*/
#include "classifyseqscommand.h"
-#include "sequence.hpp"
-#include "bayesian.h"
-#include "phylotree.h"
-#include "phylosummary.h"
-#include "knn.h"
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
+ //CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n";
helpString += "The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n";
helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method. The default is 100.\n";
+ //helpString += "The flip parameter allows you shut off mothur's The default is T.\n";
helpString += "The classify.seqs command should be in the following format: \n";
helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
}
}
//**********************************************************************************************************************
+string ClassifySeqsCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::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 == "taxonomy") { outputFileName = "taxonomy"; }
+ else if (type == "accnos") { outputFileName = "flip.accnos"; }
+ else if (type == "taxsummary") { outputFileName = "tax.summary"; }
+ else if (type == "matchdist") { outputFileName = "match.dist"; }
+ 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, "ClassifySeqsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
}
outputTypes["taxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
//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 = ""; }
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
- convert(temp, kmerSize);
+ m->mothurConvert(temp, kmerSize);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
}else if (taxonomyFileName == "not open") { abort = true; }
else { if (save) { rdb->setSavedTaxonomy(taxonomyFileName); } }
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- convert(temp, processors);
-
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "bayesian"; }
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, misMatch);
+ m->mothurConvert(temp, misMatch);
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
- convert(temp, gapOpen);
+ m->mothurConvert(temp, gapOpen);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, gapExtend);
+ m->mothurConvert(temp, gapExtend);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found"){ temp = "10"; }
- convert(temp, numWanted);
+ m->mothurConvert(temp, numWanted);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
probs = m->isTrue(temp);
+ //temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "T"; }
+ //flip = m->isTrue(temp);
+ flip = true;
+
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
- convert(temp, iters);
-
+ m->mothurConvert(temp, iters);
if ((method == "bayesian") && (search != "kmer")) {
m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
search = "kmer";
}
- }
-
+
+ if (!abort) {
+ if (namefileNames.size() == 0){
+ if (fastaFileNames.size() != 0) {
+ vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
+ parser.getNameFile(files);
+ }
+ }
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
int ClassifySeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
- else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
+
+ if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip); }
+ else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand()); }
else {
m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
m->mothurOutEndLine();
- classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
+ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);
}
if (m->control_pressed) { delete classify; return 0; }
-
for (int s = 0; s < fastaFileNames.size(); s++) {
string baseTName = taxonomyFileName;
if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy(); }
- string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
- RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
- if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
- RippedTaxName += ".";
-
+ //set rippedTaxName to
+ string RippedTaxName = "";
+ bool foundDot = false;
+ for (int i = baseTName.length()-1; i >= 0; i--) {
+ if (foundDot && (baseTName[i] != '.')) { RippedTaxName = baseTName[i] + RippedTaxName; }
+ else if (foundDot && (baseTName[i] == '.')) { break; }
+ else if (!foundDot && (baseTName[i] == '.')) { foundDot = true; }
+ }
+ if (RippedTaxName != "") { RippedTaxName += "."; }
+
if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
- string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
+ string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxonomy");
+ string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("accnos");
string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
- string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
+ string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxsummary");
if ((method == "knn") && (search == "distance")) {
- string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
+ string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("matchdist");
classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
}
outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
+ outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary);
int start = time(NULL);
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
- vector<unsigned long int> MPIPos;
+ vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_File inMPI;
MPI_File outMPINewTax;
MPI_File outMPITempTax;
+ MPI_File outMPIAcc;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outTempTax[1024];
strcpy(outTempTax, tempTaxonomyFile.c_str());
+
+ char outAcc[1024];
+ strcpy(outAcc, newaccnosFile.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, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
+ MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
if (pid == 0) { //you are the root process
//align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
for (int i = 1; i < processors; i++) {
int done;
//align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
int done = 0;
MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
MPI_File_close(&inMPI);
MPI_File_close(&outMPINewTax);
MPI_File_close(&outMPITempTax);
+ MPI_File_close(&outMPIAcc);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
+ vector<unsigned long long> 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)])); }
+#else
+ if (processors == 1) {
+ lines.push_back(new linePair(0, 1000));
+ }else {
+ positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
- 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){
- numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+ //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));
+ }
}
- else{
- processIDS.resize(0);
-
- numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
-
+#endif
+ if(processors == 1){
+ numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
+ }else{
+ numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
}
- #else
- numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
- #endif
#endif
+
+ if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
start = time(NULL);
-
+
+
#ifdef USE_MPI
if (pid == 0) { //this part does not need to be paralellized
if(namefile != "") {
m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
-
nameMap.clear(); //remove old names
-
- ifstream inNames;
- m->openInputFile(namefileNames[s], inNames);
-
- string firstCol, secondCol;
- while(!inNames.eof()) {
- inNames >> firstCol >> secondCol; m->gobble(inNames);
-
- vector<string> temp;
- m->splitAtComma(secondCol, temp);
-
- nameMap[firstCol] = temp;
- }
- inNames.close();
-
+ m->readNames(namefileNames[s], nameMap);
m->mothurOut(" Done."); m->mothurOutEndLine();
}
#endif
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
+ current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
delete classify;
+
return 0;
}
catch(exception& e) {
/**************************************************************************************************/
-int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
+int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+
int num = 0;
+ processIDS.clear();
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 1;
//loop through and create all the processes you want
while (process != processors) {
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){
- num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
+ num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
//pass numSeqs to parent
ofstream out;
}
//parent does its part
- num = driver(lines[0], taxFileName, tempTaxFile, filename);
+ num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(m->getFullPathName(tempFile));
}
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the alignData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<classifyData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ // Allocate memory for thread data.
