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libImport.py
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libImport.py
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#!/usr/bin/env python3
import pathlib, sqlite3
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import libConfig, libPrint
class sqlImporter:
def __init__(self):
self.branchStr = ""
self.testingBool = False
self.expressionInputDict = {
"sqlPath" : str(),
"count" : int(),
"rowList" : list(),
"createCommand" : str(),
"insertCommand" : str(),
}
def exportingExpression(self,clPrint):
sqlPath = self.expressionInputDict.get("sqlPath",str())
countInt = self.expressionInputDict.get("count",int())
rowList = self.expressionInputDict.get("rowList",list())
createCommandStr = self.expressionInputDict.get("createCommand",str())
insertCommandStr = self.expressionInputDict.get("insertCommand",str())
Connect = sqlite3.connect(sqlPath)
Cursor = Connect.cursor()
clPrint.printing("[SQLite3:CreateTable] "+sqlPath)
ReturnMsg = Cursor.execute(createCommandStr) # pylint: disable=unused-variable
Connect.commit()
clPrint.printing("[SQLite3:FinishCreating]")
for rowInt in range(countInt):
insertList = []
sourceList = rowList[rowInt]
insertList.append("UUID."+str(rowInt))
insertList.extend(sourceList)
ReturnMsg = Cursor.execute(insertCommandStr,insertList)
Connect.commit()
clPrint.printing("[SQLite3:Insert] "+sqlPath)
Connect.close()
clPrint.printing("[SQLite3:Close]\n")
self.expressionInputDict = {
"sqlPath" : str(),
"count" : int(),
"rowList" : list(),
"createCommand" : str(),
"insertCommand" : str(),
}
def importingStringtie(self):
# ---- Initialization for Converting ----
Target = libConfig.config()
Target.queryStr = self.branchStr
Target.folderStr = "config/"
Target.modeStr = "UPDATE"
Target.load()
branchStr = self.branchStr
controlStr = Target.storeDict.get("controlSample","")
controlSafeStr = controlStr.replace("-","_")
groupList = Target.storeDict.get("group",[])
replicationList = Target.storeDict.get("replication",[])
patternStr = Target.storeDict.get("samplePattern","")
sampleList = list()
for groupStr in groupList:
for replicationStr in replicationList:
sampleList.append(patternStr.format(group=groupStr,replication=replicationStr))
conditionList = Target.storeDict.get("conditionList",[])
methodList = Target.storeDict.get("methodList",[])
geneSourceDict = Target.storeDict.get("[sqlite]geneSourceDict",dict())
transcriptSourceDict = Target.storeDict.get("[sqlite]transcriptSourceDict",dict())
geneExpPathStr = Target.storeDict.get("[sqlite]geneSourcePathStr","")
transcriptExpPathStr = Target.storeDict.get("[sqlite]transcriptSourcePathStr","")
sqlFolderStr = Target.storeDict.get("sqlFolderStr","")
sqlPathStr = Target.storeDict.get("sqlPathStr","")
sqlLogStr = Target.storeDict.get("[sqlite]logFilename","")
for methodStr in methodList:
pathlib.Path( sqlFolderStr.format(branch=branchStr,method=methodStr) ).mkdir(parents=True,exist_ok=True)
geneFolderStr = geneSourceDict.get(methodStr,"")
transcriptFolderStr = transcriptSourceDict.get(methodStr,"")
compareSet = set()
for conditionTup in conditionList:
antStr = conditionTup[0]
trimStr = conditionTup[1]
Print = libPrint.timer()
Print.logFilenameStr = sqlLogStr.format(ant=antStr,trim=trimStr)
Print.folderStr = sqlFolderStr.format(branch=branchStr,method=methodStr)
Print.testingBool = self.testingBool
Print.startLog()
for sampleStr in sampleList:
sampleSafeStr = sampleStr.replace("-","_")
Print.phraseStr = "-- Data format conversion for Gene Expression in {} --".format(sampleStr)
Print.printTimeStamp()
geneSamplePath = geneExpPathStr.format(
folder=geneFolderStr,
branch=branchStr,
ant=antStr,
trim=trimStr,
sample=sampleStr
)
sampleDF = pd.read_csv(geneSamplePath,delimiter="\t",header=0)
Print.printing("[Pandas:Read]"+geneSamplePath)
