X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.cpp;h=70aa55d38502237388c520aeae892daf4891e73c;hp=e71c2aff6a4d8c60a3cf8f0648ecfdd2804d8544;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38 diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp index e71c2af..70aa55d 100644 --- a/seqsummarycommand.cpp +++ b/seqsummarycommand.cpp @@ -8,125 +8,708 @@ */ #include "seqsummarycommand.h" +#include "counttable.h" -//*************************************************************************************************************** - -SeqSummaryCommand::SeqSummaryCommand(){ +//********************************************************************************************************************** +vector SeqSummaryCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); - if(globaldata->getFastaFile() != "") { readSeqs = new ReadFasta(globaldata->inputFileName); } - else if(globaldata->getNexusFile() != "") { readSeqs = new ReadNexus(globaldata->inputFileName); } - else if(globaldata->getClustalFile() != "") { readSeqs = new ReadClustal(globaldata->inputFileName); } - else if(globaldata->getPhylipFile() != "") { readSeqs = new ReadPhylip(globaldata->inputFileName); } - - readSeqs->read(); - db = readSeqs->getDB(); - numSeqs = db->size(); + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SeqSummaryCommand", "setParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +string SeqSummaryCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n"; + helpString += "The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.\n"; + helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n"; + helpString += "The count parameter allows you to enter a count file associated with your fasta file. \n"; + helpString += "The summary.seqs command should be in the following format: \n"; + helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "getHelpString"); exit(1); - } + } +} +//********************************************************************************************************************** +string SeqSummaryCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "getOutputPattern"); + exit(1); + } } +//********************************************************************************************************************** +SeqSummaryCommand::SeqSummaryCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand"); + exit(1); + } +} //*************************************************************************************************************** -SeqSummaryCommand::~SeqSummaryCommand(){ +SeqSummaryCommand::SeqSummaryCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter("summary.seqs"); + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("fasta"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["fasta"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["name"] = inputDir + it->second; } + } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + + //check for required parameters + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not open") { abort = true; } + else if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setFastaFile(fastafile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { namefile = ""; abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it + } + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } + } + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand"); + exit(1); + } } - //*************************************************************************************************************** int SeqSummaryCommand::execute(){ try{ - ofstream outfile; - string summaryFile = getRootName(globaldata->inputFileName) + "summary"; - openOutputFile(summaryFile, outfile); - - vector startPosition(numSeqs, 0); - vector endPosition(numSeqs, 0); - vector seqLength(numSeqs, 0); - vector ambigBases(numSeqs, 0); - vector longHomoPolymer(numSeqs, 0); - - if(db->get(0).getIsAligned() == 1){ - outfile << "seqname\tstart\tend\tlength\tambiguities\tlonghomopolymer" << endl; - for(int i = 0; i < numSeqs; i++) { - Sequence current = db->get(i); - startPosition[i] = current.getStartPos(); - endPosition[i] = current.getEndPos(); - seqLength[i] = current.getNumBases(); - ambigBases[i] = current.getAmbigBases(); - longHomoPolymer[i] = current.getLongHomoPolymer(); - outfile << current.getName() << '\t' << startPosition[i] << '\t' << endPosition[i] << '\t' << seqLength[i] << '\t' << ambigBases[i] << '\t' << longHomoPolymer[i] << endl; - } - } - else{ - outfile << "seqname\tlength\tambiguities\tlonghomopolymer" << endl; - for(int i=0;iget(i); - seqLength[i] = current.getNumBases(); - ambigBases[i] = current.getAmbigBases(); - longHomoPolymer[i] = current.getLongHomoPolymer(); - outfile << current.getName() << '\t' << seqLength[i] << '\t' << ambigBases[i] << '\t' << longHomoPolymer[i] << endl; + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //set current fasta to fastafile + m->setFastaFile(fastafile); + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string summaryFile = getOutputFileName("summary",variables); + + int numSeqs = 0; + + vector startPosition; + vector endPosition; + vector seqLength; + vector ambigBases; + vector longHomoPolymer; + + if (namefile != "") { nameMap = m->readNames(namefile); } + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile, false, false); + nameMap = ct.getNameMap(); + } + + if (m->control_pressed) { return 0; } + +#ifdef USE_MPI + int pid, numSeqsPerProcessor; + int tag = 2001; + int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5; + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + vector MPIPos; + + MPI_Status status; + MPI_Status statusOut; + MPI_File inMPI; + MPI_File outMPI; + MPI_Comm_size(MPI_COMM_WORLD, &processors); + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + char tempFileName[1024]; + strcpy(tempFileName, fastafile.c_str()); + + char sumFileName[1024]; + strcpy(sumFileName, summaryFile.c_str()); + + MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } + + if (pid == 0) { //you are the root process + //print header + string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n"; + int length = outputString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outputString.c_str(), length); + + MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut); + delete buf2; + + MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs + + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to do + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + + //do your part + MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos); + + }else { //i am the child process + + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numSeqs+1); + MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + + //do your part + MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos); + } + + MPI_File_close(&inMPI); + MPI_File_close(&outMPI); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + if (pid == 0) { + //get the info from the child processes + for(int i = 1; i < processors; i++) { + int size; + MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); + + vector temp; temp.resize(size+1); + + for(int j = 0; j < 5; j++) { + + MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status); + int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what count this is for + + if (receiveTag == startTag) { + for (int k = 0; k < size; k++) { startPosition.push_back(temp[k]); } + }else if (receiveTag == endTag) { + for (int k = 0; k < size; k++) { endPosition.push_back(temp[k]); } + }else if (receiveTag == lengthTag) { + for (int k = 0; k < size; k++) { seqLength.push_back(temp[k]); } + }else if (receiveTag == baseTag) { + for (int k = 0; k < size; k++) { ambigBases.push_back(temp[k]); } + }else if (receiveTag == lhomoTag) { + for (int k = 0; k < size; k++) { longHomoPolymer.push_back(temp[k]); } + } + } + } + + }else{ + + //send my counts + int size = startPosition.size(); + MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); + + startPosition.push_back(startTag); + int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + endPosition.push_back(endTag); + ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + seqLength.push_back(lengthTag); + ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + ambigBases.push_back(baseTag); + ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + longHomoPolymer.push_back(lhomoTag); + ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + } + + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case +#else + vector positions; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFile(fastafile, processors); + for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); } + #else + positions = m->setFilePosFasta(fastafile, numSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; } + lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor)); + } + #endif + + + if(processors == 1){ + numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]); + }else{ + numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile); } - } + + if (m->control_pressed) { return 0; } +#endif + + #ifdef USE_MPI + if (pid == 0) { + #endif + sort(startPosition.begin(), startPosition.end()); + sort(endPosition.begin(), endPosition.end()); sort(seqLength.begin(), seqLength.end()); sort(ambigBases.begin(), ambigBases.end()); sort(longHomoPolymer.begin(), longHomoPolymer.end()); + int size = startPosition.size(); + + //find means + unsigned long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; + meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0; + for (int i = 0; i < size; i++) { + meanStartPosition += startPosition[i]; + meanEndPosition += endPosition[i]; + meanSeqLength += seqLength[i]; + meanAmbigBases += ambigBases[i]; + meanLongHomoPolymer += longHomoPolymer[i]; + } + + double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer; + + meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size; + + int ptile0_25 = int(size * 0.025); + int ptile25 = int(size * 0.250); + int ptile50 = int(size * 0.500); + int ptile75 = int(size * 0.750); + int ptile97_5 = int(size * 0.975); + int ptile100 = size - 1; + + //to compensate for blank sequences that would result in startPosition and endPostion equalling -1 + if (startPosition[0] == -1) { startPosition[0] = 0; } + if (endPosition[0] == -1) { endPosition[0] = 0; } - int median = int(numSeqs * 0.500); - int lowestPtile = int(numSeqs * 0.025); - int lowPtile = int(numSeqs * 0.250); - int highPtile = int(numSeqs * 0.750); - int