait.name)
)
result = self.cursor.fetchone()
if result:
if result[0]:
mean = result[0]
else:
mean = 0
else:
mean = 0
# XZ, 06/05/2009: It is neccessary to turn on nowrap
repr = "%2.3f" % mean
tr.append(TDCell(HT.TD(repr, Class=className, align="right", nowrap="ON"), repr, mean))
elif thisTrait.db.type == "Publish":
self.cursor.execute(
"""
select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze
where PublishData.Id = PublishXRef.DataId and
PublishXRef.Id = %s and
PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
PublishFreeze.Id = %d
"""
% (thisTrait.name, thisTrait.db.id)
)
result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
mean = result[1] / result[0]
else:
mean = 0
else:
mean = 0
repr = "%2.3f" % mean
tr.append(TDCell(HT.TD(repr, Class=className, align="right", nowrap="ON"), repr, mean))
else:
tr.append(TDCell(HT.TD("--", Class=className, align="left", nowrap="ON"), "--", 0))
# Number of cases
n_cases_value = 0
n_cases_repr = "--"
if thisTrait.db.type == "Publish":
self.cursor.execute(
"""
select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze
where PublishData.Id = PublishXRef.DataId and
PublishXRef.Id = %s and
PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
PublishFreeze.Id = %d
"""
% (thisTrait.name, thisTrait.db.id)
)
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if n_cases_value == "--":
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="left", nowrap="on"), n_cases_repr, n_cases_value
)
)
else:
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="right", nowrap="on"),
n_cases_repr,
n_cases_value,
)
)
elif thisTrait.db.type == "ProbeSet":
self.cursor.execute(
"""
select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze
where ProbeSet.Name='%s' and
ProbeSetXRef.ProbeSetId = ProbeSet.Id and
ProbeSetXRef.DataId = ProbeSetData.Id and
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
ProbeSetFreeze.Name = '%s'
"""
% (thisTrait.name, thisTrait.db.name)
)
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if n_cases_value == "--":
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="left", nowrap="on"), n_cases_repr, n_cases_value
)
)
else:
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="right", nowrap="on"),
n_cases_repr,
n_cases_value,
)
)
elif thisTrait.db.type == "Geno":
self.cursor.execute(
"""
select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain
where Geno.SpeciesId = %s and Geno.Name='%s' and
GenoXRef.GenoId = Geno.Id and
GenoXRef.DataId = GenoData.Id and
GenoXRef.GenoFreezeId = GenoFreeze.Id and
GenoData.StrainId = Strain.Id and
GenoFreeze.Name = '%s'
"""
% (
webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset),
thisTrait.name,
thisTrait.db.name,
)
)
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if n_cases_value == "--":
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="left", nowrap="on"), n_cases_repr, n_cases_value
)
)
else:
tr.append(
TDCell(
HT.TD(n_cases_repr, Class=className, align="right", nowrap="on"),
n_cases_repr,
n_cases_value,
)
)
else:
tr.append(
TDCell(HT.TD(n_cases_repr, Class=className, align="left", nowrap="on"), n_cases_repr, n_cases_value)
)
if thisTrait.db.type != "Geno":
# LRS and its location
LRS_score_repr = "--"
LRS_score_value = 0
LRS_location_repr = "--"
LRS_location_value = 1000000
LRS_flag = 1
# Max LRS and its Locus location
if hasattr(thisTrait, "lrs") and hasattr(thisTrait, "locus") and thisTrait.lrs and thisTrait.locus:
self.cursor.execute(
"""
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '%s' and
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
"""
% (species, thisTrait.locus)
)
result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
LRS_Chr = result[0]
LRS_Mb = result[1]
# XZ: LRS_location_value is used for sorting
try:
LRS_location_value = int(LRS_Chr) * 1000 + float(LRS_Mb)
except:
if LRS_Chr.upper() == "X":
LRS_location_value = 20 * 1000 + float(LRS_Mb)
else:
