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09-cd2-resultSummariser-exampleRun.py
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09-cd2-resultSummariser-exampleRun.py
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#!/usr/bin/env python3
import pandas as pd
import numpy as np
import sqlite3, json, pathlib, math
import libPrint
# Declaration of sample-dependent variables
configList = [
{
"branch" : ["speciesTreatment"],
"method" : "gffRead",
"control" : "control",
"group" : ["treat1","treat2","treat3","treat4"], # without control
"compare" : [ ["treat2","treat1"],["treat4","treat3"],["treat2","treat3"],["treat1","treat4"] ],
"note" : "All",
"annotate" : "speciesDatabase",
"trim" : "trimQ30",
"omic" : "transcript",
"attribute" : {
'description' : 'userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-attribute-description.json',
'homolog' : 'userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-attribute-homolog.json',
"GO" : "userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-GO-gene2term.json",
"KO" : "userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-KO-gene2term.json",
"EC" : "userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-EC-gene2term.json",
"TF" : "userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-TF-gene2term.json",
"SR" : "userData/08-an-annotateTranscriptome/speciesTreatment-gffRead/speciesDatabase-transcript-SR-gene2term.json",
}
},
{
"branch" : ["speciesTreatment2"],
"method" : "gffRead",
"control" : "Normal",
"group" : ["treatI","treatJ"], # without control
"compare" : [["treatI","treatJ"]],
"note" : "All",
"annotate" : "speciesDatabase",
"trim" : "trimQ30",
"omic" : "transcript",
"attribute" : {
'description' : 'userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-attribute-description.json',
'homolog' : 'userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-attribute-homolog.json',
"GO" : "userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-GO-gene2term.json",
"KO" : "userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-KO-gene2term.json",
"EC" : "userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-EC-gene2term.json",
"TF" : "userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-TF-gene2term.json",
"SR" : "userData/08-an-annotateTranscriptome/speciesTreatment2-gffRead/speciesDatabase-transcript-SR-gene2term.json",
}
},
]
# Don't touch the code below if you don't know how it works
sourceFilePathStr = 'userData/09-cd-transcriptomeSummary/{branch}-{method}/{annotate}-{trim}-{omic}Expression.db'
resultFilePathStr = 'userData/09-cd-transcriptomeSummary/{branch}-{method}-{annotate}-{trim}/ExpressionSummary-{note}-{omic}'
namePairFilePathStr = 'userData/09-cd-transcriptomeSummary/{branch}-{method}-{annotate}-{trim}/NamePair-{note}-{omic}.json'
logFolderPathStr = 'userData/09-cd-transcriptomeSummary/{branch}-{method}-{annotate}-{trim}/'
logFilePathStr = 'ExpressionSummary-{note}-{omic}'
for configDict in configList:
branchList = configDict.get("branch",[])
methodStr = configDict.get("method","")
annotateStr = configDict.get("annotate","")
trimStr = configDict.get("trim","")
omicStr = configDict.get("omic","")
noteStr = configDict.get("note","")
controlStr = configDict.get("control","")
groupList = configDict.get("group",[])
compareList = configDict.get("compare",[])
compareCStr = "; ".join([ "\t".join(sorted(x)) for x in compareList ])
