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-rwxr-xr-xweb/webqtl/textUI/__init__.py0
-rwxr-xr-xweb/webqtl/textUI/cmdClass.py224
-rwxr-xr-xweb/webqtl/textUI/cmdCorrelation.py325
-rwxr-xr-xweb/webqtl/textUI/cmdGeno.py118
-rwxr-xr-xweb/webqtl/textUI/cmdGet.py86
-rwxr-xr-xweb/webqtl/textUI/cmdHelp.py105
-rwxr-xr-xweb/webqtl/textUI/cmdInterval.py174
-rwxr-xr-xweb/webqtl/textUI/cmdMap.py144
-rwxr-xr-xweb/webqtl/textUI/cmdSearchGene.py70
-rwxr-xr-xweb/webqtl/textUI/cmdShowEditing.py50
10 files changed, 1296 insertions, 0 deletions
diff --git a/web/webqtl/textUI/__init__.py b/web/webqtl/textUI/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/textUI/__init__.py
diff --git a/web/webqtl/textUI/cmdClass.py b/web/webqtl/textUI/cmdClass.py
new file mode 100755
index 00000000..e394218e
--- /dev/null
+++ b/web/webqtl/textUI/cmdClass.py
@@ -0,0 +1,224 @@
+import string
+import os
+import MySQLdb
+
+from base import webqtlConfig
+
+#########################################
+# Basic Class
+#########################################
+class cmdClass:
+ def __init__(self,fd):
+ self.contents = []
+ self.accessError = 0
+ self.error = 0
+ self.accessCode = '###Database Code : <a href="%s%s?cmd=help">%s%s?cmd=help</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)
+ self.data = fd.formdata
+ self.cmdID = self.data.getvalue('cmd')
+ self.showurl = self.data.getvalue('url')
+ self.cursor = None
+ self.user_ip = fd.remote_ip
+
+ try:
+ if not self.openMysql():
+ self.accessError = 1
+ self.contents = ['###Error: Database is not ready']
+ return
+
+ if not self.accessCount():
+ self.accessError = 1
+ self.contents = ['###Error: You have reached maximum access today ']
+ return
+ self.accessRecord()
+ except:
+ self.accessError = 1
+ self.contents = ['###Error: Database is not ready']
+ return
+
+
+ self.probeset = self.data.getvalue('probeset')
+ self.database = self.data.getvalue('db')
+ self.probe = self.data.getvalue('probe')
+
+ self.sourcedata = []
+
+
+ try:
+ self.format = self.data.getvalue('format')[:3]
+ except:
+ self.format = 'row'
+ if not self.probeset or not self.database:
+ self.error = 1
+ return
+
+ def openMysql(self):
+ try:
+ # con = MySQLdb.Connect(db='db_webqtl', host = webqtlConfig.MYSQL_SERVER)
+ # Modified by Fan Zhang
+ con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
+ self.cursor = con.cursor()
+ return 1
+ except:
+ return 0
+
+ #XZ, 03/23/2009: The function name is confusing. This function is to get the database type(ProbeSet, Publish, Geno) id.
+ def getDBId(self,code):
+ self.cursor.execute('SELECT DBType.Name, DBList.FreezeId from DBType, DBList WHERE DBType.Id = DBList.DBTypeId and DBList.code= "%s"' % code)
+ result = self.cursor.fetchall()
+ if not result:
+ return (None, None)
+ else:
+ return result[0]
+
+ #XZ, 03/23/2009: This is to get the inbredset name.