LRS_location_value = ord(str(LRS_chr).upper()[0]) * 1000 + float(LRS_Mb)
LRS_score_repr = "%3.1f" % thisTrait.lrs
LRS_score_value = thisTrait.lrs
LRS_location_repr = "Chr%s: %.6f" % (LRS_Chr, float(LRS_Mb))
LRS_flag = 0
tr.append(
TDCell(
HT.TD(LRS_score_repr, Class=className, align="right", nowrap="on"),
LRS_score_repr,
LRS_score_value,
)
)
tr.append(
TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value)
)
if LRS_flag:
tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0))
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000))
tblobj_body.append(tr)
return tblobj_body
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 retrieveData(self, strainlist=[]):
assert self.db and self.cursor
if self.db.type == 'Temp':
query = '''
SELECT
Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
FROM
TempData, Temp, Strain
WHERE
TempData.StrainId = Strain.Id AND
TempData.Id = Temp.DataId AND
Temp.name = '%s'
Order BY
Strain.Name
''' % self.name
#XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
elif self.db.type == 'Publish':
query = '''
SELECT
Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
FROM
(PublishData, Strain, PublishXRef, PublishFreeze)
left join PublishSE on
(PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
left join NStrain on
(NStrain.DataId = PublishData.Id AND
NStrain.StrainId = PublishData.StrainId)
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.name, self.db.id)
#XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
elif self.cellid:
#Probe Data
query = '''
SELECT
Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id
FROM
(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef,
Strain, Probe, ProbeSet)
left join ProbeSE on
(ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
WHERE
Probe.Name = '%s' AND ProbeSet.Name = '%s' AND
Probe.ProbeSetId = ProbeSet.Id AND
ProbeXRef.ProbeId = Probe.Id AND
ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeXRef.DataId = ProbeData.Id AND
ProbeData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.cellid, self.name, self.db.name)
#XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
elif self.db.type == 'ProbeSet':
#ProbeSet Data
query = '''
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
FROM
(ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
WHERE
ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (self.name, self.db.name)
#XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
else:
#Geno Data
#XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
query = '''
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoFreeze.Name = '%s' AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name)
self.cursor.execute(query)
results = self.cursor.fetchall()
self.data.clear()
if results:
self.mysqlid = results[0][-1]
if strainlist:
for item in results:
if item[0] in strainlist:
val = item[1]
if val != None:
var = item[2]
ndata = None
if self.db.type in ('Publish', 'Temp'):
ndata = item[3]
self.data[item[0]] = webqtlCaseData(val, var, ndata)
#end for
else:
for item in results:
val = item[1]
if val != None:
var = item[2]
ndata = None
if self.db.type in ('Publish', 'Temp'):
ndata = item[3]
self.data[item[0]] = webqtlCaseData(val, var, ndata)
#end for
#end if
else:
pass
def updateResultPage(self, fd, thisTrait):
comments = []
ctime = time.ctime()
##Start Updating
dataID = -1
if thisTrait.db.type == 'Publish':
self.cursor.execute("SelecT PublishXRef.InbredSetId, PublishXRef.DataId, PublishXRef.PublicationId, PublishXRef.PhenotypeId, PublishXRef.Sequence from PublishXRef, PublishFreeze where PublishXRef.InbredSetId= PublishFreeze.InbredSetId and PublishFreeze.Name = '%s' and PublishXRef.Id = %s" % (thisTrait.db.name, thisTrait.name))
PInbredSetId, dataID, PublicationId, PhenotypeId, Sequence = self.cursor.fetchall()[0]
modifyField = self.formdata.getvalue('modifiedField')
###Modify Trait Informations
if modifyField:
modifyField = string.split(modifyField, '::')
