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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import os
import string
import cPickle
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
class PartialCorrInputPage(templatePage):
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 getCollectionTableHeader(self):
tblobj_header = []
className = "fs13 fwb ffl b1 cw cbrb"
tblobj_header = [[THCell(HT.TD('Index', Class=className, nowrap="on"), sort=0),
THCell(HT.TD("Primary (X)",align="center", Class="fs13 fwb ffl b1 cw cbrb", nowrap="ON"), text="primary", sort=0),
THCell(HT.TD("Control (Z)",align="center", Class="fs13 fwb ffl b1 cw cbrb", nowrap="ON"), text="control", sort=0),
THCell(HT.TD("Target (Y)",align="center", Class="fs13 fwb ffl b1 cw cbrb", nowrap="ON"), text="target", sort=0),
THCell(HT.TD("Ignored",align="center", Class="fs13 fwb ffl b1 cw cbrb", nowrap="ON"), text="target", sort=0),
THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1),
THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2),
THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=3),
THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=4),
THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=5),
THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=6),
THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=7),
THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=8)]]
return tblobj_header
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.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.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 getSortByValue(self):
sortby = ("pv", "up")
return sortby
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