+ def getRISet(self,prefix, DbId):
+ if prefix == 'ProbeSet':
+ self.cursor.execute('SELECT InbredSet.Name from InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id and ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Id = %d' % DbId)
+ else:
+ self.cursor.execute('SELECT InbredSet.Name from %sFreeze, InbredSet WHERE %sFreeze.InbredSetId = InbredSet.Id and %sFreeze.Id = %d' % (prefix, prefix, prefix, DbId))
+ result = self.cursor.fetchall()
+ if result:
+ if result[0][0] == "BXD300":
+ return "BXD"
+ else:
+ return result[0][0]
+ else:
+ return None
+
+ def accessCount(self):
+ try:
+ user_ip = self.user_ip
+ query = """SELECT count(id) FROM AccessLog WHERE ip_address = %s AND UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"""
+ self.cursor.execute(query,user_ip)
+ daycount = self.cursor.fetchall()
+ if daycount:
+ daycount = daycount[0][0]
+ if daycount > webqtlConfig.DAILYMAXIMUM:
+ return 0
+ else:
+ return 1
+ else:
+ return 1
+ except:
+ return 0
+
+ def accessRecord(self):
+ try:
+ user_ip = self.user_ip
+ self.updMysql()
+ query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)"""
+ self.cursor.execute(query,user_ip)
+ self.openMysql()
+ except:
+ pass
+
+ def __str__(self):
+ text = map(str,self.contents)
+ if self.showurl:
+ text.append('http://%s%s?%s' % (os.environ['HTTP_HOST'],os.environ['SCRIPT_NAME'],os.environ['QUERY_STRING'][:-8]))
+ text += self.sourcedata
+ return string.join(text,'\n')
+
+ def write(self):
+ if self.cursor:
+ self.cursor.close()
+ try:
+ browser = os.environ['HTTP_USER_AGENT']
+ return '<pre>%s</pre>' % str(self)
+ except:
+ return str(self)
+
+ def write2(self):
+ print str(self)
+
+ def getTraitData(self, prefix, dbId, probeset, probe = None):
+ headerDict = {'ProbeSet':'ProbeSetID', 'Publish':'RecordID', 'Geno':'Locus'}
+ if prefix == None or dbId == None:
+ return None, None
+ if probe and prefix=='ProbeSet':
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=pm&format=col
+ if string.lower(probe) in ("all","mm","pm"):
+ query = "SELECT Probe.Name from Probe, ProbeSet WHERE Probe.ProbeSetId = ProbeSet.Id and ProbeSet.Name = '%s' order by Probe.Name" % probeset
+ self.cursor.execute(query)
+ allprobes = self.cursor.fetchall()
+ if not allprobes:
+ return None, None
+
+ fetchprobes = []
+ for item in allprobes:
+ if probe == 'all':
+ fetchprobes.append(item[0])
+ else:
+ try:
+ taildigit = int(item[0][-1]) % 2
+ if probe == "pm" and taildigit == 1:
+ fetchprobes.append(item[0])
+ if probe == "mm" and taildigit == 0:
+ fetchprobes.append(item[0])
+ except:
+ pass
+ if not fetchprobes:
+ return None, None
+ #XZ, 03/05/2009: Xiaodong changed Data to ProbeData
+ query = "SELECT Strain.Name, ProbeData.value, Probe.Name from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE 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.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id and Probe.Name in (%s) order by Strain.Id, Probe.Name " % (probeset,dbId, "'" + string.join(fetchprobes, "', '") +"'")
+ self.cursor.execute(query)
+ traitdata = self.cursor.fetchall()
+ if not traitdata:
+ pass
+ else:
+ nfield = len(fetchprobes)
+ heads = [['ProbeSet'] + [probeset]*nfield]
+ heads.append(['probe'] + fetchprobes)
+ posdict = {}
+ i = 0
+ for item in fetchprobes:
+ posdict[item] = i
+ i += 1
+ prevStrain = ''
+ traitdata2 = []
+ i = -1
+ for item in traitdata:
+ if item[0] != prevStrain:
+ prevStrain = item[0]
+ i += 1
+ traitdata2.append([item[0]] + [None] * nfield)
+ else:
+ pass
+ traitdata2[i][posdict[item[-1]]+1] = item[1]
+
+ traitdata = traitdata2
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col
+ else:
+ heads = [('ProbeSetId', probeset), ('ProbeId',probe)]
+ #XZ, 03/05/2009: Xiaodong changed Data to ProbeData
+ query = "SELECT Strain.Name, ProbeData.value from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet 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.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id" % (probe,probeset,dbId)
+ #print 'Content-type: text/html\n'
+ self.cursor.execute(query)
+ traitdata = self.cursor.fetchall()
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&format=col
