*/
#include "classifyseqscommand.h"
-#include "sequence.hpp"
-#include "bayesian.h"
-#include "doTaxonomy.h"
-#include "knn.h"
-//**********************************************************************************************************************
-ClassifySeqsCommand::ClassifySeqsCommand(string option){
+
+//**********************************************************************************************************************
+vector<string> ClassifySeqsCommand::setParameters(){
try {
- // globaldata = GlobalData::getInstance();
- abort = false;
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
+ 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 pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance", "kmer", "", "", "",false,false); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
+ CommandParameter pmethod("method", "Multiple", "bayesian-knn", "bayesian", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
+ 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);
+ 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifySeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
+ helpString += "The classify.seqs command parameters are reference, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
+ helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n";
+ helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n";
+ helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
+ helpString += "The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n";
+ helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+#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";
+ helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
+ helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n";
+ 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";
+ helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
+ helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
+ 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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClassifySeqsCommand::ClassifySeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ rdb = ReferenceDB::getInstance();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
-
- //valid paramters for this command
- string AlignArray[] = {"template","fasta","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
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
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //check for required parameters
- templateFileName = validParameter.validFile(parameters, "template", true);
- if (templateFileName == "not found") {
- mothurOut("template is a required parameter for the classify.seqs command.");
- mothurOutEndLine();
- abort = true;
- }
- else if (templateFileName == "not open") { abort = true; }
+ //initialize outputTypes
+ vector<string> 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 = ""; }
- fastaFileName = validParameter.validFile(parameters, "fasta", true);
- if (fastaFileName == "not found") {
- mothurOut("fasta is a required parameter for the classify.seqs command.");
- mothurOutEndLine();
- abort = true;
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("reference");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["reference"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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 = 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") {
+ //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else {
+ 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++) {
+
+ 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 (!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]; }
+ }
+
+ 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;
+ }
+ }
+
+ 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]);
+ }
+ }
+
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ namefile = validParameter.validFile(parameters, "name", false);
+ if (namefile == "not found") { namefile = ""; }
+
+ else {
+ 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++) {
+ 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 (!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]; }
+ }
+ 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;
+ }
+ }
+
+ 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]);
+ }
+ }
+ }
+ }
+
+ if (namefile != "") {
+ if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
}
- else if (fastaFileName == "not open") { abort = true; }
- taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
- if (taxonomyFileName == "not found") {
- mothurOut("taxonomy is a required parameter for the classify.seqs command.");
- mothurOutEndLine();
- abort = true;
+ groupfile = validParameter.validFile(parameters, "group", false);
+ if (groupfile == "not found") { groupfile = ""; }
+ else {
+ 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 = 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;
+
+ ifstream in;
+ 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() + m->getSimpleName(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupfileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupfileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }else {
+ m->setGroupFile(groupfileNames[i]);
+ }
+ }
}
- else if (taxonomyFileName == "not open") { abort = true; }
+ if (groupfile != "") {
+ if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
+ }else {
+ for (int i = 0; i < fastaFileNames.size(); i++) { groupfileNames.push_back(""); }
+ }
//check for optional parameter and set defaults
// ...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);
+ 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); } }
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
- convert(temp, processors);
+ //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); } }
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"; }
+ m->mothurConvert(temp, iters);
if ((method == "bayesian") && (search != "kmer")) {
- mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); mothurOutEndLine();
+ 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) {
- errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
+ m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
-
ClassifySeqsCommand::~ClassifySeqsCommand(){
-
if (abort == false) {
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
}
}
-
-//**********************************************************************************************************************
-
-void ClassifySeqsCommand::help(){
- try {
- mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
- mothurOut("The classify.seqs command parameters are template, fasta, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend and numwanted.\n");
- mothurOut("The template, fasta and taxonomy parameters are required.\n");
- mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
- mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n");
- mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
- mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n");
- mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0.\n");
- mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n");
- mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n");
- mothurOut("The classify.seqs command should be in the following format: \n");
- mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
- mothurOut("Example classify.seqs(fasta=amazon.fasta, template=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n");
- mothurOut("The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n");
- mothurOut("The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
int ClassifySeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
-
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- if(method == "bayesian") { classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff); }
- 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 {
- mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
- mothurOutEndLine();
- classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff);
+ 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, rand(), flip);
}
-
- int numFastaSeqs = 0;
- string newTaxonomyFile = getRootName(fastaFileName) + "taxonomy";
- string tempTaxonomyFile = getRootName(fastaFileName) + "taxonomy.temp";
- string taxSummary = getRootName(fastaFileName) + "tax.summary";
+ if (m->control_pressed) { delete classify; return 0; }
+
+ for (int s = 0; s < fastaFileNames.size(); s++) {
- int start = time(NULL);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
+ m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+
+ string baseTName = taxonomyFileName;
+ if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy(); }
- lines.push_back(new linePair(0, numFastaSeqs));
+ 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 += ".";
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile);
- }
- else{
- vector<int> positions;
- processIDS.resize(0);
-
- ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
-
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
+ if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
+ string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
+ string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";
+ 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); outputTypes["matchdist"].push_back(DistName);
}
- inFASTA.close();
- numFastaSeqs = positions.size();
+ 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 numSeqsPerProcessor = numFastaSeqs / processors;
+ int start = time(NULL);
+ int numFastaSeqs = 0;
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<unsigned long long> MPIPos;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ 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 outNewTax[1024];
+ strcpy(outNewTax, newTaxonomyFile.c_str());
+
+ 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(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
+
+ if (pid == 0) { //you are the root process
+
+ MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ 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(&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;
+ MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+ }
+ }else{ //you are a child process
+ MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numFastaSeqs+1);
+ MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ 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(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
+
+ int done = 0;
+ MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ }
+
+ //close files
+ 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 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(); }
+
+ //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));
}
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
}
- createProcesses(newTaxonomyFile, tempTaxonomyFile);
-
- rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
- rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
-
- for(int i=1;i<processors;i++){
- appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
- appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
- remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
- remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
+#endif
+ if(processors == 1){
+ numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
+ }else{
+ numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
}
+#endif
- }
-#else
- ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
+ 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);
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile);
-#endif
- delete classify;
- //make taxonomy tree from new taxonomy file
- ifstream inTaxonomy;
- openInputFile(tempTaxonomyFile, inTaxonomy);
+
+ #ifdef USE_MPI
+ if (pid == 0) { //this part does not need to be paralellized
+
+ if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush(); MPIReadNamesFile(namefileNames[s]); m->mothurOut(" Done."); m->mothurOutEndLine(); }
+ #else
+ //read namefile
+ 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->mothurOut(" Done."); m->mothurOutEndLine();
+ }
+ #endif
+
+ string group = "";
+ if (groupfile != "") { group = groupfileNames[s]; }
+
+ PhyloSummary taxaSum(baseTName, group);
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
- string accession, taxaList;
- PhyloTree taxaBrowser;
+ if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
+ else {
+ ifstream in;
+ m->openInputFile(tempTaxonomyFile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ string name, taxon;
+
+ while(!in.eof()){
+ in >> name >> taxon; m->gobble(in);
+
+ itNames = nameMap.find(name);
- //read in users taxonomy file and add sequences to tree
- while(!inTaxonomy.eof()){
- inTaxonomy >> accession >> taxaList;
+ if (itNames == nameMap.end()) {
+ m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
+ }else{
+ for (int i = 0; i < itNames->second.size(); i++) {
+ taxaSum.addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
+ }
+ itNames->second.clear();
+ nameMap.erase(itNames->first);
+ }
+ }
+ in.close();
+ }
+ m->mothurRemove(tempTaxonomyFile);
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
- taxaBrowser.addSeqToTree(accession, taxaList);
+ //print summary file
+ ofstream outTaxTree;
+ m->openOutputFile(taxSummary, outTaxTree);
+ taxaSum.print(outTaxTree);
+ outTaxTree.close();
- gobble(inTaxonomy);
+ //output taxonomy with the unclassified bins added
+ ifstream inTax;
+ m->openInputFile(newTaxonomyFile, inTax);
+
+ ofstream outTax;
