X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=filterseqscommand.cpp;h=8b68988884acb408d0e72c5c3fa407a7b9f241b6;hp=e024a242ed8b35771580b00cffd66bc7dd78d66d;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=986663e2220f6b043ee83d1699cfa081dc49cbed diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index e024a24..8b68988 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -8,187 +8,1199 @@ */ #include "filterseqscommand.h" +#include "sequence.hpp" -/**************************************************************************************/ -FilterSeqsCommand::FilterSeqsCommand(){ +//********************************************************************************************************************** +vector FilterSeqsCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta); + CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard); + CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump); + CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft); + CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical); + 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); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string FilterSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n"; + helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n"; + helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n"; + helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n"; + helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n"; + helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n"; + helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n"; + helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n"; + helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n"; + helpString += "The filter.seqs command should be in the following format: \n"; + helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n"; + helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string FilterSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],filter.fasta"; } + else if (type == "filter") { pattern = "[filename],filter"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +FilterSeqsCommand::FilterSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["filter"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand"); + exit(1); + } +} +/**************************************************************************************/ +FilterSeqsCommand::FilterSeqsCommand(string option) { + try { + abort = false; calledHelp = false; + filterFileName = ""; + + //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("filter.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; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["filter"] = tempOutNames; + + //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("hard"); + //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["hard"] = inputDir + it->second; } + } + } + + //check for required parameters + fasta = validParameter.validFile(parameters, "fasta", false); + if (fasta == "not found") { + fasta = m->getFastaFile(); + if (fasta != "") { + fastafileNames.push_back(fasta); + m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); + string simpleName = m->getSimpleName(fasta); + filterFileName += simpleName.substr(0, simpleName.find_first_of('.')); + } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + } + else { + m->splitAtDash(fasta, fastafileNames); + + //go through files and make sure they are good, if not, then disregard them + for (int i = 0; i < fastafileNames.size(); i++) { + + bool ignore = false; + if (fastafileNames[i] == "current") { + fastafileNames[i] = m->getFastaFile(); + if (fastafileNames[i] != "") { m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastafileNames.erase(fastafileNames.begin()+i); + i--; + } + } + + if (!ignore) { + if (inputDir != "") { + string path = m->hasPath(fastafileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; } + } - globaldata = GlobalData::getInstance(); - - if(globaldata->getFastaFile() == "") { cout << "You must enter a fasta formatted file" << endl; } - trump = globaldata->getTrump()[0]; - numSeqs = 0; + ifstream in; + int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror"); + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]); + m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastafileNames[i] = tryPath; + } + } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]); + m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastafileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastafileNames.erase(fastafileNames.begin()+i); + i--; + }else{ + string simpleName = m->getSimpleName(fastafileNames[i]); + filterFileName += simpleName.substr(0, simpleName.find_first_of('.')); + m->setFastaFile(fastafileNames[i]); + } + in.close(); + } + } + + //make sure there is at least one valid file left + if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } + } + + if (!abort) { + //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(fastafileNames[0]); //if user entered a file with a path then preserve it + } + } + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + + string temp; + hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; } + else if (hard == "not open") { hard = ""; abort = true; } + temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; } + trump = temp[0]; + + temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; } + else { soft = (float)atoi(temp.c_str()) / 