*/
#include "classifyseqscommand.h"
-#include "sequence.hpp"
-#include "bayesian.h"
-#include "phylotree.h"
-#include "knn.h"
+
+
//**********************************************************************************************************************
+vector<string> ClassifySeqsCommand::setParameters(){
+ try {
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
-ClassifySeqsCommand::ClassifySeqsCommand(string option){
+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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 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 pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
+ 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 {
- abort = false;
+ 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, group, count, 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, align 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 count parameter allows you add a count 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: wang, knn and zap. The default is wang.\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 wang and zap 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 wang 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);
+ }
+}
+//**********************************************************************************************************************
+string ClassifySeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "taxonomy") { pattern = "[filename],[tag],[tag2],taxonomy"; }
+ else if (type == "taxsummary") { pattern = "[filename],[tag],[tag2],tax.summary"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],[tag2],flip.accnos"; }
+ else if (type == "matchdist") { pattern = "[filename],[tag],[tag2],match.dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "getOutputPattern");
+ 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(); hasName = false; hasCount=false;
//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","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters"};
- 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 = ""; }
+ //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; }
+ }
+ }
+
fastaFileName = validParameter.validFile(parameters, "fasta", false);
- if (fastaFileName == "not found") { mothurOut("fasta is a required parameter for the classify.seqs command."); mothurOutEndLine(); abort = true; }
+ 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 {
- 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++) {
- int ableToOpen;
- ifstream in;
- ableToOpen = openInputFile(fastaFileNames[i], in);
- if (ableToOpen == 1) {
- mothurOut(fastaFileNames[i] + " will be disregarded."); mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- 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]);
+ }
}
- in.close();
+
}
//make sure there is at least one valid file left
- if (fastaFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); 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;
- }
- else if (taxonomyFileName == "not open") { abort = true; }
-
-
namefile = validParameter.validFile(parameters, "name", false);
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++) {
- int ableToOpen;
- ifstream in;
- ableToOpen = openInputFile(namefileNames[i], in);
- if (ableToOpen == 1) { mothurOut("Unable to match name file with fasta file."); mothurOutEndLine(); abort = true; }
- in.close();
+ 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 (namefileNames.size() != 0) { hasName = true; }
+
if (namefile != "") {
- if (namefileNames.size() != fastaFileNames.size()) { abort = true; mothurOut("If you provide a name file, you must have one for each fasta file."); mothurOutEndLine(); }
+ 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(); }
+ }
+
+ //check for required parameters
+ countfile = validParameter.validFile(parameters, "count", false);
+ if (countfile == "not found") {
+ countfile = "";
+ }else {
+ m->splitAtDash(countfile, countfileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < countfileNames.size(); i++) {
+
+ bool ignore = false;
+ if (countfileNames[i] == "current") {
+ countfileNames[i] = m->getCountTableFile();
+ if (countfileNames[i] != "") { m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ countfileNames.erase(countfileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(countfileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { countfileNames[i] = inputDir + countfileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(countfileNames[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(countfileNames[i]);
+ m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ countfileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
+ m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ countfileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ countfileNames.erase(countfileNames.begin()+i);
+ i--;
+ }else {
+ m->setCountTableFile(countfileNames[i]);
+ }
+ }
+ }
+ }
+
+ if (countfileNames.size() != 0) { hasCount = true; if (countfileNames.size() != fastaFileNames.size()) {m->mothurOut("If you provide a count file, you must have one for each fasta file."); m->mothurOutEndLine(); } }
+
+ //make sure there is at least one valid file left
+ if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->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++) {
+
+ bool ignore = false;
+ if (groupfileNames[i] == "current") {
+ groupfileNames[i] = m->getGroupFile();
+ if (groupfileNames[i] != "") { m->mothurOut("Using " + groupfileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(groupfileNames[i]);
+ cout << path << '\t' << inputDir << endl;
+ //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();
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }else {
+ m->setGroupFile(groupfileNames[i]);
+ }
+ }
+
+ }
+ }
+
+ 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(); }
+ if (hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
+ }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);
+ 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();
+ }
- 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
+ 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); } }
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
- method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "bayesian"; }
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "wang"; }
+
+ temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){
+ temp = "8";
+ if (method == "zap") { temp = "7"; }
+ }