+ elif prefix=='ProbeSet': #XZ: probeset data
+ heads = [(headerDict[prefix], probeset)]
+ query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix)
+ self.cursor.execute(query)
+ traitdata = self.cursor.fetchall()
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=10834&db=BXDPublish&format=col
+ elif prefix=='Publish':
+ heads = [(headerDict[prefix], probeset)]
+ #XZ, 03/05/2009: Xiaodong changed Data to PublishData
+ query = "SELECT Strain.Name, PublishData.value from PublishData, Strain, PublishXRef, PublishFreeze WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishFreeze.Id = %d and PublishData.StrainId = Strain.Id" % (probeset, dbId)
+ self.cursor.execute(query)
+ traitdata = self.cursor.fetchall()
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=rs13475701&db=BXDGeno&format=col
+ else: #XZ: genotype data
+ heads = [(headerDict[prefix], probeset)]
+ RISet = self.getRISet(prefix, dbId)
+ self.cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet)
+ speciesId = self.cursor.fetchone()[0]
+ #XZ, 03/05/2009: Xiaodong changed Data to %sData
+ query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.SpeciesId=%s and %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, speciesId, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix)
+ self.cursor.execute(query)
+ traitdata = self.cursor.fetchall()
+ if traitdata:
+ return traitdata, heads
+ else:
+ return None, None
diff --git a/web/webqtl/textUI/cmdCorrelation.py b/web/webqtl/textUI/cmdCorrelation.py
new file mode 100755
index 00000000..04595fc5
--- /dev/null
+++ b/web/webqtl/textUI/cmdCorrelation.py
@@ -0,0 +1,325 @@
+# 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
+from math import *
+import time
+
+import reaper
+
+from base import webqtlConfig
+from utility import webqtlUtil
+from cmdClass import cmdClass
+
+
+#########################################
+# Correlation Class
+#########################################
+class cmdCorrelation(cmdClass):
+
+ calFunction = 'webqtlUtil.calCorrelation'
+
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+
+ if self.accessError:
+ return
+
+ self.searchDB = self.data.getvalue('searchdb')
+ if not self.searchDB or self.error:
+ self.contents.append("###Error: source trait doesn't exist or no target database was given")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ try:
+ self.returnNumber = int(self.data.getvalue('return'))
+ except:
+ self.returnNumber = None
+
+ self.sort = self.data.getvalue('sort')
+
+ prefix, dbId = self.getDBId(self.database)
+ if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ RISet = self.getRISet(prefix, dbId)
+ prefix2, dbId2 = self.getDBId(self.searchDB)
+ if not prefix2 or not dbId2:
+ self.contents.append("###Error: target database doesn't exist.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ RISet2 = self.getRISet(prefix2, dbId2)
+ if RISet2 != RISet:
+ self.contents.append("###Error: target database has different Mouse InbredSet.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ if not traitdata:
+ self.contents.append("###Error: source trait doesn't exist.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ StrainNames = []
+ sourceTrait = []
+ StrainIds = []
+
+ #XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation.
+ for item in traitdata:
+ one_strain_name = item[0]
+ one_strain_value = item[1]
+
+ self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2))
+ Results = self.cursor.fetchall()
+ if Results:
+ StrainIds.append('%d' % Results[0][0])
+ StrainNames.append( one_strain_name )
+ sourceTrait.append( one_strain_value )
+
+ correlationArray = []
+
+ useFastMethod = False
+ if prefix2 == "ProbeSet":
+ DatabaseFileName = self.getFileName( target_db_id=dbId2 )
+ DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists
+ if DatabaseFileName in DirectoryList:
+ useFastMethod = True
+
+ if useFastMethod:
+ datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
+
+ #XZ, 01/08/2009: read the first line
+ line = datasetFile.readline()
+ dataset_strains = webqtlUtil.readLineCSV(line)[1:]
+
+ #XZ, 01/08/2009: This step is critical. It is necessary for this new method.
