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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 string
#from base.templatePage import templatePage
#from basicStatistics.BasicStatisticsPage import BasicStatisticsPage
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from utility import webqtlUtil
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from DataEditingPage import DataEditingPage
#class ShowBestTrait(BasicStatisticsPage, templatePage):
class ShowBestTrait(DataEditingPage):
def __init__(self,fd):
########## geneName means symbol ##########
geneName = fd.formdata.getvalue('gene')
if geneName:
geneName = string.strip(geneName)
refseq = fd.formdata.getvalue('refseq')
if refseq:
refseq = string.strip(refseq)
genbankid = fd.formdata.getvalue('genbankid')
if genbankid:
genbankid = string.strip(genbankid)
geneid = fd.formdata.getvalue('geneid')
if geneid:
geneid = string.strip(geneid)
species = fd.formdata.getvalue('species')
tissue = fd.formdata.getvalue('tissue')
database = fd.formdata.getvalue('database')
########## searchAlias is just a singal, so it doesn't need be stripped ##########
searchAlias = fd.formdata.getvalue('searchAlias')
if not self.openMysql():
return
if database:
if geneName:
if searchAlias:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE)
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneName))
else:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.symbol = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneName))
elif refseq:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.RefSeq_TranscriptId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, refseq))
elif genbankid:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.GenbankId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, genbankid))
elif geneid:
self.cursor.execute(""" SELECT ProbeSetXRef.*
FROM
ProbeSet, ProbeSetXRef, DBList
WHERE
ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
(DBList.Name=%s or DBList.Code=%s) AND
ProbeSet.GeneId = %s
ORDER BY ProbeSetXRef.mean DESC
""" , (database, database, geneid))
Results = self.cursor.fetchone()
########## select the Data that match the selection(currently, only max mean available) ##########
if Results:
ProbeSetFreezeId = Results[0]
ProbeSetId = Results[1]
DataId = Results[2]
self.cursor.execute("""
select
InbredSet.Name
from
InbredSet, ProbeFreeze, ProbeSetFreeze
where
InbredSet.Id=ProbeFreeze.InbredSetId and
ProbeFreeze.Id=ProbeSetFreeze.ProbeFreezeId and
ProbeSetFreeze.Id=%s
""", ProbeSetFreezeId)
fd.RISet = self.cursor.fetchone()[0]
#fd.RISet = Results[0]
self.cursor.execute("select Name, FullName from ProbeSetFreeze where Id=%s", ProbeSetFreezeId)
fd.database, fd.identification = self.cursor.fetchone()
self.cursor.execute("select Name, symbol, description from ProbeSet where Id=%s", ProbeSetId)
fd.ProbeSetID, fd.symbol, fd.description = self.cursor.fetchone()
fd.identification += ' : '+fd.ProbeSetID
fd.formdata['fullname'] = fd.database+'::'+fd.ProbeSetID
#XZ, 03/03/2009: Xiaodong changed Data to ProbeSetData
self.cursor.execute("select Strain.Name, ProbeSetData.Value from Strain, ProbeSetData where Strain.Id=ProbeSetData.StrainId and ProbeSetData.Id=%s", DataId)
Results = self.cursor.fetchall()
fd.allstrainlist = []
for item in Results:
fd.formdata[item[0]] = item[1]
fd.allstrainlist.append(item[0])
#XZ, 03/12/2009: Xiaodong changed SE to ProbeSetSE
self.cursor.execute("select Strain.Name, ProbeSetSE.error from Strain, ProbeSetSE where Strain.Id = ProbeSetSE.StrainId and ProbeSetSE.DataId=%s", DataId)
Results = self.cursor.fetchall()
for item in Results:
fd.formdata['V'+item[0]] = item[1]
else:
fd.RISet = 'BXD'
fd.database = 'KI_2A_0405_Rz'
fd.ProbeSetID = '1367452_at'
else:
fd.RISet = 'BXD'
fd.database = 'KI_2A_0405_Rz'
fd.ProbeSetID = '1367452_at'
#BasicStatisticsPage.__init__(self, fd)
thisTrait = webqtlTrait(db=fd.database, name=fd.ProbeSetID, cursor=self.cursor)
thisTrait.retrieveInfo()
thisTrait.retrieveData()
DataEditingPage.__init__(self, fd, thisTrait)
self.dict['title'] = '%s: Display Trait' % fd.identification
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