100.0; } + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + vertical = validParameter.validFile(parameters, "vertical", false); + if (vertical == "not found") { + if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char. + else { vertical = "F"; } + } + + numSeqs = 0; + } + + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand"); + exit(1); + } } - /**************************************************************************************/ -void FilterSeqsCommand::doHard() { +int FilterSeqsCommand::execute() { + try { - string hardName = globaldata->getHard(); - string hardFilter = ""; + if (abort == true) { if (calledHelp) { return 0; } return 2; } - ifstream fileHandle; - openInputFile(hardName, fileHandle); - - fileHandle >> filter; + ifstream inFASTA; + m->openInputFile(fastafileNames[0], inFASTA); + + Sequence testSeq(inFASTA); + alignmentLength = testSeq.getAlignLength(); + inFASTA.close(); + + ////////////create filter///////////////// + m->mothurOut("Creating Filter... "); m->mothurOutEndLine(); + + filter = createFilter(); + + m->mothurOutEndLine(); m->mothurOutEndLine(); + + if (m->control_pressed) { outputTypes.clear(); return 0; } + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output the filter + #endif + + ofstream outFilter; + + //prevent giantic file name + map variables; + variables["[filename]"] = outputDir + filterFileName + "."; + if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; } + string filterFile = getOutputFileName("filter", variables); + + m->openOutputFile(filterFile, outFilter); + outFilter << filter << endl; + outFilter.close(); + outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile); + + #ifdef USE_MPI + } + #endif + + ////////////run filter///////////////// + + m->mothurOut("Running Filter... "); m->mothurOutEndLine(); + + filterSequences(); + + m->mothurOutEndLine(); m->mothurOutEndLine(); + + int filteredLength = 0; + for(int i=0;icontrol_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine(); + m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine(); + m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine(); + m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "execute"); + exit(1); + } } - /**************************************************************************************/ +int FilterSeqsCommand::filterSequences() { + try { + + numSeqs = 0; + + for (int s = 0; s < fastafileNames.size(); s++) { + + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])); + string filteredFasta = getOutputFileName("fasta", variables); +#ifdef USE_MPI + int pid, numSeqsPerProcessor, num; + int tag = 2001; + vectorMPIPos; + + MPI_Status status; + MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + MPI_File outMPI; + MPI_File inMPI; + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; + + char outFilename[1024]; + strcpy(outFilename, filteredFasta.c_str()); + + char inFileName[1024]; + strcpy(inFileName, fastafileNames[s].c_str()); + + MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); -void FilterSeqsCommand::doTrump(Sequence seq) { - - string curAligned = seq.getAligned(); - - for(int j = 0; j < alignmentLength; j++) { - if(curAligned[j] == trump){ - filter[j] = '0'; + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } + + if (pid == 0) { //you are the root process + + MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs + numSeqs += num; + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to do + numSeqsPerProcessor = num / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + + + //do your part + driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } + + //wait on chidren + for(int i = 1; i < processors; i++) { + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); + } + + }else { //you are a child process + MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(num+1); + numSeqs += num; + MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = num / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + + + //align your part + driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } + + char buf[5]; + strcpy(buf, "done"); + + //tell parent you are done. + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + } + + MPI_File_close(&outMPI); + MPI_File_close(&inMPI); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + +#else + + vector positions; + if (savedPositions.size() != 0) { positions = savedPositions[s]; } + else { +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFile(fastafileNames[s], processors); +#else + if(processors != 1){ + int numFastaSeqs = 0; + positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); + if (positions.size() < processors) { processors = positions.size(); } + } +#endif + } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //vector positions = m->divideFile(fastafileNames[s], processors); + + for (int i = 0; i < (positions.size()-1); i++) { + lines.push_back(new linePair(positions[i], positions[(i+1)])); + } + + if(processors == 1){ + int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]); + numSeqs += numFastaSeqs; + }else{ + int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta); + numSeqs += numFastaSeqs; + } + + if (m->control_pressed) { return 1; } + #else + if(processors == 1){ + lines.push_back(new linePair(0, 1000)); + int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]); + numSeqs += numFastaSeqs; + }else { + int numFastaSeqs = positions.size()-1; + //positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numFastaSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; } + lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor)); + } + + numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta); + numSeqs += numFastaSeqs; + } + + if (m->control_pressed) { return 1; } + #endif +#endif + outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta); } - } + return 0; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "filterSequences"); + exit(1); + } } - +#ifdef USE_MPI /**************************************************************************************/ +int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos) { + try { + string outputString = ""; + int count = 0; + MPI_Status status; + + 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 seq(iss); m->gobble(iss); + + if (seq.getName() != "") { + string align = seq.getAligned(); + string filterSeq = ""; + + for(int j=0;jerrorOut(e, "FilterSeqsCommand", "driverRunFilter"); + exit(1); } - } - +#endif /**************************************************************************************/ +int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) { + try { + ofstream out; + m->openOutputFile(outputFilename, out); + + ifstream in; + m->openInputFile(inputFilename, in); + + in.seekg(filePos->start); -void FilterSeqsCommand::doSoft() { - - int threshold = int (soft * numSeqs); - bool keep = 0; + bool done = false; + int count = 0; - for(int i=0;i= threshold) { keep = 1; } - else if(t[i] >= threshold) { keep = 1; } - else if(g[i] >= threshold) { keep = 1; } - else if(c[i] >= threshold) { keep = 1; } + while (!done) { + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + Sequence seq(in); m->gobble(in); + if (seq.getName() != "") { + string align = seq.getAligned(); + string filterSeq = ""; + + for(int j=0;j' << seq.getName() << endl << filterSeq << endl; + count++; + } + + #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 + + //report progress + if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); } + } + //report progress + if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); } + + + out.close(); + in.close(); - if(keep == 0) { filter[i] = 0; } + return count; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "driverRunFilter"); + exit(1); } } +/**************************************************************************************************/ +int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) { + 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){ + string filteredFasta = filename + toString(getpid()) + ".temp"; + num = driverRunFilter(F, filteredFasta, filename, lines[process]); + + //pass numSeqs to parent + ofstream out; + string tempFile = filename + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + out << num << 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); + } + } + + num = driverRunFilter(F, filteredFastaName, filename, lines[0]); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFile, in); + if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } + in.close(); m->mothurRemove(tempFile); + + m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName); + m->mothurRemove((filename + toString(processIDS[i]) + ".temp")); + } + +#else + + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the filterData 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 F. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; istart, lines[i]->end, alignmentLength, i); + pDataArray.push_back(tempFilter); + processIDS.push_back(i); + + hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); + } + + num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[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; + } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + for (int i = 1; i < processors; i++) { + m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName); + m->mothurRemove((filteredFastaName + toString(i) + ".temp")); + } +#endif + + return num; + + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter"); + exit(1); + } +} /**************************************************************************************/ +string FilterSeqsCommand::createFilter() { + try { + string filterString = ""; + Filters F; + + if (soft != 0) { F.setSoft(soft); } + if (trump != '*') { F.setTrump(trump); } + + F.setLength(alignmentLength); + + if(trump != '*' || m->isTrue(vertical) || soft != 0){ + F.initialize(); + } + + if(hard.compare("") != 0) { F.doHard(hard); } + else { F.setFilter(string(alignmentLength, '1')); } + + numSeqs = 0; + if(trump != '*' || m->isTrue(vertical) || soft != 0){ + for (int s = 0; s < fastafileNames.size(); s++) { + + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + +#ifdef USE_MPI + int pid, numSeqsPerProcessor, num; + int tag = 2001; + vector MPIPos; + + MPI_Status status; + MPI_File inMPI; + MPI_Comm_size(MPI_COMM_WORLD, &processors); + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + //char* tempFileName = new char(fastafileNames[s].length()); + //tempFileName = &(fastafileNames[s][0]); + + char tempFileName[1024]; + strcpy(tempFileName, fastafileNames[s].c_str()); + + MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + + if (m->control_pressed) { MPI_File_close(&inMPI); return 0; } + + if (pid == 0) { //you are the root process + MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs + numSeqs += num; + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to do + numSeqsPerProcessor = num / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + + + //do your part + MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); return 0; } + + }else { //i am the child process + MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(num+1); + numSeqs += num; + MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = num / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + + + //do your part + MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); return 0; } + } + + MPI_File_close(&inMPI); + 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(fastafileNames[s], processors); + for (int i = 0; i < (positions.size()-1); i++) { + lines.push_back(new linePair(positions[i], positions[(i+1)])); + } + + if(processors == 1){ + int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]); + numSeqs += numFastaSeqs; + }else{ + int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]); + numSeqs += numFastaSeqs; + } + #else + if(processors == 1){ + lines.push_back(new linePair(0, 1000)); + int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]); + numSeqs += numFastaSeqs; + }else { + int numFastaSeqs = 0; + positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numFastaSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; } + lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor)); + } + + numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]); + numSeqs += numFastaSeqs; + } + #endif + //save the file positions so we can reuse them in the runFilter function + savedPositions[s] = positions; + + if (m->control_pressed) { return filterString; } +#endif + + } + } -void FilterSeqsCommand::getFreqs(Sequence seq) { - string curAligned = seq.getAligned();; - - for(int j=0;jisTrue(vertical) || soft != 0){ + + if (pid == 0) { //only one process should output the filter + + vector temp; temp.resize(alignmentLength+1); + + //get the frequencies from the child processes + for(int i = 1; i < processors; i++) { + + for (int j = 0; j < 5; j++) { + + MPI_Recv(&temp[0], (alignmentLength+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 letter count this is for + + if (receiveTag == Atag) { //you are recieveing the A frequencies + for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; } + }else if (receiveTag == Ttag) { //you are recieveing the T frequencies + for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; } + }else if (receiveTag == Ctag) { //you are recieveing the C frequencies + for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; } + }else if (receiveTag == Gtag) { //you are recieveing the G frequencies + for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; } + }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies + for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; } + } + } + } + }else{ + + //send my fequency counts + F.a.push_back(Atag); + int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + F.t.push_back(Ttag); + ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + F.c.push_back(Ctag); + ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + F.g.push_back(Gtag); + ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + F.gap.push_back(Gaptag); + ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); + } + + } + + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + if (pid == 0) { //only one process should output the filter +#endif + + F.setNumSeqs(numSeqs); + if(m->isTrue(vertical) == 1) { F.doVertical(); } + if(soft != 0) { F.doSoft(); } + filterString = F.getFilter(); + +#ifdef USE_MPI + //send filter string to kids + //for(int i = 1; i < processors; i++) { + // MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + //} + MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); + }else{ + //recieve filterString + char* tempBuf = new char[alignmentLength]; + //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); + + filterString = tempBuf; + if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); } + delete tempBuf; } + MPI_Barrier(MPI_COMM_WORLD); +#endif + + return filterString; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "createFilter"); + exit(1); + } } - /**************************************************************************************/ +int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) { + try { + + ifstream in; + m->openInputFile(filename, in); + + in.seekg(filePos->start); -int FilterSeqsCommand::execute() { + bool done = false; + int count = 0; + + while (!done) { + + if (m->control_pressed) { in.close(); return 1; } + + Sequence seq(in); m->gobble(in); + if (seq.getName() != "") { + if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + + if(trump != '*') { F.doTrump(seq); } + if(m->isTrue(vertical) || soft != 0) { F.getFreqs(seq); } + cout.flush(); + count++; + } + + #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 + + //report progress + if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); } + } + //report progress + if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); } + in.