X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=6a4732cf72cd4222e539beb93c6b0b45226d2a08;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=584e9874fd4cea4136d45c184a4c0662973c3b25;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp index 584e987..6a4732c 100644 --- a/chimeracheckcommand.cpp +++ b/chimeracheckcommand.cpp @@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraCheckCommand::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 = "chimeracheck.chimeras"; } + 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); + } +} +//********************************************************************************************************************** ChimeraCheckCommand::ChimeraCheckCommand(){ try { abort = true; calledHelp = true; @@ -281,7 +301,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { string 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, "save", false); if (temp == "not found"){ temp = "f"; } save = m->isTrue(temp); @@ -306,14 +326,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } - convert(temp, ksize); + m->mothurConvert(temp, ksize); temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } svg = m->isTrue(temp); if (nameFileNames.size() != 0) { svg = true; } temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } - convert(temp, increment); + m->mothurConvert(temp, increment); } } catch(exception& e) { @@ -342,14 +362,14 @@ int ChimeraCheckCommand::execute(){ if (m->control_pressed) { delete chimera; return 0; } if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera"); outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); #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 @@ -370,7 +390,7 @@ int ChimeraCheckCommand::execute(){ 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); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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); 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 MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs @@ -390,7 +410,7 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } //wait on chidren for(int j = 1; j < processors; j++) { @@ -410,7 +430,7 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } //tell parent you are done. char buf[5]; @@ -424,18 +444,20 @@ int ChimeraCheckCommand::execute(){ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = m->divideFile(fastaFileNames[i], processors); - - for (int s = 0; s < (positions.size()-1); s++) { - lines.push_back(new linePair(positions[s], positions[(s+1)])); - } + //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + vector positions = m->divideFile(fastaFileNames[i], processors); + + for (int s = 0; s < (positions.size()-1); s++) { + lines.push_back(new linePair(positions[s], positions[(s+1)])); + } + if(processors == 1){ numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); @@ -447,11 +469,11 @@ int ChimeraCheckCommand::execute(){ //append output files for(int j=1;jappendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName); - remove((outputFileName + toString(processIDS[j]) + ".temp").c_str()); + m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp")); } if (m->control_pressed) { - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); + for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); delete chimera; return 0; @@ -459,9 +481,10 @@ int ChimeraCheckCommand::execute(){ } #else + lines.push_back(new linePair(0, 1000)); numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } #endif #endif delete chimera; @@ -519,8 +542,8 @@ int ChimeraCheckCommand::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; } @@ -528,6 +551,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi //report progress if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + count++; } //report progress if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } @@ -544,7 +568,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ +int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ try { MPI_File outAccMPI; MPI_Status status; @@ -596,7 +620,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 0; int num = 0; @@ -636,7 +660,7 @@ int ChimeraCheckCommand::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;