comments += modifyField
updateHomologeneid = False
if thisTrait.db.type == 'Publish':
PhenotypeItemUpdate = []
PhenotypeItemValues = []
PublicationItemUpdate = []
PublicationItemValues = []
for item in modifyField:
itemvalue = self.formdata.getvalue(item)
#XZ: identify Phenotype items
if item in ['pre_publication_description', 'post_publication_description', 'original_description', 'pre_publication_abbreviation', 'post_publication_abbreviation', 'lab_code', 'submitter', 'owner', 'authorized_users', 'units']:
if itemvalue != None: #XZ: the problem is that the item value can not be deleted
PhenotypeItemUpdate.append('%s=%%s' % item)
PhenotypeItemValues.append(itemvalue)
continue #XZ: this is important to distinguish Phenotype item and Publication item
elif item == "pubmed_id":
#Only integer allowed in this field
try:
itemvalue = int(itemvalue)
except:
itemvalue = None
#whether old PMID exists
self.cursor.execute("SelecT PubMed_ID from Publication where Id = %d" % PublicationId)
oldPMID = self.cursor.fetchone()
if oldPMID:
oldPMID = oldPMID[0]
#whether new PMID already exists
newPMID = None
self.cursor.execute("SelecT Id from Publication where PubMed_ID = %d" % itemvalue)
newPMID = self.cursor.fetchone()
if newPMID:
newPMID = newPMID[0]
##the logic is still not very clear here
if newPMID:
#new PMID in record
self.cursor.execute("Update PublishXRef set PublicationId = %d where InbredSetId=%d and PhenotypeId=%d and PublicationId=%d and Sequence=%d" % (newPMID, PInbredSetId, PhenotypeId, PublicationId, Sequence))
#no need to update other fields
PublicationItemUpdate = []
break
elif itemvalue:
#have new PMID, but not in record or need to change
self.cursor.execute("Update Publication set pubmed_id=%d where Id = %s" % (itemvalue,PublicationId))
else:
#no new PMID
if oldPMID:
#remove a pubmed_id, don't know if this ever gonna happen
self.cursor.execute("SelecT max(Id) from Publication")
maxId = self.cursor.fetchone()[0] + 1
self.cursor.execute("SelecT * from Publication where Id = %d" % PublicationId)
oldRecs = list(self.cursor.fetchone())
oldRecs[0] = maxId
oldRecs[1] = None
NFields = ['%s'] * len(oldRecs)
query = "insert into Publication Values (%s)" % string.join(NFields, ',')
self.cursor.execute(query, tuple(oldRecs))
self.cursor.execute("Update PublishXRef set PublicationId = %d where InbredSetId=%d and PhenotypeId=%d and PublicationId=%d and Sequence=%d" % (maxId, PInbredSetId, PhenotypeId, PublicationId, Sequence))
PublicationId = maxId
pass
else:
pass
continue
else:
pass
if itemvalue:
PublicationItemUpdate.append('%s=%%s' % item)
PublicationItemValues.append(itemvalue)
if PhenotypeItemUpdate:
updateStr= string.join(PhenotypeItemUpdate,',')
query = "Update Phenotype set %s where Id = %s" % (updateStr, PhenotypeId)
self.cursor.execute(query,tuple(PhenotypeItemValues))
if PublicationItemUpdate:
updateStr= string.join(PublicationItemUpdate,',')
query = "Update Publication set %s where Id = %s" % (updateStr, PublicationId)
self.cursor.execute(query,tuple(PublicationItemValues))
else: #ProbeSet or Genotype Data
itemValues = []
itemUpdate = []
for item in modifyField:
itemvalue = self.formdata.getvalue(item)
if itemvalue != None:
itemvalue = string.strip(itemvalue)
else:
pass
if item == 'homologeneid':
updateHomologeneid = True
new_homologeneid = 0
if itemvalue and len(itemvalue) > 0:
try:
new_homologeneid = int(itemvalue)
except:
heading = "Record Updating Result"
detail = ["Can't update database. Homologeneid must be integer!"]
self.error(heading=heading,detail=detail,error="Error")
return
else:
itemUpdate.append('%s=%%s' % item) #XZ: Use %% to put a % in the output string
itemValues.append(itemvalue)
if itemUpdate:
updateStr= string.join(itemUpdate,', ')
comments = "%s modified %s at %s\n" % (self.userName, string.join(comments, ', '), ctime)
if thisTrait.db.type == "ProbeSet":#XZ, June 29, 2010: The algorithm is not good. Need to fix it later.