rowList = sampleDF.values.tolist()
countInt = len(rowList)
# check
compareList = list()
for rowInt in range(countInt):
insertList = []
sourceList = rowList[rowInt]
insertList.append("UUID."+str(rowInt))
insertList.extend(sourceList[0:7])
compareStr = "\t".join([str(x) for x in insertList])
compareList.append(compareStr)
if compareSet == set():
Print.printing(" "+sampleStr+": Empty")
compareSet = set(compareList)
elif compareSet != set(compareList):
Print.printing(" "+sampleStr+": Same")
elif compareSet == set(compareList):
Print.printing(" "+sampleStr+": Different")
sqlPath = sqlPathStr.format(branch=branchStr,method=methodStr,ant=antStr,trim=trimStr)
createCommandStr = """CREATE TABLE GeneExpression_{}
('UUID' TEXT PRIMARY KEY NOT NULL,
'GeneID' TEXT NOT NULL,
'GeneName' TEXT NOT NULL,
'Reference' TEXT NOT NULL,
'Strand' TEXT NOT NULL,
'Start' INTEGER NOT NULL,
'End' INTEGER NOT NULL,
'Coverage' REAL NOT NULL,
'FPKM' REAL NOT NULL,
'TPM' REAL NOT NULL);""".format(sampleSafeStr)
insertCommandStr = "INSERT INTO GeneExpression_{} ('UUID','GeneID','GeneName','Reference','Strand','Start','End','Coverage','FPKM','TPM')\
VALUES (?,?,?,?,?,?,?,?,?,?)".format(sampleSafeStr)
self.expressionInputDict = {
"sqlPath" : sqlPath,
"count" : countInt,
"rowList" : rowList,
"createCommand" : createCommandStr,
"insertCommand" : insertCommandStr,
}
self.exportingExpression(Print)
# Transcript
Print.phraseStr = "-- Data format conversion for Transcript Expression in {} --".format(sampleStr)
Print.printTimeStamp()
transcriptSamplePath = transcriptExpPathStr.format(
folder=transcriptFolderStr,
branch=branchStr,
ant=antStr,
trim=trimStr,
sample=sampleStr
)
sampleDF = pd.read_csv(transcriptSamplePath,delimiter="\t",header=0)
Print.printing("[Pandas:Read] "+transcriptSamplePath)
rowList = sampleDF.values.tolist()
countInt = len(rowList)
# check
compareList = list()
for rowInt in range(countInt):
insertList = []
sourceList = rowList[rowInt]
insertList.append("UUID."+str(rowInt))
insertList.extend(sourceList[0:10])
compareStr = "\t".join([str(x) for x in insertList])
compareList.append(compareStr)
if compareSet == set():
Print.printing(" "+sampleStr+": Empty")
compareSet = set(compareList)
elif compareSet != set(compareList):
Print.printing(" "+sampleStr+": Same")
elif compareSet == set(compareList):
Print.printing(" "+sampleStr+": Different")
sqlPath = sqlPathStr.format(branch=branchStr,method=methodStr,ant=antStr,trim=trimStr)
createCommandStr = """CREATE TABLE TranscriptExpression_{}
('UUID' TEXT PRIMARY KEY NOT NULL,
'TranscriptID' INTEGER NOT NULL,
'Chromosome' TEXT,
'Strand' TEXT NOT NULL,
'Start' INTEGER NOT NULL,
'End' INTEGER NOT NULL,
'TranscriptName' TEXT NOT NULL,
'ExonCount' INTEGER NOT NULL,
'Length' INTEGER NOT NULL,
'GeneID' TEXT NOT NULL,
'GeneName' TEXT NOT NULL,
'Coverage' REAL NOT NULL,
'FPKM' REAL NOT NULL);""".format(sampleSafeStr)
insertCommandStr = "INSERT INTO TranscriptExpression_{} ('UUID','TranscriptID','Chromosome','Strand','Start','End','TranscriptName','ExonCount','Length','GeneID','GeneName','Coverage','FPKM')\
VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)".format(sampleSafeStr)
self.expressionInputDict = {
"sqlPath" : sqlPath,
"count" : countInt,
"rowList" : rowList,
"createCommand" : createCommandStr,
"insertCommand" : insertCommandStr,
}
self.exportingExpression(Print)
Print.phraseStr = "-- Summarising for Gene Expression --"
Print.printTimeStamp()
createComStr = "CREATE TABLE GeneExpressionSummary ({})"
createColumnList = [
"'UUID' TEXT PRIMARY KEY NOT NULL",
"'GeneID' TEXT",
"'GeneName' TEXT",
]
insertColumnList = ["UUID", "GeneID", "GeneName"]
for targetStr in ["FPKM","TPM"]:
for sampleStr in sampleList:
sampleSafeStr = sampleStr.replace("-","_")
columnStr = "{target}_{sample} REAL".format(target=targetStr,sample=sampleSafeStr)
createColumnList.append(columnStr)