+ string unclass = newTaxonomyFile + ".unclass.temp";
+ m->openOutputFile(unclass, outTax);
+
+ //get maxLevel from phylotree so you know how many 'unclassified's to add
+ int maxLevel = taxaSum.getMaxLevel();
+
+ //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++) { m->mothurRemove(outputNames[i]); } m->mothurRemove(unclass); delete classify; return 0; }
+
+ inTax >> name >> taxon; m->gobble(inTax);
+
+ string newTax = addUnclassifieds(taxon, maxLevel);
+
+ outTax << name << '\t' << newTax << endl;
+ }
+ inTax.close();
+ outTax.close();
+
+ m->mothurRemove(newTaxonomyFile);
+ rename(unclass.c_str(), newTaxonomyFile.c_str());
+
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
}
- inTaxonomy.close();
- remove(tempTaxonomyFile.c_str());
- taxaBrowser.assignHeirarchyIDs(0);
-
- ofstream outTaxTree;
- openOutputFile(taxSummary, outTaxTree);
+ //set taxonomy file as new current taxonomyfile
+ string current = "";
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
- taxaBrowser.print(outTaxTree);
+ current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
- mothurOutEndLine();
- mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
+ delete classify;
return 0;
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "execute");
+ m->errorOut(e, "ClassifySeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
+ try{
+ string newTax, taxon;
+ int level = 0;
+
+ //keep what you have counting the levels
+ while (tax.find_first_of(';') != -1) {
+ //get taxon
+ taxon = tax.substr(0,tax.find_first_of(';'))+';';
+ tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+ newTax += taxon;
+ level++;
+ }
+
+ //add "unclassified" until you reach maxLevel
+ while (level < maxlevel) {
+ newTax += "unclassified;";
+ level++;
+ }
+
+ return newTax;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
exit(1);
}
}
+
/**************************************************************************************************/
-void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile) {
+int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
- // processIDS.resize(0);
+
+ 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){
- driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp");
+ num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + 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("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }
}
+ //parent does its part
+ num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
+
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
-#endif
+
+ 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(); 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);
+ 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"));
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(accnos, out);
+ out.close();
+ }
+
+ return num;
+
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "createProcesses");
+ m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
exit(1);
}
}
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; }
output.close();
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
+ m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
exit(1);
}
}
//**********************************************************************************************************************
-int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName){
+int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
try {
ofstream outTax;
- openOutputFile(taxFName, outTax);
+ m->openOutputFile(taxFName, outTax);
ofstream outTaxSimple;
- openOutputFile(tempTFName, outTaxSimple);
+ m->openOutputFile(tempTFName, outTaxSimple);
+
+ ofstream outAcc;
+ m->openOutputFile(accnos, outAcc);
ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
-
- inFASTA.seekg(line->start);
+ m->openInputFile(filename, inFASTA);
string taxonomy;
- for(int i=0;i<line->numSeqs;i++){
-
- Sequence* candidateSeq = new Sequence(inFASTA);
+ inFASTA.seekg(filePos->start);
- taxonomy = classify->getTaxonomy(candidateSeq);
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+ if (m->control_pressed) {
+ inFASTA.close();
+ outTax.close();
+ outTaxSimple.close();
+ outAcc.close(); return 0; }
+
+ Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
+
+ if (candidateSeq->getName() != "") {
- if (taxonomy != "bad seq") {
- outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
+ taxonomy = classify->getTaxonomy(candidateSeq);
+
+ if (m->control_pressed) { delete candidateSeq; return 0; }
+
+ 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((i+1) % 100 == 0){
- mothurOut("Classifying sequence " + toString(i+1)); mothurOutEndLine();
- }
+ #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(); }
+
}
-
+ //report progress
+ if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+
inFASTA.close();
outTax.close();
outTaxSimple.close();
+ outAcc.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+#ifdef USE_MPI
+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;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ string taxonomy;
+ string outputString;
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
+
+ Sequence* candidateSeq = new Sequence(iss);
+
+ if (candidateSeq->getName() != "") {
+ taxonomy = classify->getTaxonomy(candidateSeq);
+
+ 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) {
+ 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);
+
+ 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;
+
+ if((i+1) % 100 == 0){ cout << "Classifying sequence " << (i+1) << endl; }
+ }
+
+ if(num % 100 != 0){ cout << "Classifying sequence " << (num) << endl; }
+
return 1;
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "driver");
+ m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
exit(1);
}
}
+//**********************************************************************************************************************
+int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
+ try {
+
+ nameMap.clear(); //remove old names
+
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ //char* inFileName = new char[nameFilename.length()];
+ //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, nameFilename.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ MPI_File_get_size(inMPI, &size);
+ //delete inFileName;
+
+ char* buffer = new char[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buffer;
+
+ string firstCol, secondCol;
+ while(!iss.eof()) {
+ iss >> firstCol >> secondCol; m->gobble(iss);
+
+ vector<string> temp;
+ m->splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
+ }
+
+ MPI_File_close(&inMPI);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
+ exit(1);
+ }
+}
+#endif
/**************************************************************************************************/