if thisTrait.chipid in (2,4):
if thisTrait.name[-2:] == '_A':
thisTrait.name = string.replace(thisTrait.name, '_A', '')
elif thisTrait.name[-2:] == '_B':
thisTrait.name = string.replace(thisTrait.name, '_B', '')
else:
pass
query = "Update %s set %s where Name like '%s%%%%'" % (thisTrait.db.type,updateStr,thisTrait.name)
self.cursor.execute(query,tuple(itemValues))
self.cursor.execute("Update %s set comments = CONCAT(comments,'%s') where Name like '%s%%%%'" % (thisTrait.db.type, comments, thisTrait.name))
elif thisTrait.sequence:
query = "Update %s set %s where BlatSeq='%s'" % (thisTrait.db.type,updateStr,thisTrait.sequence)
self.cursor.execute(query,tuple(itemValues))
self.cursor.execute("Update %s set comments = CONCAT(comments,'%s') where BlatSeq='%s'" % (thisTrait.db.type, comments, thisTrait.sequence))
else:
query = "Update %s set %s where Name='%s'" % (thisTrait.db.type,updateStr,thisTrait.name)
self.cursor.execute(query,tuple(itemValues))
self.cursor.execute("Update %s set comments = CONCAT(comments,'%s') where Name='%s'" % (thisTrait.db.type, comments, thisTrait.name))
else: #XZ: Genotype
query = "Update %s set %s where SpeciesId=%s and Name='%s'" % (thisTrait.db.type,updateStr, webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name)
self.cursor.execute(query,tuple(itemValues))
if updateHomologeneid: #XZ: to update homologene id must be after updating geneid.
#XZ: In one species, one homologeneid can have multiple geneid. One geneid only can have one homologeneid.
#XZ: In Homologene table, GeneId is unique.
#XZ: Geneid might just being updated.
thisTrait = webqtlTrait(fullname=self.formdata.getvalue('fullname'), cursor=self.cursor)
thisTrait.retrieveInfo()
if not thisTrait.geneid:
heading = "Record Updating Result"
detail = ["There is no geneid associated with this trait. Can't update homologeneid info"]
self.error(heading=heading,detail=detail,error="Error")
return
else:
query = """
SELECT Species.TaxonomyId
FROM Species, InbredSet
WHERE InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id
""" % thisTrait.db.riset
self.cursor.execute(query)
taxonomyId = self.cursor.fetchone()[0]
if not new_homologeneid:
query = """DELETE FROM Homologene WHERE GeneId=%s""" % thisTrait.geneid
self.cursor.execute(query)
else:
query = """SELECT GeneId FROM Homologene WHERE GeneId=%s""" % thisTrait.geneid
self.cursor.execute(query)
result = self.cursor.fetchone()
if not result:
query = """INSERT into Homologene (HomologeneId, GeneId, TaxonomyId) VALUES (%s, %s, %s)""" % (new_homologeneid, thisTrait.geneid, taxonomyId)
self.cursor.execute(query)
else:
query = """UPDATE Homologene SET HomologeneId=%s WHERE GeneId=%s""" % (new_homologeneid, thisTrait.geneid)
self.cursor.execute(query)
#XZ: It's critical to get lasted info first, then update gene level info across traits by geneid.