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter"); + exit(1); + } +} +#ifdef USE_MPI +/**************************************************************************************/ +int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector& MPIPos) { try { - ifstream inFASTA; - openInputFile(globaldata->getFastaFile(), inFASTA); - Sequence testSeq(inFASTA); - alignmentLength = testSeq.getAlignLength(); - inFASTA.seekg(0); + MPI_Status status; + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - if(globaldata->getSoft() != "" || isTrue(globaldata->getVertical())){ - a.assign(alignmentLength, 0); - t.assign(alignmentLength, 0); - g.assign(alignmentLength, 0); - c.assign(alignmentLength, 0); - gap.assign(alignmentLength, 0); - } - if(globaldata->getSoft() != ""){ - soft = (float)atoi(globaldata->getSoft().c_str()) / 100.0; + 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 seq(iss); + + if (seq.getAligned().length() != alignmentLength) { cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1); } + + if(trump != '*'){ F.doTrump(seq); } + if(m->isTrue(vertical) || soft != 0){ F.getFreqs(seq); } + cout.flush(); + + //report progress + if((i+1) % 100 == 0){ cout << (i+1) << endl; } } - if(globaldata->getHard().compare("") != 0) { doHard(); } - else { filter = string(alignmentLength, '1'); } - - if(globaldata->getTrump().compare("") != 0 || isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ + //report progress + if((num) % 100 != 0){ cout << num << endl; } - while(!inFASTA.eof()){ - Sequence seq(inFASTA); - if(globaldata->getTrump().compare("") != 0) { doTrump(seq); } - if(isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ getFreqs(seq); } - numSeqs++; - cout.flush(); + return 0; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter"); + exit(1); + } +} +#endif +/**************************************************************************************************/ + +int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) { + 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){ + //reset child's filter counts to 0; + F.a.clear(); F.a.resize(alignmentLength, 0); + F.t.clear(); F.t.resize(alignmentLength, 0); + F.g.clear(); F.g.resize(alignmentLength, 0); + F.c.clear(); F.c.resize(alignmentLength, 0); + F.gap.clear(); F.gap.resize(alignmentLength, 0); + + num = driverCreateFilter(F, filename, lines[process]); + + //write out filter counts to file + filename += toString(getpid()) + "filterValues.temp"; + ofstream out; + m->openOutputFile(filename, out); + + out << num << endl; + out << F.getFilter() << endl; + for (int k = 0; k < alignmentLength; k++) { out << F.a[k] << '\t'; } out << endl; + for (int k = 0; k < alignmentLength; k++) { out << F.t[k] << '\t'; } out << endl; + for (int k = 0; k < alignmentLength; k++) { out << F.g[k] << '\t'; } out << endl; + for (int k = 0; k < alignmentLength; k++) { out << F.c[k] << '\t'; } out << endl; + for (int k = 0; k < alignmentLength; k++) { out << F.gap[k] << '\t'; } out << endl; + + //cout << F.getFilter() << 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); } + } + //parent do your part + num = driverCreateFilter(F, filename, lines[0]); + + //force parent to wait until all the processes are done + for (int i=0;i<(processors-1);i++) { + int temp = processIDS[i]; + wait(&temp); } - inFASTA.close(); - if(isTrue(globaldata->getVertical()) == 1) { doVertical(); } - if(globaldata->getSoft().compare("") != 0) { doSoft(); } + //parent reads in and combines Filter info + for (int i = 0; i < processIDS.size(); i++) { + string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp"; + ifstream in; + m->openInputFile(tempFilename, in); + + int temp, tempNum; + string tempFilterString; - ofstream outFilter; - string filterFile = getRootName(globaldata->inputFileName) + "filter"; - openOutputFile(filterFile, outFilter); - outFilter << filter << endl; - outFilter.close(); - + in >> tempNum; m->gobble(in); num += tempNum; - openInputFile(globaldata->getFastaFile(), inFASTA); - string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta"; - ofstream outFASTA; - openOutputFile(filteredFasta, outFASTA); + in >> tempFilterString; + F.mergeFilter(tempFilterString); - numSeqs = 0; - while(!inFASTA.eof()){ - Sequence seq(inFASTA); - string align = seq.getAligned(); - string filterSeq = ""; - - for(int j=0;j' << seq.getName() << endl << filterSeq << endl; - numSeqs++; - gobble(inFASTA); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in); + + in.close(); + m->mothurRemove(tempFilename); } - outFASTA.close(); - inFASTA.close(); - int filteredLength = 0; - for(int i=0;i pDataArray; + DWORD dwThreadIdArray[processors]; + HANDLE hThreadArray[processors]; - globaldata->clear(); + //Create processor worker threads. + for( int i=0; istart, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i); + pDataArray.push_back(tempFilter); + processIDS.push_back(i); + + hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); + } + + //Wait until all threads have terminated. + WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE); - return 0; + //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; + } + F.mergeFilter(pDataArray[i]->F.getFilter()); + + for (int k = 0; k < alignmentLength; k++) { F.a[k] += pDataArray[i]->F.a[k]; } + for (int k = 0; k < alignmentLength; k++) { F.t[k] += pDataArray[i]->F.t[k]; } + for (int k = 0; k < alignmentLength; k++) { F.g[k] += pDataArray[i]->F.g[k]; } + for (int k = 0; k < alignmentLength; k++) { F.c[k] += pDataArray[i]->F.c[k]; } + for (int k = 0; k < alignmentLength; k++) { F.gap[k] += pDataArray[i]->F.gap[k]; } + + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } +#endif + return num; + } 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"; - 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"; + m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter"); exit(1); } } - /**************************************************************************************/