+ _newvals = []
+ for item in dataset_strains:
+ if item in StrainNames:
+ _newvals.append(sourceTrait[StrainNames.index(item)])
+ else:
+ _newvals.append('None')
+
+ nnCorr = len(_newvals)
+
+
+ for line in datasetFile:
+ traitdata=webqtlUtil.readLineCSV(line)
+ traitdataName = traitdata[0]
+ traitvals = traitdata[1:]
+
+ corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
+ traitinfo = [traitdataName,corr,nOverlap]
+ correlationArray.append( traitinfo )
+
+ #calculate correlation with slow method
+ else:
+ correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) )
+
+ correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step
+
+ if not self.returnNumber:
+ correlationArray = correlationArray[:100]
+ else:
+ if self.returnNumber < len(correlationArray):
+ correlationArray = correlationArray[:self.returnNumber]
+ NN = len(correlationArray)
+ for i in range(NN):
+ nOverlap = correlationArray[i][-1]
+ corr = correlationArray[i][-2]
+ if nOverlap < 3:
+ corrPValue = 1.0
+ else:
+ if abs(corr) >= 1.0:
+ corrPValue = 0.0
+ else:
+ ZValue = 0.5*log((1.0+corr)/(1.0-corr))
+ ZValue = ZValue*sqrt(nOverlap-3)
+ corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
+ correlationArray[i].append(corrPValue)
+ if self.sort == 'pvalue':
+ correlationArray.sort(self.cmpPValue)
+
+ if prefix2 == 'Publish':
+ self.contents.append("RecordID\tCorrelation\t#Strains\tp-value")
+ elif prefix2 == 'Geno':
+ self.contents.append("Locus\tCorrelation\t#Strains\tp-value")
+ else:
+ pass
+
+ if prefix2 == 'Publish' or prefix2 == 'Geno':
+ for item in correlationArray:
+ self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
+ else:
+ id = self.data.getvalue('id')
+ if id == 'yes':
+ self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID")
+ for item in correlationArray:
+ query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
+ self.cursor.execute(query)
+ results = self.cursor.fetchall()
+ if not results:
+ item = item + [None]
+ else:
+ item = item + list(results[0])
+ self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item))
+ elif id == 'only':
+ self.contents.append("GenID")
+ for item in correlationArray:
+ query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
+ self.cursor.execute(query)
+ results = self.cursor.fetchall()
+ if not results:
+ self.contents.append('None')
+ else:
+ self.contents.append(results[0][0])
+ else:
+ self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value")
+ for item in correlationArray:
+ self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
+
+
+
+
+ def getFileName(self, target_db_id):
+
+ query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Id = %s' % target_db_id
+ self.cursor.execute(query)
+ result = self.cursor.fetchone()
+ Id = result[0]
+ FullName = result[1]
+ FullName = FullName.replace(' ','_')
+ FullName = FullName.replace('/','_')
+
+ FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt'
+
+ return FileName
+
+
+
+ def calCorrelation(self,source,target):
+ allcorrelations = []
+ NN = len(source)
+
+ if len(source) != len(target[0]) - 1:
+ return allcorrelations
+ else:
+ for traitData in target:
+ corr,nOverlap = eval("%s(traitData[1:],source,NN)" % self.calFunction)
+ traitinfo = [traitData[0],corr,nOverlap]
+ allcorrelations.append(traitinfo)
+
+ return allcorrelations
+
+ def cmpCorr(self,A,B):
+ try:
+ if abs(A[1]) < abs(B[1]):
+ return 1
+ elif abs(A[1]) == abs(B[1]):
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+ def cmpPValue(self,A,B):
+ try:
+ if A[-1] > B[-1]:
+ return 1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+
+ def readDB(self, StrainIds=[], prefix2='', dbId2=''):
+
+ #retrieve data from target database
+ nnn = len(StrainIds) / 25
+ if len(StrainIds) % 25:
+ nnn += 1
+ oridata = []
+ for step in range(nnn):
+ temp = []
+ StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
+ for item in StrainIdstep:
+ temp.append('T%s.value' % item)
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue
+ if prefix2 == "Publish":
+ query = "SELECT PublishXRef.Id, "
+ dataStartPos = 1
+ query += string.join(temp,', ')
+ query += ' from (PublishXRef, PublishFreeze)\n'
+ #XZ, 03/05/2009: Xiaodong changed Data to PublishData
+ for item in StrainIdstep:
+ query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item)
+ query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d" % (dbId2, )
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=HC_M2_1005_M&return=500&sort=pvalue
+ #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDGeno&return=500&sort=pvalue
+ else:
+ query = "SELECT %s.Name," % prefix2
+ query += string.join(temp,', ')
+ query += ' from (%s, %sXRef, %sFreeze) \n' % (prefix2,prefix2,prefix2)
+ #XZ, 03/05/2009: Xiaodong changed Data to %sData
+ for item in StrainIdstep:
+ query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(prefix2,item,item,prefix2,item,item)
+ query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Id = %d and %s.Id = %sXRef.%sId" % (prefix2, prefix2, prefix2, prefix2, dbId2, prefix2, prefix2, prefix2)
+ self.cursor.execute(query)
+ results = self.cursor.fetchall()
+ if not results:
+ self.contents.append("###Error: target database doesn't exist.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ oridata.append(results)
+
+ datasize = len(oridata[0])
+ targetTrait = []
+ for j in range(datasize):
+ traitdata = list(oridata[0][j])
+ for i in range(1,nnn):
+ traitdata += list(oridata[i][j][1:])
+ targetTrait.append(traitdata)
+
+ return targetTrait
+
diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
new file mode 100755
index 00000000..8dd0f924
--- /dev/null
+++ b/web/webqtl/textUI/cmdGeno.py
@@ -0,0 +1,118 @@
+# 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
+import os
+
+import reaper
+
+from base import webqtlConfig
+from cmdClass import cmdClass
+
+#########################################
+# Geno Class
+#########################################
+class cmdGeno(cmdClass):
+
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+ if self.accessError:
+ return
+ self.error = 0
+ self.RISet = None
+ self.chr = None
+ self.dataset = None
+ self.strainList = []
+ try:
+ self.RISet = self.data.getvalue('riset')
+ if not self.RISet:
+ raise ValueError
+ except:
+ self.error = 1
+ self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
+ return
+ try:
+ self.format = self.data.getvalue('format')[:3]
+ except:
+ self.format = 'row'
+
+ try:
+ self.dataset = reaper.Dataset()
+ try:
+ self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
+ except:
+ self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
+ self.strainList = list(self.dataset.prgy)
+ except:
+ self.error = 1
+ #traceback.print_exc()
+ self.contents.append('###The name of RISet is incorrect')
+ return
+
+ try:
+ self.chr = self.data.getvalue('chr')
+ if self.chr:
+ if self.chr == 'X' or self.chr == 'x':
+ self.chr = '20'
+ self.chr = int(self.chr)
+ except:
+ pass
+
+ self.readGeno()
+
+ def readGeno(self):
+ try:
+ table = [['Chr'] + ['Locus'] + self.strainList]
+ if self.chr:
+ chr = self.dataset[self.chr-1]
+ for locus in chr:
+ items = string.split(string.join(locus.genotext, " "))
+ items = [chr.name] + [locus.name] + items
+ table += [items]
+ else:
+ for chr in self.dataset:
+ for locus in chr:
+ items = string.split(string.join(locus.genotext, " "))
+ items = [chr.name] + [locus.name] + items
+ table += [items]
+ if self.format == 'col':
+ table = [[r[col] for r in table] for col in range(1, len(table[0]))]
+ table[0][0] = 'Line'
+ lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n')
+ self.contents.append(lines)
+ except:
+ self.contents =['###Error: Read file error or name of chromosome is incorrect']
+ #traceback.print_exc()
+ return
+
+
+
diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.py
new file mode 100755
index 00000000..a11c97a3
--- /dev/null
+++ b/web/webqtl/textUI/cmdGet.py
@@ -0,0 +1,86 @@
+# 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 import webqtlConfig
+from cmdClass import cmdClass
+
+#########################################
+# Get trait value Class
+#########################################
+class cmdGet(cmdClass):
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+ if self.accessError:
+ return
+ if not self.error:
+ self.readDB()
+ else:
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+
+ def readDB(self):
+ prefix, dbId = self.getDBId(self.database)
+
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ try:
+ if not traitdata:
+ raise ValueError
+ traitdata = heads + list(traitdata)
+ if self.format == 'col':
+ self.formatCols(traitdata)
+ else:
+ self.formatRows(traitdata)
+ except:
+ self.contents.append('Error: no record was found')
+ self.contents.append(self.accessCode)
+ return
+
+ def formatCols(self, traitdata):
+ for item in traitdata:
+ lines = []
+ for item2 in item:
+ lines.append(item2)
+ lines = string.join(map(str,lines), '\t')
+ self.contents.append(lines)
+
+ def formatRows(self, traitdata):
+ for i in range(len(traitdata[0])):
+ lines = []
+ for j in range(len(traitdata)):
+ lines.append(traitdata[j][i])
+ lines = string.join(map(str,lines), '\t')
+ self.contents.append(lines)
+
+
diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py
new file mode 100755
index 00000000..754ff5b5
--- /dev/null
+++ b/web/webqtl/textUI/cmdHelp.py
@@ -0,0 +1,105 @@
+# 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 import webqtlConfig
+from base.admin import ADMIN_tissue_alias
+from cmdClass import cmdClass
+
+#########################################
+# Help Class
+#########################################
+
+#XZ, 03/23/2009: There are several issues need attention.