#XZ: Need to build index on GeneId. Otherwise, it's too slow.
if thisTrait.db.type == 'ProbeSet':
thisTrait = webqtlTrait(fullname=self.formdata.getvalue('fullname'), cursor=self.cursor)
thisTrait.retrieveInfo()
if thisTrait.geneid:
if 'symbol' in modifyField:
if thisTrait.symbol:
query = """UPDATE ProbeSet SET Symbol='%s' WHERE GeneId=%s""" % (thisTrait.symbol, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET Symbol=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'alias' in modifyField:
if thisTrait.alias:
newalias = []
for alias in re.split('[,;|\s]+', thisTrait.alias):
if alias and 0<len(alias):
newalias.append(alias)
thisTrait.alias = '; '.join(newalias)
query = """UPDATE ProbeSet SET alias='%s' WHERE GeneId=%s""" % (thisTrait.alias, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET alias=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'description' in modifyField:
if thisTrait.description: #XZ: Attention, we must use "%s" instead of '%s'. Otherwise, to insert 3'UTR will generate error.
query = """UPDATE ProbeSet SET description="%s" WHERE GeneId=%s""" % (thisTrait.description, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET description=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'strand_gene' in modifyField:
if thisTrait.strand_gene:
query = """UPDATE ProbeSet SET Strand_Gene='%s' WHERE GeneId=%s""" % (thisTrait.strand_gene, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET Strand_Gene=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'unigeneid' in modifyField:
if thisTrait.unigeneid:
query = """UPDATE ProbeSet SET UniGeneId='%s' WHERE GeneId=%s""" % (thisTrait.unigeneid, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET UniGeneId=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'refseq_transcriptid' in modifyField:
if thisTrait.refseq_transcriptid:
query = """UPDATE ProbeSet SET RefSeq_TranscriptId='%s' WHERE GeneId=%s""" % (thisTrait.refseq_transcriptid, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET RefSeq_TranscriptId=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'genbankid' in modifyField:
if thisTrait.genbankid:
query = """UPDATE ProbeSet SET GenbankId='%s' WHERE GeneId=%s""" % (thisTrait.genbankid, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET GenbankId=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
if 'omim' in modifyField:
if thisTrait.omim:
query = """UPDATE ProbeSet SET OMIM='%s' WHERE GeneId=%s""" % (thisTrait.omim, thisTrait.geneid)
else:
query = """UPDATE ProbeSet SET OMIM=NULL WHERE GeneId=%s""" % (thisTrait.geneid)
self.cursor.execute(query)
###Modify Trait Data
if thisTrait.db.type == 'Publish' and dataID > 0 and fd.formdata.getvalue("modifiedDataField"):
StrainIds = []
for item in fd.strainlist:
self.cursor.execute('SelecT Id from Strain where Name = "%s"' % item)
StrainId = self.cursor.fetchone()
if not StrainId:
raise ValueError
else:
StrainIds.append(StrainId[0])
comments.append('Trait Value')
#XZ, 03/05/2009: Xiaodong changed Data to PublishData, SE to PublishSE
self.cursor.execute('delete from PublishData where Id = %d' % dataID)
self.cursor.execute('delete from PublishSE where DataId = %d' % dataID)
self.cursor.execute('delete from NStrain where DataId = %d' % dataID)
for i, strain in enumerate(fd.strainlist):
sId = StrainIds[i]
if fd.allTraitData.has_key(strain):
tdata = fd.allTraitData[strain]
_val, _var, _N = tdata.val, tdata.var, tdata.N
if _val != None:
#XZ, 03/05/2009: Xiaodong changed Data to PublishData, SE to PublishSE
self.cursor.execute('insert into PublishData values(%d, %d, %s)' % (dataID, sId, _val))
if _var != None:
self.cursor.execute('insert into PublishSE values(%d, %d, %s)' % (dataID, sId, _var))
if _N != None:
self.cursor.execute('insert into NStrain values(%d, %d, %s)' % (dataID, sId, _N))
else:
pass
#end for
else:
pass
TD_LR = HT.TD(valign="top", bgcolor="#eeeeee",height=200,width="100%")
main_title = HT.Paragraph(" Record Updating Result", Class="title")
TD_LR.append(main_title,HT.Blockquote('Successfully updated record %s in database ' % thisTrait.name, thisTrait.db.genHTML(), '.'))
