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Diffstat (limited to 'web/webqtl/showTrait/ShowBestTrait.py')
| -rwxr-xr-x | web/webqtl/showTrait/ShowBestTrait.py | 195 |
1 files changed, 0 insertions, 195 deletions
diff --git a/web/webqtl/showTrait/ShowBestTrait.py b/web/webqtl/showTrait/ShowBestTrait.py deleted file mode 100755 index 9eb42923..00000000 --- a/web/webqtl/showTrait/ShowBestTrait.py +++ /dev/null @@ -1,195 +0,0 @@ -# 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 - - |