attriDict = configDict.get("attribute",dict())
descriDict = dict()
descriList = list(attriDict.keys())
for labelStr in descriList:
labelDict = json.load(open(attriDict[labelStr]))
descriDict.update({ labelStr : labelDict })
for branchStr in branchList:
infoDict = {
"branch" : branchStr,
"method" : methodStr,
"annotate" : annotateStr,
"trim" : trimStr,
"omic" : omicStr,
"note" : noteStr
}
sourcePathStr = sourceFilePathStr.format(**infoDict)
resultPathStr = resultFilePathStr.format(**infoDict)
logFolderPath = logFolderPathStr.format(**infoDict)
logPathStr = logFilePathStr.format(**infoDict)
pathlib.Path( logFolderPath ).mkdir(parents=True,exist_ok=True)
Print = libPrint.timer()
Print.logFilenameStr = logPathStr
Print.folderStr = logFolderPath
Print.testingBool = False
Print.startLog()
Print.printing("branch = {branch}\nmethod = {method}\nannotate = {annotate}\ntrim = {trim}\ntype = {omic}".format(**infoDict))
Print.printing("[SQL-load] open expression database")
Connect = sqlite3.connect(sourcePathStr)
Cursor = Connect.cursor()
selectStr = "SELECT * FROM Expression"
expExc = Cursor.execute(selectStr)
Print.printing("[Compare] adjust combination")
columnSet = {'[Object ID]'}
resultDict = dict()
countInt = 0
for expList in expExc:
tempList = list(expList)
testIDStr = tempList[1]
geneidStr = tempList[2]
sampleAStr = tempList[5]
sampleBStr = tempList[6]
sampleStr = "\t".join(sorted([sampleAStr, sampleBStr]))
testStr = tempList[7]
fpkmAFlt = tempList[8]
fpkmBFlt = tempList[9]
foldFlt = tempList[10]
pvFlt = tempList[12]
qvFlt = tempList[13]
sigStr = tempList[14]
errorInt = 0
subDict = resultDict.get(testIDStr,dict())
# haveSignalBool = (fpkmAFlt > 0) or (fpkmBFlt > 0)
# if controlStr in sampleStr and haveSignalBool:
if controlStr in sampleStr:
if sampleAStr == controlStr:
aStr = sampleAStr
bStr = sampleBStr
faFlt = fpkmAFlt
fbFlt = fpkmBFlt
fcFlt = foldFlt
diFlt = fbFlt - faFlt
elif sampleBStr == controlStr:
aStr = sampleBStr
bStr = sampleAStr
faFlt = fpkmBFlt
fbFlt = fpkmAFlt
fcFlt = foldFlt * -1
diFlt = fbFlt - faFlt
else:
errorInt = errorInt + 1
print("[ERROR{}:A!=Control,B!=Control]".format(str(errorInt)))
if faFlt == 0.0:
logaEle = "noSignal"
else:
logaEle = math.log10(faFlt)
if fbFlt == 0.0:
logbEle = "noSignal"
else:
logbEle = math.log10(fbFlt)
inputDict = {
'[Gene ID]' : geneidStr,
"[FPKM:{}]".format(aStr) : faFlt,
"[FPKM:{}]".format(bStr) : fbFlt,
"[log10(FPKM:{})]".format(aStr) : logaEle,
"[log10(FPKM:{})]".format(bStr) : logbEle,
"[diff:{}-{}]".format(bStr,aStr) : diFlt,
"[ratio:{}/{}]".format(bStr,aStr) : fcFlt,
"[pass:{}/{}]".format(bStr,aStr) : testStr,
"[pVal:{}/{}]".format(bStr,aStr) : pvFlt,
"[qVal:{}/{}]".format(bStr,aStr) : qvFlt,
"[signi:{}/{}]".format(bStr,aStr) : sigStr,
}
subDict.update(inputDict)
columnSet.update(set(inputDict.keys()))
resultDict.update({ testIDStr : subDict })
# elif sampleStr in compareCStr and haveSignalBool:
elif sampleStr in compareCStr:
for compareSubList in compareList:
baseStr = compareSubList[0]
elemStr = compareSubList[1]
if (baseStr in sampleStr) and (elemStr in sampleStr):
if sampleAStr == baseStr:
aStr = sampleAStr
bStr = sampleBStr
faFlt = fpkmAFlt
fbFlt = fpkmBFlt
fcFlt = foldFlt
diFlt = fbFlt - faFlt
elif sampleBStr == baseStr:
aStr = sampleBStr
bStr = sampleAStr
faFlt = fpkmBFlt
fbFlt = fpkmAFlt
fcFlt = foldFlt * -1
diFlt = fbFlt - faFlt
else:
errorInt = errorInt + 1
print("[ERROR{}:A!=Control,B!=Control]".format(str(errorInt)))