highestPtile = int(numSeqs * 0.975); - int max = numSeqs - 1; - - cout << endl; - if(db->get(0).getIsAligned() == 1){ - sort(startPosition.begin(), startPosition.end()); - sort(endPosition.begin(), endPosition.end()); + if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine(); + m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine(); + m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine(); + m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine(); + m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine(); + m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine(); + m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine(); + m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine(); + m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine(); + + if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } + else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); } + + if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); + m->mothurOutEndLine(); + + #ifdef USE_MPI + } + #endif + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("summary"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "execute"); + exit(1); + } +} +/**************************************************************************************/ +int SeqSummaryCommand::driverCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, string filename, string sumFile, linePair* filePos) { + try { + + ofstream outSummary; + m->openOutputFile(sumFile, outSummary); + + //print header if you are process 0 + if (filePos->start == 0) { + outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl; + } + + ifstream in; + m->openInputFile(filename, in); + + in.seekg(filePos->start); + + bool done = false; + int count = 0; + + + while (!done) { + + if (m->control_pressed) { in.close(); outSummary.close(); return 1; } + + if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n"); } + + Sequence current(in); m->gobble(in); + + if (current.getName() != "") { + + if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); } + + int num = 1; + if ((namefile != "") || (countfile != "")) { + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(current.getName()); - cout << "\t\tStart\tEnd\tLength\tN's\tPolymer" << endl; - cout << "Minimum:\t" << startPosition[0] << '\t' << endPosition[0] << '\t' << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl; - cout << "2.5%-tile:\t" << startPosition[lowestPtile] << '\t' << endPosition[lowestPtile] << '\t' << seqLength[lowestPtile] << '\t' << ambigBases[lowestPtile] << '\t' << longHomoPolymer[lowestPtile] << endl; - cout << "25%-tile:\t" << startPosition[lowPtile] << '\t' << endPosition[lowPtile] << '\t' << seqLength[lowPtile] << '\t' << ambigBases[lowPtile] << '\t' << longHomoPolymer[lowPtile] << endl; - cout << "Median: \t" << startPosition[median] << '\t' << endPosition[median] << '\t' << seqLength[median] << '\t' << ambigBases[median] << '\t' << longHomoPolymer[median] << endl; - cout << "75%-tile:\t" << startPosition[highPtile] << '\t' << endPosition[highPtile] << '\t' << seqLength[highPtile] << '\t' << ambigBases[highPtile] << '\t' << longHomoPolymer[highPtile] << endl; - cout << "97.5%-tile:\t" << startPosition[highestPtile] << '\t' << endPosition[highestPtile] << '\t' << seqLength[highestPtile] << '\t' << ambigBases[highestPtile] << '\t' << longHomoPolymer[highestPtile] << endl; - cout << "Maximum:\t" << startPosition[max] << '\t' << endPosition[max] << '\t' << seqLength[max] << '\t' << ambigBases[max] << '\t' << longHomoPolymer[max] << endl; + if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + for (int i = 0; i < num; i++) { + startPosition.push_back(current.getStartPos()); + endPosition.push_back(current.getEndPos()); + seqLength.push_back(current.getNumBases()); + ambigBases.push_back(current.getAmbigBases()); + longHomoPolymer.push_back(current.getLongHomoPolymer()); + } + count++; + outSummary << current.getName() << '\t'; + outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t'; + outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t'; + outSummary << current.getLongHomoPolymer() << '\t' << num << endl; + + if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); } + } + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = in.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + #else + if (in.eof()) { break; } + #endif } - else{ - cout << "\t\tLength\tN's\tPolymer" << endl; - cout << "Minimum:\t" << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl; - cout << "2.5%-tile:\t" << seqLength[lowestPtile] << '\t' << ambigBases[lowestPtile] << '\t' << longHomoPolymer[lowestPtile] << endl; - cout << "25%-tile:\t" << seqLength[lowPtile] << '\t' << ambigBases[lowPtile] << '\t' << longHomoPolymer[lowPtile] << endl; - cout << "Median: \t" << seqLength[median] << '\t' << ambigBases[median] << '\t' << longHomoPolymer[median] << endl; - cout << "75%-tile:\t"<< seqLength[highPtile] << '\t' << ambigBases[highPtile] << '\t' << longHomoPolymer[highPtile] << endl; - cout << "97.5%-tile:\t"<< seqLength[highestPtile] << '\t' << ambigBases[highestPtile] << '\t' << longHomoPolymer[highestPtile] << endl; - cout << "Maximum:\t" << seqLength[max] << '\t' << ambigBases[max] << '\t' << longHomoPolymer[max] << endl; + + in.