if thisTrait.db.type == 'Publish':
comments = "%s modified %s at %s\n" % (self.userName, string.join(comments, ', '), ctime)
self.cursor.execute("Update PublishXRef set comments = CONCAT(comments,'%s') where InbredSetId=%d and PhenotypeId=%d and PublicationId=%d and Sequence=%d" % (comments, PInbredSetId, PhenotypeId, PublicationId, Sequence))
if 0:
heading = "Record Updating Result"
detail = ["Can't update database. The server may be down at this time or you don't have the permission"]
self.error(heading=heading,detail=detail,error="Error")
return
self.dict['body'] = str(TD_LR)
def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''):
tblobj_body = []
className = "fs12 fwn b1 c222"
for thisTrait in traitList:
tr = []
if not thisTrait.haveinfo:
thisTrait.retrieveInfo(QTL=1)
if thisTrait.riset != RISet:
continue
trId = str(thisTrait)
#XZ: check box column
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId))
#XZ: Dataset column
tr.append(TDCell(HT.TD(thisTrait.db.displayname, Class="fs12 fwn b1 c222"), thisTrait.db.displayname, thisTrait.db.displayname.upper()))
#XZ: Trait ID column
if thisTrait.cellid:
tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid))
else:
tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
#XZ: Symbol column and Description column
if (thisTrait.db.type == "Publish"):
AbbreviationString = "--"
if (thisTrait.post_publication_abbreviation != None):
AbbreviationString = thisTrait.post_publication_abbreviation
PhenotypeString = thisTrait.post_publication_description
if thisTrait.confidential:
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
if thisTrait.pre_publication_abbreviation:
AbbreviationString = thisTrait.pre_publication_abbreviation
else:
AbbreviationString = "--"
PhenotypeString = thisTrait.pre_publication_description
if AbbreviationString == "--":
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
else:
tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper()))
if PhenotypeString:
PhenotypeString_upper = PhenotypeString.upper()
else:
PhenotypeString_upper = PhenotypeString
tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString_upper))
elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"):
description_string = str(thisTrait.description).strip()
if (thisTrait.db.type == "ProbeSet"):
if (thisTrait.symbol != None):
if thisTrait.geneid:
symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn")
else:
symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn")
tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol))
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
target_string = str(thisTrait.probe_target_description).strip()
description_display = ''
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
else:
description_display = thisTrait.symbol
if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
description_display = description_display + '; ' + target_string.strip()
description_string = description_display
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
else:
if (thisTrait.name != None):
tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name))
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
#XZ: Location column
if (thisTrait.db.type == "Publish"):
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
else:
if thisTrait.db.type == "ProbeSet" and thisTrait.cellid:
EnsemblProbeSetID = thisTrait.name
if '_at' in thisTrait.name:
EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3]
#These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10.
self.cursor.execute('''
SELECT EnsemblProbeLocation.*
FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze
WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End'''
,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id))
LocationFields = self.cursor.fetchall()
Chr=''
Mb=''
Start=''
End=''
if (len(LocationFields)>=1):
Chr,Start,Start_2016,End,End_2016,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0])
Start /= 1000000.0
End /= 1000000.0
Mb = Start
if (len(LocationFields)>1):
self.cursor.execute('''
SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze
WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id'''
,(thisTrait.name, thisTrait.db.id))
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, ProbeSetFreeze
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 ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1'''
,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id))
NewLocationFields = self.cursor.fetchall()
if (len(NewLocationFields)>0):
Chr,Start,Start_2016,End,End_2016,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0])
Start /= 1000000.0
End /= 1000000.0
Mb = Start
#ZS: trait_location_value is used for sorting
trait_location_repr = "--"
trait_location_value = 1000000
if Chr and Mb:
try:
trait_location_value = int(Chr)*1000 + Mb
except:
if Chr.upper() == "X":
trait_location_value = 20*1000 + Mb
else:
trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb
trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) )
tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
else:
#ZS: trait_location_value is used for sorting