inputDict = {
"[compare:{}/{}]".format(bStr,aStr) : fcFlt,
"[diff:{}-{}]".format(bStr,aStr) : diFlt,
"[pass:{}/{}]".format(bStr,aStr) : testStr,
"[pVal:{}/{}]".format(bStr,aStr) : pvFlt,
"[qVal:{}/{}]".format(bStr,aStr) : qvFlt,
"[signi:{}/{}]".format(bStr,aStr) : sigStr,
}
subDict.update(inputDict)
columnSet.update(set(inputDict.keys()))
resultDict.update({ testIDStr : subDict })
countInt = countInt + 1
print("[{}]".format(countInt),end='\r')
print("")
Print.printing("[Finish] scan throught {} lines (with \"OK\")".format(str(countInt)))
Connect.close()
Print.printing("[Organise] create list of column names")
columnList = ['[Object ID]','[Gene ID]']
columnList.extend(descriList)
columnList.append("[FPKM:{}]".format(controlStr))
columnList.extend(["[FPKM:{}]".format(x) for x in groupList])
columnList.append("[log10(FPKM:Total)]")
columnList.append("[log10(FPKM:{})]".format(controlStr))
sampleSectionList = [
"[diff:{}-{}]",
"[ratio:{}/{}]",
"[pass:{}/{}]",
"[pVal:{}/{}]",
"[qVal:{}/{}]",
"[signi:{}/{}]",
]
for groupStr in groupList:
columnList.append("[log10(FPKM:{})]".format(groupStr))
for sampleSectionStr in sampleSectionList:
columnList.append(sampleSectionStr.format(groupStr,controlStr))
compareSectionList = [
"[diff:{}-{}]",
"[compare:{}/{}]",
"[pass:{}/{}]",
"[pVal:{}/{}]",
"[qVal:{}/{}]",
"[signi:{}/{}]",
]
for compareSubList in compareList:
for compareSectionStr in compareSectionList:
baseStr = compareSubList[0]
elemStr = compareSubList[1]
columnList.append(compareSectionStr.format(elemStr,baseStr))
Print.printing("[Arrange] fill the values into DataFrame")
testList = list(resultDict.keys())
nameListDict = dict()
resultDF = pd.DataFrame(index=range(len(testList)), columns=columnList)
for rowInt in range(len(testList)):
print("[{}/{}]".format(str(rowInt),str(len(testList))),end="\r")
testStr = testList[rowInt]
resultDF.at[rowInt, '[Object ID]'] = testStr
valueDict = resultDict[testList[rowInt]]
geneIDStr = valueDict.get(columnList[1],np.NaN)
if testStr != geneIDStr:
nameListDict.update({ testStr : geneIDStr })
for titleStr in [ x for x in columnList if x != '[Object ID]' ]:
resultDF.at[rowInt, titleStr] = valueDict.get(titleStr,np.NaN)
sumFlt = 0.0
fpkmList = [ x for x in columnList if "[FPKM:" in x ]
for titleStr in fpkmList:
sumFlt = sumFlt + valueDict.get(titleStr,np.NaN)
if sumFlt == 0.0:
resultDF.at[rowInt, "[log10(FPKM:Total)]"] = "noSignal"
else:
resultDF.at[rowInt, "[log10(FPKM:Total)]"] = math.log10(sumFlt)
for labelStr in descriList:
descriEle = descriDict.get(labelStr,dict()).get(testStr,np.NaN)
if type(descriEle) == type(list()):
descriStr = "; ".join(descriEle)
elif type(descriEle) == type(str()):
descriStr = descriEle
else:
descriStr = np.NaN
resultDF.at[rowInt, labelStr] = descriStr
print("")
Print.printing("[Export] export as expressionSummary.db")
if pathlib.Path(resultPathStr+".db").exists():
pathlib.Path(resultPathStr+".db").unlink()
Connect = sqlite3.connect(resultPathStr+".db")
resultDF.to_sql(name='Summary', con=Connect)
Connect.commit()
Connect.close()
Print.printing("[Export] export as expressionSummary.tsv")
resultDF.to_csv(resultPathStr+".tsv", index=False, sep='\t', encoding='utf-8')
if nameListDict != dict():
Print.printing("[Export] export namePair.json")
with open(namePairFilePathStr.format(**infoDict),"w") as targetHandle:
json.dump(nameListDict,targetHandle,indent=1)
Print.stopLog()
print("\n")