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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 2010/11/10
#
# Last updated by Ning Liu, 2011/01/26
#tissueCorrelationMatrix: funciton part for TissueCorrelationPage.py
from htmlgen import HTMLgen2 as HT
from correlation import correlationFunction
from dbFunction import webqtlDatabaseFunction
import sys
#########################################
# Tissue Correlation Page
#########################################
class tissueCorrelationMatrix:
def __init__(self,tissueProbeSetFreezeId=None):
#initialize parameters
self.tProbeSetFreezeId = tissueProbeSetFreezeId
self.cursor = webqtlDatabaseFunction.getCursor()
#retreive dataSet info from database table TissueProbeSetFreeze to get all TissueProbeSetFreezeId(List), Name(List) and FullName(List)
def getTissueDataSet(self):
tissProbeSetFreezeIds,Names,fullNames = webqtlDatabaseFunction.getTissueDataSet(cursor=self.cursor)
return tissProbeSetFreezeIds,Names,fullNames
#retrieve DatasetName, DatasetFullName based on TissueProbeSetFreezeId, return DatasetName(string), DatasetFullName(string)
def getFullnameofCurrentDataset(self):
DatasetName, DatasetFullName =webqtlDatabaseFunction.getDatasetNamesByTissueProbeSetFreezeId(cursor=self.cursor, TissueProbeSetFreezeId=self.tProbeSetFreezeId)
return DatasetName, DatasetFullName
#retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId, return TissueCount(int)
def getTissueCountofCurrentDataset(self):
TissueCount =webqtlDatabaseFunction.getTissueCountByTissueProbeSetFreezeId(cursor=self.cursor,TissueProbeSetFreezeId=self.tProbeSetFreezeId)
return TissueCount
#retrieve corrArray(array), pvArray(array) for display by calling calculation function:calZeroOrderCorrForTiss
def getTissueCorrPvArray(self,geneNameLst=None,dataIdDict=None):
#retrieve SymbolValuePairDict(Dict), dictionary of Symbol and Value Pair.key is symbol, value is one list of expression values of one probeSet
symbolValuepairDict =correlationFunction.getGeneSymbolTissueValueDict(cursor=self.cursor,symbolList=geneNameLst,dataIdDict=dataIdDict)
corrArray,pvArray = correlationFunction.getCorrPvArray(cursor=self.cursor,priGeneSymbolList=geneNameLst,symbolValuepairDict=symbolValuepairDict)
return corrArray,pvArray
#retrieve symbolList,geneIdList,dataIdList,ChrList,MbList,descList,pTargetDescList (all are list type) to
#get multi lists for short and long label functions, and for getSymbolValuePairDict and
#getGeneSymbolTissueValueDict to build dict to get CorrPvArray
def getTissueProbeSetXRefInfo(self,GeneNameLst=[]):
symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict =correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=self.tProbeSetFreezeId)
return symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict
#retrieve corrArray(array), pvArray(array) for gene symbol pair
def getCorrPvArrayForGeneSymbolPair(self,geneNameLst=None):
corrArray = None
pvArray = None
if len(geneNameLst) == 2:
#retrieve SymbolValuePairDict(Dict), dictionary of Symbol and Value Pair.key is symbol, value is one list of expression values of one probeSet
symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict =correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=geneNameLst,TissueProbeSetFreezeId=self.tProbeSetFreezeId)
symbolValuepairDict =correlationFunction.getGeneSymbolTissueValueDict(cursor=self.cursor,symbolList=geneNameLst,dataIdDict=dataIdDict)
corrArray,pvArray = correlationFunction.getCorrPvArray(cursor=self.cursor,priGeneSymbolList=geneNameLst,symbolValuepairDict=symbolValuepairDict)
return corrArray,pvArray
#retrieve symbolCorrDict(dict), symbolPvalueDict(dict) to get all tissues' correlation value and P value; key is symbol
def calculateCorrOfAllTissueTrait(self, primaryTraitSymbol=None, method='0'):
symbolCorrDict, symbolPvalueDict = correlationFunction.calculateCorrOfAllTissueTrait(cursor=self.cursor, primaryTraitSymbol=primaryTraitSymbol, TissueProbeSetFreezeId=self.tProbeSetFreezeId,method=method)
return symbolCorrDict, symbolPvalueDict
#Translate GeneId to gene symbol and keep the original order.
def getGeneSymbolLst(self, geneSymbols=None):
geneSymbolLst=[]
geneIdLst=[]
#split the input string at every occurrence of the delimiter '\r', and return the substrings in an array.
tokens=geneSymbols.strip().split('\r')
#Ning: To keep the original order of input symbols and GeneIds
for i in tokens:
i=i.strip()
if (len(i) >0) and (i not in geneSymbolLst):
geneSymbolLst.append(i)
# if input includes geneId(s), then put it/them into geneIdLst
if i.isdigit():
geneIdLst.append(i)
#Ning: Replace GeneId with symbol if applicable
if len(geneIdLst)>0:
# if input includes geneId(s), replace geneId by geneSymbol;
geneIdSymbolPair =webqtlDatabaseFunction.getGeneIdSymbolPairByGeneId(cursor=self.cursor, geneIdLst =geneIdLst)
for geneId in geneIdLst:
if geneIdSymbolPair[geneId]:
index = geneSymbolLst.index(geneId)
geneSymbolLst[index] =geneIdSymbolPair[geneId]
return geneSymbolLst
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