+#1. Some probeset datasets are not added into DBList.
+#2. Do NOT show confidential datasets.
+#3. Get rid of ADMIN_tissue_alias. We should use info from database instead.
+
+class cmdHelp(cmdClass):
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+
+ machineParse = self.data.getvalue('parse')
+ topic = self.data.getvalue('topic')
+ if topic:
+ topic = topic.lower()
+ if topic == 'tissue':
+ self.contents.append("%s%s| %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations"))
+ self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)"))
+ self.contents.append("%s|%s" %('_'*50, '_'*40))
+
+ keys = ADMIN_tissue_alias.keys()
+ keys.sort()
+ for key in keys:
+ self.contents.append("%s%s| %s" % (key , ' '*(50-len(key)), string.join(ADMIN_tissue_alias[key], " ")))
+ self.contents.append("%s|%s" %('_'*50, '_'*40))
+ else:
+ pass
+ else:
+ self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use",
+ "#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)]
+ self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time
+ from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
+ DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id and
+ ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id)
+ UNION
+ (SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time
+ from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
+ DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by
+ PublishFreeze.CreateTime ,DBList.Name, DBList.Id)
+ UNION
+ (SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime
+ from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and
+ DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by
+ GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH)
+ dbs = self.cursor.fetchall()
+ if machineParse =="machine":
+ pass
+ else:
+ self.contents.append("\n")
+ self.contents.append("%s%s| %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name"))
+ self.contents.append("%s|%s" %('_'*50, '_'*40))
+ for dbInfo in dbs:
+ self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH))
+ results = self.cursor.fetchall()
+ if not results:
+ pass
+ else:
+ if machineParse =="machine":
+ self.contents.append(results[0][0]+ ',' +dbInfo[2])
+ else:
+ self.contents.append("%s%s| %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2]))
+ self.contents.append("%s|%s" %('_'*50, '_'*40))
+
+
+
diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py
new file mode 100755
index 00000000..0b97c7c3
--- /dev/null
+++ b/web/webqtl/textUI/cmdInterval.py
@@ -0,0 +1,174 @@
+# 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
+import os
+
+import reaper
+
+from base import webqtlConfig
+from cmdClass import cmdClass
+
+#########################################
+# Interval Mapping Class
+#########################################
+class cmdInterval(cmdClass):
+
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+ if self.accessError:
+ return
+ self.sort = None
+ self.step = 0.01
+ self.peak = 1
+ self.chr = None
+ self.sort = None
+ self.returnnumber = 20
+ if self.error:
+ self.error = 1
+ self.contents.append(self.example)
+ return
+ else:
+ try:
+ self.sort = self.data.getvalue('sort')
+ if string.lower(self.sort) == 'pos':
+ self.sort = 'pos'
+ else:
+ self.sort = 'lrs'
+ except:
+ self.sort = None
+
+ try:
+ self.returnnumber = int(self.data.getvalue('return'))
+ except:
+ self.returnnumber = 20
+ try:
+ self.chr = self.data.getvalue('chr')
+ except:
+ self.chr = None
+
+ self.readDB()
+
+ def readDB(self):
+ prefix, dbId = self.getDBId(self.database)
+ if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ RISet = self.getRISet(prefix, dbId)
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ if not traitdata:
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ dataset0 = reaper.Dataset()
+ dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
+ strainList = list(dataset0.prgy)
+ dataset = dataset0.addinterval()
+ if self.chr != None:
+ for _chr in dataset:
+ if string.lower(_chr.name) == string.lower(self.chr):
+ dataset.chromosome = [_chr]