insertColumnList.append("{target}_{sample}".format(target=targetStr,sample=sampleSafeStr))
Connect = sqlite3.connect(sqlPath)
Cursor = Connect.cursor()
ReturnMsg = Cursor.execute(createComStr.format(",".join(createColumnList))) # pylint: disable=unused-variable
Connect.commit()
Print.printing("[SQLite3:CreateTable] "+sqlPath)
resultDict = dict()
controlExc = Cursor.execute("SELECT UUID, GeneID, GeneName from GeneExpression_{}".format(controlSafeStr))
for rowList in controlExc:
uuid, geneid, genename = rowList
subDict = {
"UUID" : uuid,
"GeneID" : geneid,
"GeneName" : genename
}
resultDict.update({ uuid : subDict })
for sampleStr in sampleList:
sampleSafeStr = sampleStr.replace("-","_")
sampleExc = Cursor.execute("SELECT UUID, FPKM, TPM from GeneExpression_{}".format(sampleSafeStr))
for rowList in sampleExc:
uuid, fpkm, tpm = rowList
subDict = resultDict[uuid]
subDict.update({
"FPKM_{}".format(sampleSafeStr) : fpkm,
"TPM_{}".format(sampleSafeStr) : tpm
})
resultDict.update({ uuid : subDict })
insertComStr = "INSERT INTO GeneExpressionSummary ({column}) VALUES ({value})"
for uuid in resultDict.keys():
valueList = list()
for posInt in range(len(insertColumnList)):
valueList.append(resultDict[uuid][insertColumnList[posInt]])
insertCommand = insertComStr.format(column=",".join(insertColumnList),value=(("?,"*(len(valueList)-1)))+"?")
ReturnMsg = Cursor.execute(insertCommand,valueList)
Connect.commit()
Print.printing("[SQLite3:Insert] "+sqlPath)
Connect.close()
Print.printing("[SQLite3:Close]\n")
# Transcript
Print.phraseStr = "-- Summarising for Gene Expression --"
Print.printTimeStamp()
createComStr = "CREATE TABLE TranscriptExpressionSummary ({})"
createColumnList = [
"'UUID' TEXT PRIMARY KEY NOT NULL",
"'TranscriptID' INTEGER",
"'TranscriptName' TEXT",
"'GeneID' TEXT",
"'GeneName' TEXT",
]
insertColumnList = ["UUID", "TranscriptID", "TranscriptName", "GeneID", "GeneName"]
for sampleStr in sampleList:
sampleSafeStr = sampleStr.replace("-","_")
columnStr = "FPKM_{sample} REAL".format(sample=sampleSafeStr)
createColumnList.append(columnStr)
insertColumnList.append("FPKM_{sample}".format(sample=sampleSafeStr))
Connect = sqlite3.connect(sqlPath)
Cursor = Connect.cursor()
ReturnMsg = Cursor.execute(createComStr.format(",".join(createColumnList)))
Connect.commit()
Print.printing("[SQLite3:CreateTable] "+sqlPath)
resultDict = dict()
controlExc = Cursor.execute("SELECT UUID, TranscriptID, TranscriptName, GeneID, GeneName from TranscriptExpression_{}".format(controlSafeStr))
for rowList in controlExc:
uuid, tid, tname, geneid, genename = rowList
subDict = {
"UUID" : uuid,
"TranscriptID" : tid,
"TranscriptName" : tname,
"GeneID" : geneid,
"GeneName" : genename
}
resultDict.update({ uuid : subDict })
for sampleStr in sampleList:
sampleSafeStr = sampleStr.replace("-","_")
sampleExc = Cursor.execute("SELECT UUID, FPKM from TranscriptExpression_{}".format(sampleSafeStr))
for rowList in sampleExc:
uuid, fpkm = rowList
subDict = resultDict[uuid]
subDict.update({
"FPKM_{}".format(sampleSafeStr) : fpkm
})
resultDict.update({ uuid : subDict })
insertComStr = "INSERT INTO TranscriptExpressionSummary ({column}) VALUES ({value})"
for uuid in resultDict.keys():
valueList = list()
for posInt in range(len(insertColumnList)):
valueList.append(resultDict[uuid][insertColumnList[posInt]])
insertCommand = insertComStr.format(column=",".join(insertColumnList),value=(("?,"*(len(valueList)-1)))+"?")
ReturnMsg = Cursor.execute(insertCommand,valueList)
Connect.commit()
Print.printing("[SQLite3:Insert] "+sqlPath)
Connect.close()
Print.printing("[SQLite3:Close]\n")
Print.stopLog()
def importingCuffdiff(self):
# ---- Initialization for Converting ----
Target = libConfig.config()
Target.queryStr = self.branchStr
Target.folderStr = "config/"
Target.modeStr = "UPDATE"
Target.load()