trait_location_repr = "--"
trait_location_value = 1000000
if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb:
try:
trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb
except:
if thisTrait.chr.upper() == "X":
trait_location_value = 20*1000 + thisTrait.mb
else:
trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb
trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) )
tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
#XZ: Mean column
if (thisTrait.db.type == "ProbeSet"):
if thisTrait.cellid:
mean = -10000.0
try:
thisTrait.retrieveData()
mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1])
except:
pass
repr = '%2.3f' % mean
mean = '%2.2f' % mean
tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
else:
self.cursor.execute("""
select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %d and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
ProbeSet.Name = '%s'
""" % (thisTrait.db.id, thisTrait.name))
result = self.cursor.fetchone()
if result:
if result[0]:
mean = result[0]
else:
mean=0
else:
mean = 0
#XZ, 06/05/2009: It is neccessary to turn on nowrap
repr = "%2.3f" % mean
tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
elif (thisTrait.db.type == "Publish"):
self.cursor.execute("""
select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze
where PublishData.Id = PublishXRef.DataId and
PublishXRef.Id = %s and
PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
PublishFreeze.Id = %d
""" % (thisTrait.name, thisTrait.db.id))
result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
mean = result[1]/result[0]
else:
mean = 0
else:
mean = 0
repr = "%2.3f" % mean
tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
else:
tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0))
#Number of cases
n_cases_value = 0
n_cases_repr = "--"
if (thisTrait.db.type == "Publish"):
self.cursor.execute("""
select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze
where PublishData.Id = PublishXRef.DataId and
PublishXRef.Id = %s and
PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
PublishFreeze.Id = %d
""" % (thisTrait.name, thisTrait.db.id))
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if (n_cases_value == "--"):
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
else:
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
elif (thisTrait.db.type == "ProbeSet"):
self.cursor.execute("""
select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze
where ProbeSet.Name='%s' and
ProbeSetXRef.ProbeSetId = ProbeSet.Id and
ProbeSetXRef.DataId = ProbeSetData.Id and
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
ProbeSetFreeze.Name = '%s'
""" % (thisTrait.name, thisTrait.db.name))
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if (n_cases_value == "--"):
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
else:
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
elif (thisTrait.db.type == "Geno"):
self.cursor.execute("""
select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain
where Geno.SpeciesId = %s and Geno.Name='%s' and
GenoXRef.GenoId = Geno.Id and
GenoXRef.DataId = GenoData.Id and
GenoXRef.GenoFreezeId = GenoFreeze.Id and
GenoData.StrainId = Strain.Id and
GenoFreeze.Name = '%s'
""" % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name))
result = self.cursor.fetchone()
if result:
if result[0]:
n_cases_value = result[0]
n_cases_repr = result[0]
if (n_cases_value == "--"):
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
else:
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
else:
tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
#XZ: Max LRS column and Max LRS Location column
if (thisTrait.db.type != "Geno"):
#LRS value
LRS_score_repr = '--'
LRS_score_value = 0
if hasattr(thisTrait, 'lrs') and thisTrait.lrs:
LRS_score_repr = '%3.1f' % thisTrait.lrs
LRS_score_value = thisTrait.lrs
tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value))
#LRS location
LRS_location_repr = '--'
LRS_location_value = 1000000
LRS_flag = 1
#Max LRS and its Locus location
if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus:
self.cursor.execute("""
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '%s' and
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, thisTrait.locus))
result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
LRS_Chr = result[0]
LRS_Mb = result[1]
#XZ: LRS_location_value is used for sorting
try:
LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
except:
if LRS_Chr.upper() == 'X':
LRS_location_value = 20*1000 + float(LRS_Mb)
else:
LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
LRS_flag = 0
tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
if LRS_flag:
tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
else:
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0))
tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000))
try:
additive = '%3.3f' % thisTrait.additive
except Exception:
additive = ''
tr.append(TDCell(HT.TD(additive, Class=className, align="right", nowrap="on"), additive, additive))
tblobj_body.append(tr)
return tblobj_body