+ break
+
+ strains = []
+ trait = []
+ _prgy = dataset.prgy
+ for item in traitdata:
+ if item[0] in _prgy:
+ strains.append(item[0])
+ trait.append(item[1])
+
+ qtlscan = dataset.regression(strains, trait)
+ LRS = dataset.permutation(strains, trait)
+ nperm = len(LRS)
+
+ #print inter1[0]
+ returnPeak = []
+ nqtl = len(qtlscan)
+ if self.peak:
+ for i in range(nqtl):
+ if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
+ if qtlscan[i].lrs < qtlscan[i+1].lrs:
+ continue
+ elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
+ if qtlscan[i].lrs < qtlscan[i-1].lrs:
+ continue
+ else:
+ if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
+ continue
+ returnPeak.append(qtlscan[i])
+ else:
+ returnPeak = qtlscan[:]
+
+ if returnPeak:
+ self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM")
+ qtlresult = []
+ for item in returnPeak:
+ p_value = reaper.pvalue(item.lrs,LRS)
+ qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
+ if self.sort == 'lrs':
+ qtlresult.sort(self.cmpLRS2)
+ for item in qtlresult:
+ self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
+ else:
+ self.contents.append("###Error: Error occurs while regression.")
+ return
+
+ def cmpPValue(self,A,B):
+ try:
+ if A[-1] > B[-1]:
+ return 1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+ def cmpLRS2(self,A,B):
+ try:
+ if A[1] < B[1]:
+ return 1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+
diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py
new file mode 100755
index 00000000..1fbff5a5
--- /dev/null
+++ b/web/webqtl/textUI/cmdMap.py
@@ -0,0 +1,144 @@
+# 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
+import os
+
+import reaper
+
+from base import webqtlConfig
+from cmdClass import cmdClass
+
+
+#########################################
+# Mapping Class
+#########################################
+class cmdMap(cmdClass):
+
+ def __init__(self,fd=None):
+
+ cmdClass.__init__(self,fd)
+
+ if not webqtlConfig.TEXTUI:
+ self.contents.append("Please send your request to http://robot.genenetwork.org")
+ return
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+ if self.accessError:
+ return
+ try:
+ self.returnnumber = int(self.data.getvalue('return'))
+ except:
+ self.returnnumber = None
+
+ if self.error:
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ else:
+ self.sort = self.data.getvalue('sort')
+ self.readDB()
+
+ def readDB(self):
+ prefix, dbId = self.getDBId(self.database)
+ if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ RISet = self.getRISet(prefix, dbId)
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ if not traitdata:
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ dataset = reaper.Dataset()
+ dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
+ strainList = list(dataset.prgy)
+
+ strains = []
+ trait = []
+ _prgy = dataset.prgy
+ for item in traitdata:
+ if item[0] in _prgy:
+ strains.append(item[0])
+ trait.append(item[1])
+
+ qtlscan = dataset.regression(strains, trait)
+ LRS = dataset.permutation(strains, trait)
+ nperm = len(LRS)
+ if qtlscan:
+ self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value")
+ qtlresult = []
+ if self.returnnumber:
+ self.returnnumber = min(self.returnnumber,len(qtlscan))
+ if self.sort == 'lrs':
+ qtlscan.sort(self.cmpLRS)
+ for item in qtlscan[:self.returnnumber]:
+ p_value = reaper.pvalue(item.lrs,LRS)
+ qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
+ else:#sort by position
+ qtlscan2 = qtlscan[:]
+ qtlscan2.sort(self.cmpLRS)
+ LRSthresh = qtlscan2[self.returnnumber].lrs
+ for item in qtlscan:
+ if item.lrs >= LRSthresh:
+ p_value = reaper.pvalue(item.lrs,LRS)
+ qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
+ else:
+ for item in qtlscan:
+ p_value = reaper.pvalue(item.lrs,LRS)
+ qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
+ if self.sort == 'lrs':
+ qtlresult.sort(self.cmpLRS2)
+ for item in qtlresult:
+ self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item)
+ else:
+ self.contents.append("###Error: Error occurs while regression.")
