From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 8 May 2012 18:39:56 -0500 Subject: Add all the source codes into the github. --- web/webqtl/textUI/__init__.py | 0 web/webqtl/textUI/cmdClass.py | 224 +++++++++++++++++++++++++ web/webqtl/textUI/cmdCorrelation.py | 325 ++++++++++++++++++++++++++++++++++++ web/webqtl/textUI/cmdGeno.py | 118 +++++++++++++ web/webqtl/textUI/cmdGet.py | 86 ++++++++++ web/webqtl/textUI/cmdHelp.py | 105 ++++++++++++ web/webqtl/textUI/cmdInterval.py | 174 +++++++++++++++++++ web/webqtl/textUI/cmdMap.py | 144 ++++++++++++++++ web/webqtl/textUI/cmdSearchGene.py | 70 ++++++++ web/webqtl/textUI/cmdShowEditing.py | 50 ++++++ 10 files changed, 1296 insertions(+) create mode 100755 web/webqtl/textUI/__init__.py create mode 100755 web/webqtl/textUI/cmdClass.py create mode 100755 web/webqtl/textUI/cmdCorrelation.py create mode 100755 web/webqtl/textUI/cmdGeno.py create mode 100755 web/webqtl/textUI/cmdGet.py create mode 100755 web/webqtl/textUI/cmdHelp.py create mode 100755 web/webqtl/textUI/cmdInterval.py create mode 100755 web/webqtl/textUI/cmdMap.py create mode 100755 web/webqtl/textUI/cmdSearchGene.py create mode 100755 web/webqtl/textUI/cmdShowEditing.py (limited to 'web/webqtl/textUI') diff --git a/web/webqtl/textUI/__init__.py b/web/webqtl/textUI/__init__.py new file mode 100755 index 00000000..e69de29b 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 : %s%s?cmd=help' % (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 '
%s
' % 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 : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue' % (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 : %s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all' % (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 : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12' % (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 : %s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20' % (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" + -- cgit v1.2.3