X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=a7d42b331bc3044de372c030175da4663f9e3a9c;hb=e98d56be8369a799e61a411bc13d3bd1fa3451e5;hp=613dfda1dbbfcc74bea7e218fff53850c366fd7c;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index 613dfda..a7d42b3 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -78,6 +78,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { //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(); @@ -124,7 +125,12 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { 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(); } + 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 { @@ -189,6 +195,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { }else{ string simpleName = m->getSimpleName(fastafileNames[i]); filterFileName += simpleName.substr(0, simpleName.find_first_of('.')); + m->setFastaFile(fastafileNames[i]); } in.close(); } @@ -220,7 +227,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); vertical = validParameter.validFile(parameters, "vertical", false); if (vertical == "not found") { @@ -296,7 +303,7 @@ int FilterSeqsCommand::execute() { if(filter[i] == '1'){ filteredLength++; } } - if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } m->mothurOutEndLine(); @@ -339,7 +346,7 @@ int FilterSeqsCommand::filterSequences() { #ifdef USE_MPI int pid, numSeqsPerProcessor, num; int tag = 2001; - vectorMPIPos; + vectorMPIPos; MPI_Status status; MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running @@ -418,32 +425,56 @@ int FilterSeqsCommand::filterSequences() { MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = m->divideFile(fastafileNames[s], processors); - + + 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 defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]); numSeqs += numFastaSeqs; }else{ - int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]); + int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta); numSeqs += numFastaSeqs; - - rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str()); - - //append fasta files - for(int i=1;iappendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta); - remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str()); - } } 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 @@ -460,7 +491,7 @@ int FilterSeqsCommand::filterSequences() { } #ifdef USE_MPI /**************************************************************************************/ -int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos) { +int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos) { try { string outputString = ""; int count = 0; @@ -565,8 +596,8 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i count++; } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - unsigned long int pos = in.tellg(); + #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; } @@ -591,12 +622,15 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i } /**************************************************************************************************/ -int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) { +int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; + + 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) { @@ -624,8 +658,10 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) { } } + 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(); remove(tempFile.c_str()); + 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); - return num; -#endif + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + num += pDataArray[i]->count; + 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"); @@ -674,7 +755,7 @@ string FilterSeqsCommand::createFilter() { #ifdef USE_MPI int pid, numSeqsPerProcessor, num; int tag = 2001; - vector MPIPos; + vector MPIPos; MPI_Status status; MPI_File inMPI; @@ -734,12 +815,14 @@ string FilterSeqsCommand::createFilter() { MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - 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 defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + 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; @@ -747,13 +830,32 @@ string FilterSeqsCommand::createFilter() { int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]); numSeqs += numFastaSeqs; } - - if (m->control_pressed) { return filterString; } #else - int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]); - numSeqs += numFastaSeqs; - if (m->control_pressed) { return filterString; } + 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 } @@ -840,7 +942,7 @@ string FilterSeqsCommand::createFilter() { MPI_Barrier(MPI_COMM_WORLD); #endif - + return filterString; } catch(exception& e) { @@ -874,8 +976,8 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* count++; } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - unsigned long int pos = in.tellg(); + #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; } @@ -897,7 +999,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* } #ifdef USE_MPI /**************************************************************************************/ -int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector& MPIPos) { +int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector& MPIPos) { try { MPI_Status status; @@ -946,11 +1048,12 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 1; + 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(); @@ -1022,11 +1125,53 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in); in.close(); - remove(tempFilename.c_str()); + m->mothurRemove(tempFilename); + } + + +#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]; + HANDLE hThreadArray[processors]; + + //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); + + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + num += pDataArray[i]->count; + 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]; } - return num; -#endif +#endif + return num; + } catch(exception& e) { m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");