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+
+ classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip);
+ pDataArray.push_back(tempclass);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MyClassThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+
+ }
+
+ //parent does its part
+ num = driver(lines[processors-1], taxFileName + toString(processors-1) + ".temp", tempTaxFile + toString(processors-1) + ".temp", accnos + toString(processors-1) + ".temp", filename);
+ processIDS.push_back((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;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ #endif
+ vector<string> nonBlankAccnosFiles;
+ if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
+ else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
+
for(int i=0;i<processIDS.size();i++){
- appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
- appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+ m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
+ m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+ if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
+ }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp")); }
+
m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
}
- return num;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream input;
- m->openOutputFileAppend(filename, output);
- m->openInputFile(temp, input);
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ m->appendFiles(nonBlankAccnosFiles[h], accnos);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(accnos, out);
+ out.close();
}
+
+ return num;
- input.close();
- output.close();
}
catch(exception& e) {
- m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
+ m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
exit(1);
}
}
-
//**********************************************************************************************************************
-int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
+int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
try {
ofstream outTax;
m->openOutputFile(taxFName, outTax);
ofstream outTaxSimple;
m->openOutputFile(tempTFName, outTaxSimple);
+
+ ofstream outAcc;
+ m->openOutputFile(accnos, outAcc);
ifstream inFASTA;
m->openInputFile(filename, inFASTA);
int count = 0;
while (!done) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) {
+ inFASTA.close();
+ outTax.close();
+ outTaxSimple.close();
+ outAcc.close(); return 0; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
taxonomy = classify->getTaxonomy(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 0; }
-
- if (taxonomy != "bad seq") {
- //output confidence scores or not
- if (probs) {
- outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
- }else{
- outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
- }
-
- outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
+
+ if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
+
+ //output confidence scores or not
+ if (probs) {
+ outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
+ }else{
+ outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
}
+
+ if (classify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
+
+ outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
+
count++;
}
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; }
inFASTA.close();
outTax.close();
outTaxSimple.close();
+ outAcc.close();
return count;
}
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
+int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, MPI_File& accFile, vector<unsigned long long>& MPIPos){
try {
MPI_Status statusNew;
MPI_Status statusTemp;
+ MPI_Status statusAcc;
MPI_Status status;
int pid;
if (candidateSeq->getName() != "") {
taxonomy = classify->getTaxonomy(candidateSeq);
- if (taxonomy != "bad seq") {
- //output confidence scores or not
- if (probs) {
- outputString = candidateSeq->getName() + "\t" + taxonomy + "\n";
- }else{
- outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
- }
-
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
+ if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
- MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
- delete buf2;
-
+ //output confidence scores or not
+ if (probs) {
+ outputString = candidateSeq->getName() + "\t" + taxonomy + "\n";
+ }else{
outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
- length = outputString.length();
- char* buf = new char[length];
- memcpy(buf, outputString.c_str(), length);
+ }
+
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
- MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
- delete buf;
+ MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
+ delete buf2;
+
+ outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
+ length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
+ delete buf;
+
+ if (classify->getFlipped()) {
+ outputString = candidateSeq->getName() + "\n";
+ length = outputString.length();
+ char* buf3 = new char[length];
+ memcpy(buf3, outputString.c_str(), length);
+
+ MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
+ delete buf3;
}
+
}
delete candidateSeq;
projects / mothur.git / blobdiff