X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerapintailcommand.cpp;h=9d492afe950713cefd4d1fad7fcd72a6da74640c;hp=b11887d8cdddc110490e436777422dc0b0d86105;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7 diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp index b11887d..9d492af 100644 --- a/chimerapintailcommand.cpp +++ b/chimerapintailcommand.cpp @@ -10,21 +10,23 @@ #include "chimerapintailcommand.h" #include "pintail.h" + //********************************************************************************************************************** vector ChimeraPintailCommand::setParameters(){ try { - CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pconservation); - CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pquantile); - CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter); - CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow); - CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement); - CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta); + CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation); + CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile); + CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter); + CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow); + CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement); + CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask); + 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); + CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave); + vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; @@ -50,6 +52,7 @@ string ChimeraPintailCommand::getHelpString(){ #ifdef USE_MPI helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n"; #endif + helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f."; helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=300. \n"; helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n"; helpString += "The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n"; @@ -66,6 +69,22 @@ string ChimeraPintailCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraPintailCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "chimera") { pattern = "[filename],[tag],pintail.chimeras-[filename],pintail.chimeras"; } + else if (type == "accnos") { pattern = "[filename],[tag],pintail.accnos-[filename],pintail.accnos"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** ChimeraPintailCommand::ChimeraPintailCommand(){ try { abort = true; calledHelp = true; @@ -73,6 +92,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(){ vector tempOutNames; outputTypes["chimera"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + } catch(exception& e) { m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand"); @@ -83,9 +103,11 @@ ChimeraPintailCommand::ChimeraPintailCommand(){ ChimeraPintailCommand::ChimeraPintailCommand(string option) { try { abort = false; calledHelp = false; + rdb = ReferenceDB::getInstance(); //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(); @@ -104,6 +126,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { vector tempOutNames; outputTypes["chimera"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -204,6 +227,8 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; + }else { + m->setFastaFile(fastaFileNames[i]); } } } @@ -218,13 +243,35 @@ ChimeraPintailCommand::ChimeraPintailCommand(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, "increment", false); if (temp == "not found") { temp = "25"; } - convert(temp, increment); + m->mothurConvert(temp, increment); + + temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; } + save = m->isTrue(temp); + rdb->save = save; + if (save) { //clear out old references + rdb->clearMemory(); + } + + //this has to go after save so that if the user sets save=t and provides no reference we abort + templatefile = validParameter.validFile(parameters, "reference", true); + if (templatefile == "not found") { + //check for saved reference sequences + if (rdb->referenceSeqs.size() != 0) { + templatefile = "saved"; + }else { + m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); + m->mothurOutEndLine(); + abort = true; + } + }else if (templatefile == "not open") { abort = true; } + else { if (save) { rdb->setSavedReference(templatefile); } } + maskfile = validParameter.validFile(parameters, "mask", false); if (maskfile == "not found") { maskfile = ""; } @@ -271,10 +318,6 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { //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 = ""; } - templatefile = validParameter.validFile(parameters, "reference", true); - if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; } - consfile = validParameter.validFile(parameters, "conservation", true); if (consfile == "not open") { abort = true; } else if (consfile == "not found") { @@ -326,15 +369,18 @@ int ChimeraPintailCommand::execute(){ if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); } //check for quantile to save the time + string baseName = templatefile; + if (templatefile == "saved") { baseName = rdb->getSavedReference(); } + string tempQuan = ""; if ((!filter) && (maskfile == "")) { - tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan"; }else if ((!filter) && (maskfile != "")) { - tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan"; }else if ((filter) && (maskfile != "")) { - tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; }else if ((filter) && (maskfile == "")) { - tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; } ifstream FileTest(tempQuan.c_str()); @@ -347,13 +393,13 @@ int ChimeraPintailCommand::execute(){ string tryPath = m->getDefaultPath(); string tempQuan = ""; if ((!filter) && (maskfile == "")) { - tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan"; + tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan"; }else if ((!filter) && (maskfile != "")) { - tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan"; + tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan"; }else if ((filter) && (maskfile != "")) { - tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; + tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; }else if ((filter) && (maskfile == "")) { - tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; + tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; } ifstream FileTest2(tempQuan.c_str()); @@ -364,20 +410,18 @@ int ChimeraPintailCommand::execute(){ } } } - chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir); 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])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos"; - }else { - outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.accnos"; - } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])); + if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); } + outputFileName = getOutputFileName("chimera", variables); + accnosFileName = getOutputFileName("accnos", variables); + - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); @@ -389,7 +433,7 @@ int ChimeraPintailCommand::execute(){ #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 @@ -415,7 +459,7 @@ int ChimeraPintailCommand::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) { outputTypes.clear(); 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()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; } if (pid == 0) { //you are the root process @@ -435,7 +479,7 @@ int ChimeraPintailCommand::execute(){ //do your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { outputTypes.clear(); 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()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); 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]); } delete chimera; return 0; } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -450,7 +494,7 @@ int ChimeraPintailCommand::execute(){ //do your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { outputTypes.clear(); 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()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; } } //close files @@ -459,19 +503,20 @@ int ChimeraPintailCommand::execute(){ MPI_File_close(&outMPIAccnos); 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)])); - } - + //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) { outputTypes.clear(); remove(outputFileName.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]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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]; } lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); @@ -484,19 +529,19 @@ int ChimeraPintailCommand::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; @@ -504,9 +549,10 @@ int ChimeraPintailCommand::execute(){ } #else + lines.push_back(new linePair(0, 1000)); numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.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]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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]; } lines.clear(); delete chimera; return 0; } #endif #endif @@ -582,18 +628,18 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string } 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; } #endif //report progress - if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } } //report progress - if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } out.close(); out2.close(); @@ -608,7 +654,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ +int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ try { MPI_Status status; @@ -649,10 +695,10 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi delete candidateSeq; //report progress - if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); } + if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; } } //report progress - if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); } + if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; } return 0; @@ -668,7 +714,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi int ChimeraPintailCommand::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; @@ -708,7 +754,7 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam 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;