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary"); + exit(1); + } +} +#ifdef USE_MPI +/**************************************************************************************/ +int SeqSummaryCommand::MPICreateSummary(int start, int num, vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos) { + try { + + int pid; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + for(int i=0;icontrol_pressed) { return 0; } + + //read next sequence + int length = MPIPos[start+i+1] - MPIPos[start+i]; + + char* buf4 = new char[length]; + MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); + + string tempBuf = buf4; + if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } + istringstream iss (tempBuf,istringstream::in); + delete buf4; + + Sequence current(iss); + + if (current.getName() != "") { + + int num = 1; + if ((namefile != "") || (countfile != "")) { + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(current.getName()); + + if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + for (int j = 0; j < num; j++) { + startPosition.push_back(current.getStartPos()); + endPosition.push_back(current.getEndPos()); + seqLength.push_back(current.getNumBases()); + ambigBases.push_back(current.getAmbigBases()); + longHomoPolymer.push_back(current.getLongHomoPolymer()); + } + + string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t"; + outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n"; + + //output to file + length = outputString.length(); + char* buf3 = new char[length]; + memcpy(buf3, outputString.c_str(), length); + + MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status); + delete buf3; + } } - cout << "# of Seqs:\t" << numSeqs << endl; return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +#endif +/**************************************************************************************************/ +int SeqSummaryCommand::createProcessesCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, string filename, string sumFile) { + try { + int process = 1; + int num = 0; + processIDS.clear(); + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later + process++; + }else if (pid == 0){ + num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]); + + //pass numSeqs to parent + ofstream out; + string tempFile = fastafile + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + + out << num << endl; + out << startPosition.size() << endl; + for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl; + for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl; + for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl; + for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl; + for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl; + + out.close(); + + exit(0); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } + } + + //do your part + num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFilename, in); + + int temp, tempNum; + in >> tempNum; m->gobble(in); num += tempNum; + in >> tempNum; m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in); + + in.close(); + m->mothurRemove(tempFilename); + + m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile); + m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp")); + } + +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the seqSumData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to allow both threads to add info to vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + bool hasNameMap = false; + if ((namefile !="") || (countfile != "")) { hasNameMap = true; } + + //Create processor worker threads. + for( int i=0; istart, lines[i]->end, hasNameMap, nameMap); + pDataArray.push_back(tempSum); + + //MySeqSumThreadFunction is in header. It must be global or static to work with the threads. + //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier + hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); + } + + //do your part + num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]); + processIDS.push_back(processors-1); + + //Wait until all threads have terminated. + WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); + + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + num += pDataArray[i]->count; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } + for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); } + for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); } + for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); } + for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) { ambigBases.push_back(pDataArray[i]->ambigBases[k]); } + for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) { longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + //append files + for(int i=0;iappendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile); + m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp")); + } +#endif + return num; + } + catch(exception& e) { + m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary"); exit(1); } - } +/**********************************************************************************************************************/ -//***************************************************************************************************************