OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("classify.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
it = parameters.find("template");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["template"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(fastaFileName, fastaFileNames);
+ m->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(fastaFileNames[i]);
+ string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
- #ifdef USE_MPI
- int pid;
- MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
ifstream in;
- ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
fastaFileNames[i] = tryPath;
}
}
in.close();
- #ifdef USE_MPI
- for (int j = 1; j < processors; j++) {
- MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
- }
- }else{
- MPI_Status status;
- MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
- }
-
- #endif
-
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
if (namefile == "not found") { namefile = ""; }
else {
- splitAtDash(namefile, namefileNames);
+ m->splitAtDash(namefile, namefileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < namefileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(namefileNames[i]);
+ string path = m->hasPath(namefileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
}
int ableToOpen;
- #ifdef USE_MPI
- int pid;
- MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
ifstream in;
- ableToOpen = openInputFile(namefileNames[i], in, "noerror");
+ ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(namefileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
namefileNames[i] = tryPath;
}
}
in.close();
- #ifdef USE_MPI
- for (int j = 1; j < processors; j++) {
- MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
- }
- }else{
- MPI_Status status;
- MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
- }
-
- #endif
-
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
//erase from file list
groupfile = validParameter.validFile(parameters, "group", false);
if (groupfile == "not found") { groupfile = ""; }
else {
- splitAtDash(groupfile, groupfileNames);
+ m->splitAtDash(groupfile, groupfileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < groupfileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(groupfileNames[i]);
+ string path = m->hasPath(groupfileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
}
int ableToOpen;
- #ifdef USE_MPI
- int pid;
- MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
ifstream in;
- ableToOpen = openInputFile(groupfileNames[i], in, "noerror");
+ ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(groupfileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
groupfileNames[i] = tryPath;
}
}
in.close();
- #ifdef USE_MPI
- for (int j = 1; j < processors; j++) {
- MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
- }
- }else{
- MPI_Status status;
- MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
- }
-
- #endif
-
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
//erase from file list
convert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
- probs = isTrue(temp);
+ probs = m->isTrue(temp);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
convert(temp, iters);
m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
- if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
- string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
- string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
- string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
+ string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
+ RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
+ if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
+ RippedTaxName += ".";
+
+ if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
+ string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
+ string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
+ string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
+
+ if ((method == "knn") && (search == "distance")) {
+ string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
+ classify->setDistName(DistName); outputNames.push_back(DistName);
+ }
outputNames.push_back(newTaxonomyFile);
outputNames.push_back(taxSummary);
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) { //you are the root process
- MPIPos = setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
+ MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
+
+ vector<unsigned long int> 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){
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+ numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
}
else{
- vector<unsigned long int> positions;
processIDS.resize(0);
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
-
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
- }
- inFASTA.close();
-
- numFastaSeqs = positions.size();
-
- int numSeqsPerProcessor = numFastaSeqs / processors;
-
- for (int i = 0; i < processors; i++) {
- unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
- createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+ numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
}
#else
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+ numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
#endif
#endif
nameMap.clear(); //remove old names
ifstream inNames;
- openInputFile(namefileNames[s], inNames);
+ m->openInputFile(namefileNames[s], inNames);
string firstCol, secondCol;
while(!inNames.eof()) {
- inNames >> firstCol >> secondCol; gobble(inNames);
+ inNames >> firstCol >> secondCol; m->gobble(inNames);
vector<string> temp;
- splitAtComma(secondCol, temp);
+ m->splitAtComma(secondCol, temp);
nameMap[firstCol] = temp;
}
if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
else {
ifstream in;
- openInputFile(tempTaxonomyFile, in);
+ m->openInputFile(tempTaxonomyFile, in);
//read in users taxonomy file and add sequences to tree
string name, taxon;
while(!in.eof()){
- in >> name >> taxon; gobble(in);
+ in >> name >> taxon; m->gobble(in);
itNames = nameMap.find(name);
//print summary file
ofstream outTaxTree;
- openOutputFile(taxSummary, outTaxTree);
+ m->openOutputFile(taxSummary, outTaxTree);
taxaSum.print(outTaxTree);
outTaxTree.close();
//output taxonomy with the unclassified bins added
ifstream inTax;
- openInputFile(newTaxonomyFile, inTax);
+ m->openInputFile(newTaxonomyFile, inTax);
ofstream outTax;
string unclass = newTaxonomyFile + ".unclass.temp";
- openOutputFile(unclass, outTax);
+ m->openOutputFile(unclass, outTax);
//get maxLevel from phylotree so you know how many 'unclassified's to add
int maxLevel = taxaSum.getMaxLevel();
while (!inTax.eof()) {
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
- inTax >> name >> taxon; gobble(inTax);
+ inTax >> name >> taxon; m->gobble(inTax);
string newTax = addUnclassifieds(taxon, maxLevel);
/**************************************************************************************************/
-void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
+int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
- // processIDS.resize(0);
+ int num = 0;
//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){
- driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
+ num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
int temp = processIDS[i];
wait(&temp);
}
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = filename + 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());
+ }
+
+ return num;
#endif
}
catch(exception& e) {
ofstream output;
ifstream input;
- openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ m->openOutputFileAppend(filename, output);
+ m->openInputFile(temp, input);
while(char c = input.get()){
if(input.eof()) { break; }
//**********************************************************************************************************************
-int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName, string filename){
+int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
try {
ofstream outTax;
- openOutputFile(taxFName, outTax);
+ m->openOutputFile(taxFName, outTax);
ofstream outTaxSimple;
- openOutputFile(tempTFName, outTaxSimple);
+ m->openOutputFile(tempTFName, outTaxSimple);
ifstream inFASTA;
- openInputFile(filename, inFASTA);
-
- inFASTA.seekg(line->start);
+ m->openInputFile(filename, inFASTA);
string taxonomy;
- for(int i=0;i<line->numSeqs;i++){
+ inFASTA.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
if (m->control_pressed) { return 0; }
- Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+ Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
if (candidateSeq->getName() != "") {
taxonomy = classify->getTaxonomy(candidateSeq);
outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
}
- }
+ count++;
+ }
delete candidateSeq;
- if((i+1) % 100 == 0){
- m->mothurOut("Classifying sequence " + toString(i+1)); m->mothurOutEndLine();
- }
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+
+ //report progress
+ if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
}
-
+ //report progress
+ if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+
inFASTA.close();
outTax.close();
outTaxSimple.close();
- return 1;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "driver");
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<long>& MPIPos){
+int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
try {
MPI_Status statusNew;
MPI_Status statusTemp;
string firstCol, secondCol;
while(!iss.eof()) {
- iss >> firstCol >> secondCol; gobble(iss);
+ iss >> firstCol >> secondCol; m->gobble(iss);
vector<string> temp;
- splitAtComma(secondCol, temp);
+ m->splitAtComma(secondCol, temp);
nameMap[firstCol] = temp;
}
projects / mothur.git / blobdiff