X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=942635ea183cedee17550fd85df3c3daa68d9979;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=fd80ec965b4040f78dce01579e1974760fbb2a89;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp index fd80ec9..942635e 100644 --- a/chimeraccodecommand.cpp +++ b/chimeraccodecommand.cpp @@ -64,6 +64,28 @@ string ChimeraCcodeCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraCcodeCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "chimera") { outputFileName = "ccode.chimeras"; } + else if (type == "mapinfo") { outputFileName = "mapinfo"; } + else if (type == "accnos") { outputFileName = "ccode.accnos"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** ChimeraCcodeCommand::ChimeraCcodeCommand(){ try { abort = true; calledHelp = true; @@ -223,13 +245,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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); temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; } - convert(temp, window); + m->mothurConvert(temp, window); temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; } - convert(temp, numwanted); + m->mothurConvert(temp, numwanted); temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; } save = m->isTrue(temp); @@ -284,22 +306,24 @@ int ChimeraCcodeCommand::execute(){ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it string outputFileName, accnosFileName; if (maskfile != "") { - outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("chimera"); + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("accnos"); }else { - outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera"); + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos"); + } - string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo"; + string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("mapinfo"); + - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); return 0; } + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; } #ifdef USE_MPI int pid, numSeqsPerProcessor; int tag = 2001; - vector MPIPos; + vector MPIPos; MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are @@ -325,7 +349,7 @@ int ChimeraCcodeCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } if (pid == 0) { //you are the root process string outTemp = "For full window mapping info refer to " + mapInfo + "\n"; @@ -355,7 +379,7 @@ int ChimeraCcodeCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -371,7 +395,7 @@ int ChimeraCcodeCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } } //close files @@ -390,19 +414,21 @@ int ChimeraCcodeCommand::execute(){ outHeader.close(); - 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)])); - } + //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #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){ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); @@ -415,19 +441,19 @@ int ChimeraCcodeCommand::execute(){ //append output files for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); - remove((outputFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp")); } //append output files for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); - remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp")); } if (m->control_pressed) { - remove(outputFileName.c_str()); - remove(accnosFileName.c_str()); - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); + m->mothurRemove(outputFileName); + m->mothurRemove(accnosFileName); + for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; @@ -436,15 +462,16 @@ int ChimeraCcodeCommand::execute(){ } #else + lines.push_back(new linePair(0, 1000)); numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } #endif m->appendFiles(outputFileName, tempHeader); - remove(outputFileName.c_str()); + m->mothurRemove(outputFileName); rename(tempHeader.c_str(), outputFileName.c_str()); #endif @@ -521,8 +548,8 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi } delete candidateSeq; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - unsigned long int pos = inFASTA.tellg(); + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = inFASTA.tellg(); if ((pos == -1) || (pos >= filePos->end)) { break; } #else if (inFASTA.eof()) { break; } @@ -547,7 +574,7 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ +int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ try { MPI_Status status; @@ -608,7 +635,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 0; int num = 0; @@ -648,7 +675,7 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp"; m->openInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } - in.close(); remove(tempFile.c_str()); + in.close(); m->mothurRemove(tempFile); } return num;