+ return
+
+ def cmpLRS(self,A,B):
+ try:
+ if A.lrs < B.lrs:
+ return 1
+ elif A.lrs == B.lrs:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+ def cmpLRS2(self,A,B):
+ try:
+ if A[1] < B[1]:
+ return 1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
diff --git a/web/webqtl/textUI/cmdSearchGene.py b/web/webqtl/textUI/cmdSearchGene.py
new file mode 100755
index 00000000..c2c71815
--- /dev/null
+++ b/web/webqtl/textUI/cmdSearchGene.py
@@ -0,0 +1,70 @@
+# 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 cmdClass import cmdClass
+from search.TextSearchPage import TextSearchPage
+
+#########################################
+# Search Gene Symbol PAGE
+#########################################
+class cmdSearchGene(cmdClass):
+ def __init__(self,fd):
+ #example
+ cmdClass.__init__(self,fd)
+ self.page = None
+ self.text = ""
+ fd.geneName = fd.formdata.getvalue('gene')
+ fd.returnFmt = fd.formdata.getvalue('format', 'html')
+ if fd.geneName:
+ fd.geneName = string.strip(fd.geneName)
+ fd.refseq = fd.formdata.getvalue('refseq')
+ if fd.refseq:
+ fd.refseq = string.strip(fd.refseq)
+ fd.genbankid = fd.formdata.getvalue('genbankid')
+ if fd.genbankid:
+ fd.genbankid = string.strip(fd.genbankid)
+ fd.geneid = fd.formdata.getvalue('geneid')
+ if fd.geneid:
+ fd.geneid = string.strip(fd.geneid)
+ if 1:
+ if not (fd.geneName or fd.refseq or fd.genbankid or fd.geneid):
+ raise "ValueError"
+ fd.searchAlias = fd.formdata.getvalue('alias')
+ if fd.searchAlias != '1':
+ fd.searchAlias = None
+ self.page = TextSearchPage(fd)
+ if fd.returnFmt != 'text':
+ pass
+ else:
+ self.text = self.page.output
+ self.page = None
+ elif "ValueError":
+ self.text = "You need to submit a Gene name, a Refseq ID, or a GenBank ID"
+ else:
+ self.text = "Error occurs while searching the database"
+
diff --git a/web/webqtl/textUI/cmdShowEditing.py b/web/webqtl/textUI/cmdShowEditing.py
new file mode 100755
index 00000000..918e83a7
--- /dev/null
+++ b/web/webqtl/textUI/cmdShowEditing.py
@@ -0,0 +1,50 @@
+# 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
+
+from cmdClass import cmdClass
+from showTrait.ShowTraitPage import ShowTraitPage
+
+
+#########################################
+# SHOW DATA-EDITING PAGE
+#########################################
+class cmdShowEditing(cmdClass):
+ def __init__(self,fd):
+ ###example = http://www.webqtl.org/cgi-bin/beta/WebQTL?cmd=snp&chr=1&start=0&end=21345677
+ cmdClass.__init__(self,fd)
+ self.page = None
+ prefix, dbId = self.getDBId(self.database)
+ try:
+ if not prefix or not dbId:
+ raise ValueError
+ self.cursor.execute('SELECT Name from %sFreeze WHERE Id=%d' % (prefix, dbId))
+ database = self.cursor.fetchall()[0][0]
+ traitInfos = (database,self.probeset,self.probe)
+ self.page = ShowTraitPage(fd,traitInfos)
+ #self = page
+ except:
+ print "Database Name Incorrect"
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 14:08:55 +0000