def replaceFiles(folderName, replacedName): commandList = [] commandList.append("cp " + folderName + "improved3.fasta " + folderName + "improved3_backup.fasta") commandList.append("cp " + folderName + "improved3_Double.fasta " + folderName + "improved3_backup.fasta") IORobot.writeToFile_Double1(folderName, replacedName[0:-6] + ".fasta", replacedName[0:-6] + "_Double.fasta", "contig") commandList.append("cp " + folderName + replacedName + " " + folderName + "improved3.fasta") command = "perl -pe 's/>[^\$]*$/\">Segkk\" . $n++ .\"\n\"/ge' " + folderName + "improved3.fasta > " + folderName + "newImproved3.fasta " commandList.append(command) command = "cp " + folderName + "newImproved3.fasta " + folderName + "improved3.fasta " commandList.append(command) commandList.append("cp " + folderName + replacedName[0:-6] + "_Double.fasta " + folderName + "improved3_Double.fasta") for eachcommand in commandList: print eachcommand os.system(eachcommand)
def replaceFiles( folderName, replacedName) : commandList = [] commandList.append("cp " + folderName + "improved3.fasta " + folderName + "improved3_backup.fasta") commandList.append("cp " + folderName + "improved3_Double.fasta " + folderName + "improved3_backup.fasta") IORobot.writeToFile_Double1(folderName, replacedName[0:-6]+".fasta", replacedName[0:-6]+"_Double.fasta", "contig") commandList.append("cp " + folderName + replacedName + " "+folderName + "improved3.fasta") command = "perl -pe 's/>[^\$]*$/\">Segkk\" . $n++ .\"\n\"/ge' "+folderName+"improved3.fasta > "+folderName+"newImproved3.fasta " commandList.append(command) command = "cp " +folderName+"newImproved3.fasta "+folderName+"improved3.fasta " commandList.append(command) commandList.append("cp " + folderName + replacedName[0:-6]+"_Double.fasta " + folderName + "improved3_Double.fasta") for eachcommand in commandList: print eachcommand os.system(eachcommand)
def formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, graphName, needAlignment=True): ''' Input : all_associated_reads.fasta, improved3.fasta Output : (G) String Graph linking the reads and contigs Algorithm: a) Form double reads and contigs V b) Mummer the data and extract dataList three times V c) Use the subroutine to output a graph V d) Output the graph to a file phasing_String_graph.graph V ''' G = [] IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta", contigFilename + "_Double.fasta", "contig") IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta", readsetFilename + "_Double.fasta", "reads") header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta", contigFilename + "_Double.fasta" #if needAlignment: # alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile) if needAlignment: alignerRobot.useMummerAlignBatch( mummerLink, folderName, [[header, referenceFile, queryFile, ""]], houseKeeper.globalParallel) lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta") dataListCC = alignerRobot.extractMumData(folderName, header + "Out") dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC) header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta", readsetFilename + "_Double.fasta" lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta") if not abunHouseKeeper.abunGlobalRRDisable: if needAlignment: alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink, header) dataListRR = alignerRobot.extractMumData(folderName, header + "Out") dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR) dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR) else: dataListRR = [] header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta", readsetFilename + "_Double.fasta" if needAlignment: alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink, header) lenDicCR = dict(lenDicCC.items() + lenDicRR.items()) dataListCR = alignerRobot.extractMumData(folderName, header + "Out") dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR) numberOfNodes = len(lenDicCR) G = graphLib.seqGraph(numberOfNodes) N1, N2 = len(lenDicCC), len(lenDicRR) print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes ''' e.g. of dataListCC[0], dataListRR[0], dataListCR[0] [1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d'] [1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p'] [1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d'] ''' addDataToList(dataListCC, G, 0, 0, 'C', 'C') addDataToList(dataListRR, G, N1, N1, 'R', 'R') addDataToList(dataListCR, G, 0, N1, 'C', 'R') Gnew = formExtraEdges(folderName, optTypeFileHeader, contigFilename, G, N1) Gnew.saveToFile(folderName, graphName) print "len(Gnew.graphNodesList)", len(Gnew.graphNodesList)
def formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, graphName): ''' Input : all_associated_reads.fasta, improved3.fasta Output : (G) String Graph linking the reads and contigs Algorithm: a) Form double reads and contigs V b) Mummer the data and extract dataList three times V c) Use the subroutine to output a graph V d) Output the graph to a file phasing_String_graph.graph V ''' G = [] IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta", contigFilename + "_Double.fasta", "contig") IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta", readsetFilename + "_Double.fasta", "reads") header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta" , contigFilename + "_Double.fasta" if True: alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile) lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta") dataListCC = alignerRobot.extractMumData(folderName, header + "Out") dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC) header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta" , readsetFilename + "_Double.fasta" lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta") if not abunHouseKeeper.abunGlobalRRDisable: if True: alignerSubRoutine(folderName ,referenceFile, queryFile, mummerLink, header ) dataListRR = alignerRobot.extractMumData(folderName, header + "Out") dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR) for eachitem in dataListRR: if eachitem[-2] == "Read164_p" and eachitem[-1] == "Read159_p" : print "debug" , eachitem if eachitem[-1] == "Read164_p" and eachitem[-2] == "Read159_p" : print "debug" , eachitem dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR) else: dataListRR = [] header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta" , readsetFilename + "_Double.fasta" if True: alignerSubRoutine(folderName ,referenceFile, queryFile, mummerLink, header ) #alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile) lenDicCR = dict(lenDicCC.items() + lenDicRR.items()) dataListCR = alignerRobot.extractMumData(folderName, header + "Out") dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR) numberOfNodes = len(lenDicCR) G = graphLib.seqGraph(numberOfNodes) N1, N2 = len(lenDicCC), len(lenDicRR) print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes ''' e.g. of dataListCC[0], dataListRR[0], dataListCR[0] [1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d'] [1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p'] [1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d'] ''' # print dataListCC[0] # print dataListRR[0] # print dataListCR[0] # for eachitem in dataListCC: # print eachitem addDataToList(dataListCC, G, 0, 0, 'C', 'C') # for eachitem in dataListRR[0:10]: # print eachitem , lenDicRR[eachitem[-2]], lenDicRR[eachitem[-1]] addDataToList(dataListRR, G, N1, N1, 'R', 'R') addDataToList(dataListCR, G, 0, N1, 'C', 'R') # G.reportEdge() G.saveToFile(folderName, graphName) checkGraphLength(G, N1, lenDicRR) # print len(G.graphNodesList[0].listOfPrevNodes), len(G.graphNodesList[0].listOfNextNodes) print "len(G.graphNodesList)", len(G.graphNodesList)
def formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, graphName): ''' Input : all_associated_reads.fasta, improved3.fasta Output : (G) String Graph linking the reads and contigs Algorithm: a) Form double reads and contigs V b) Mummer the data and extract dataList three times V c) Use the subroutine to output a graph V d) Output the graph to a file phasing_String_graph.graph V ''' G = [] IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta", contigFilename + "_Double.fasta", "contig") IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta", readsetFilename + "_Double.fasta", "reads") header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta", contigFilename + "_Double.fasta" if True: alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile) lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta") dataListCC = alignerRobot.extractMumData(folderName, header + "Out") dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC) header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta", readsetFilename + "_Double.fasta" lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta") if not abunHouseKeeper.abunGlobalRRDisable: if True: alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink, header) dataListRR = alignerRobot.extractMumData(folderName, header + "Out") dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR) for eachitem in dataListRR: if eachitem[-2] == "Read164_p" and eachitem[-1] == "Read159_p": print "debug", eachitem if eachitem[-1] == "Read164_p" and eachitem[-2] == "Read159_p": print "debug", eachitem dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR) else: dataListRR = [] header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta", readsetFilename + "_Double.fasta" if True: alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink, header) #alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile) lenDicCR = dict(lenDicCC.items() + lenDicRR.items()) dataListCR = alignerRobot.extractMumData(folderName, header + "Out") dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR) numberOfNodes = len(lenDicCR) G = graphLib.seqGraph(numberOfNodes) N1, N2 = len(lenDicCC), len(lenDicRR) print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes ''' e.g. of dataListCC[0], dataListRR[0], dataListCR[0] [1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d'] [1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p'] [1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d'] ''' # print dataListCC[0] # print dataListRR[0] # print dataListCR[0] # for eachitem in dataListCC: # print eachitem addDataToList(dataListCC, G, 0, 0, 'C', 'C') # for eachitem in dataListRR[0:10]: # print eachitem , lenDicRR[eachitem[-2]], lenDicRR[eachitem[-1]] addDataToList(dataListRR, G, N1, N1, 'R', 'R') addDataToList(dataListCR, G, 0, N1, 'C', 'R') # G.reportEdge() G.saveToFile(folderName, graphName) checkGraphLength(G, N1, lenDicRR) # print len(G.graphNodesList[0].listOfPrevNodes), len(G.graphNodesList[0].listOfNextNodes) print "len(G.graphNodesList)", len(G.graphNodesList)