#include "knn.h"
+
//**********************************************************************************************************************
vector<string> ClassifySeqsCommand::setParameters(){
try {
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);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
#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 match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
ClassifySeqsCommand::ClassifySeqsCommand(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<string> myArray = setParameters();
}
}
- //check for required parameters
- templateFileName = validParameter.validFile(parameters, "reference", true);
- if (templateFileName == "not found") {
- m->mothurOut("reference is a required parameter for the classify.seqs command.");
- m->mothurOutEndLine();
- abort = true;
- }
- else if (templateFileName == "not open") { abort = true; }
-
-
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") {
//if there is a current fasta file, use it
//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 = 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;
-
- ifstream in;
- 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() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
}
}
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ 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]; }
}
- }
-
- in.close();
+
+ int ableToOpen;
+
+ ifstream in;
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
+ }
}
}
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
-
- taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
- if (taxonomyFileName == "not found") {
- m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
- m->mothurOutEndLine();
- abort = true;
- }
- else if (taxonomyFileName == "not open") { abort = true; }
-
-
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
//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 = 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;
-
- ifstream in;
- 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() + m->getSimpleName(namefileNames[i]);
- m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- namefileNames[i] = tryPath;
+ bool ignore = false;
+ if (namefileNames[i] == "current") {
+ namefileNames[i] = m->getNameFile();
+ if (namefileNames[i] != "") { m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ namefileNames.erase(namefileNames.begin()+i);
+ i--;
}
}
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
- m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- namefileNames[i] = tryPath;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ 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]; }
}
- }
- in.close();
+ int ableToOpen;
+
+ ifstream in;
+ ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
- //erase from file list
- namefileNames.erase(namefileNames.begin()+i);
- i--;
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
+ m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ namefileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
+ m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ namefileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
+ //erase from file list
+ namefileNames.erase(namefileNames.begin()+i);
+ i--;
+ }else {
+ m->setNameFile(namefileNames[i]);
+ }
}
-
}
}
//erase from file list
groupfileNames.erase(groupfileNames.begin()+i);
i--;
+ }else {
+ m->setGroupFile(groupfileNames[i]);
}
}
}
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
convert(temp, kmerSize);
+ 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
+ templateFileName = validParameter.validFile(parameters, "reference", true);
+ if (templateFileName == "not found") {
+ //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templateFileName = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (templateFileName == "not open") { abort = true; }
+ else { if (save) { rdb->setSavedReference(templateFileName); } }
+
+ //this has to go after save so that if the user sets save=t and provides no reference we abort
+ taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxonomyFileName == "not found") {
+ //check for saved reference sequences
+ if (rdb->wordGenusProb.size() != 0) {
+ taxonomyFileName = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }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);
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()); }
+ 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());
}
if (m->control_pressed) { delete classify; return 0; }
m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
- string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
+ 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 += ".";
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, 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++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
+ 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; }
for (int i = 1; i < processors; i++) {
int done;
string group = "";
if (groupfile != "") { group = groupfileNames[s]; }
- PhyloSummary taxaSum(taxonomyFileName, group);
+ PhyloSummary taxaSum(baseTName, group);
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
else {
}
in.close();
}
- remove(tempTaxonomyFile.c_str());
+ m->mothurRemove(tempTaxonomyFile);
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
//print summary file
ofstream outTaxTree;
//read taxfile - this reading and rewriting is done to preserve the confidence scores.
string name, taxon;
while (!inTax.eof()) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->mothurRemove(unclass); delete classify; return 0; }
inTax >> name >> taxon; m->gobble(inTax);
inTax.close();
outTax.close();
- remove(newTaxonomyFile.c_str());
+ m->mothurRemove(newTaxonomyFile);
rename(unclass.c_str(), newTaxonomyFile.c_str());
m->mothurOutEndLine();
process++;
}else if (pid == 0){
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";
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());
+ in.close(); m->mothurRemove(m->getFullPathName(tempFile));
}
for(int i=0;i<processIDS.size();i++){
appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
- remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
- remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
+ m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
}
return num;
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