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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/showTrait/ShowBestTrait.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/showTrait/ShowBestTrait.py')
-rwxr-xr-xweb/webqtl/showTrait/ShowBestTrait.py195
1 files changed, 0 insertions, 195 deletions
diff --git a/web/webqtl/showTrait/ShowBestTrait.py b/web/webqtl/showTrait/ShowBestTrait.py
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--- a/web/webqtl/showTrait/ShowBestTrait.py
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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
-
-