+ m->mothurConvert(temp, kmerSize);
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 = isTrue(temp);
+ probs = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "shortcuts", false); if (temp == "not found"){ temp = "true"; }
+ writeShortcuts = 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")) {
- mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); mothurOutEndLine();
+ if ((method == "wang") && (search != "kmer")) {
+ m->mothurOut("The wang method requires the kmer search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
- }
-
+
+ if ((method == "zap") && ((search != "kmer") && (search != "align"))) {
+ m->mothurOut("The zap method requires the kmer or align search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
+ search = "kmer";
+ }
+
+ if (!abort) {
+ if (!hasCount) {
+ 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, numwanted and probs.\n");
- mothurOut("The template, 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");
- 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 -2.0.\n");
- mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\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 probs parameter shut off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be run.\n");
- mothurOut("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");
- 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(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 (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ string outputMethodTag = method;
+ if(method == "wang"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts); }
+ else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand()); }
+ else if(method == "zap"){
+ outputMethodTag = search + "_" + outputMethodTag;
+ if (search == "kmer") { classify = new KmerTree(templateFileName, taxonomyFileName, kmerSize, cutoff); }
+ else { classify = new AlignTree(templateFileName, taxonomyFileName, cutoff); }
+ }
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, iters);
+ m->mothurOut(search + " is not a valid method option. I will run the command using wang.");
+ m->mothurOutEndLine();
+ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);
}
-
+
+ if (m->control_pressed) { delete classify; return 0; }
for (int s = 0; s < fastaFileNames.size(); s++) {
- //read namefile
- if(namefile != "") {
- nameMap.clear(); //remove old names
-
- ifstream inNames;
- openInputFile(namefileNames[s], inNames);
-
- string firstCol, secondCol;
- while(!inNames.eof()) {
- inNames >> firstCol >> secondCol; gobble(inNames);
- nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
- }
- inNames.close();
+ m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+
+ string baseTName = m->getSimpleName(taxonomyFileName);
+ if (taxonomyFileName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
+
+ //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]); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ variables["[tag]"] = RippedTaxName;
+ variables["[tag2]"] = outputMethodTag;
+ string newTaxonomyFile = getOutputFileName("taxonomy", variables);
+ string newaccnosFile = getOutputFileName("accnos", variables);
+ string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
+ string taxSummary = getOutputFileName("taxsummary", variables);
+
+ if ((method == "knn") && (search == "distance")) {
+ string DistName = getOutputFileName("matchdist", variables);
+ classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
}
-
- mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); mothurOutEndLine();
- string newTaxonomyFile = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "taxonomy";
- string tempTaxonomyFile = getRootName(fastaFileNames[s]) + "taxonomy.temp";
- string taxSummary = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "tax.summary";
+
+ outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
+ outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary);
int start = time(NULL);
int numFastaSeqs = 0;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<unsigned long long> MPIPos;
- lines.push_back(new linePair(0, numFastaSeqs));
+ 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;
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
- }
- else{
- vector<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] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
- }
- inFASTA.close();
+ char outNewTax[1024];
+ strcpy(outNewTax, newTaxonomyFile.c_str());
- numFastaSeqs = positions.size();
+ char outTempTax[1024];
+ strcpy(outTempTax, tempTaxonomyFile.c_str());
+
+ char outAcc[1024];
+ strcpy(outAcc, newaccnosFile.c_str());
- int numSeqsPerProcessor = numFastaSeqs / processors;
+ 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);
- for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ 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);
}
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+
+ //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);
}
- 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());
+ //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
- 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());
- }
+#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));
+ }
}
-#else
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
+#endif
+ if(processors == 1){
+ numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
+ }else{
+ numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
+ }
+#endif
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
-#endif
- //make taxonomy tree from new taxonomy file
- PhyloTree taxaBrowser;
+ if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
+ outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
+ }else { m->mothurRemove(newaccnosFile); }
+
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ start = time(NULL);
- ifstream in;
- openInputFile(tempTaxonomyFile, in);
- //read in users taxonomy file and add sequences to tree
- string name, taxon;
- while(!in.eof()){
- in >> name >> taxon; gobble(in);
-
- if (namefile != "") {
- itNames = nameMap.find(name);
-
- if (itNames == nameMap.end()) {
- mothurOut(name + " is not in your name file please correct."); mothurOutEndLine(); exit(1);
- }else{
- for (int i = 0; i < itNames->second; i++) {
- taxaBrowser.addSeqToTree(name+toString(i), taxon); //add it as many times as there are identical seqs
- }
- }
- }else { taxaBrowser.addSeqToTree(name, taxon); } //add it once
+
+ #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
+ m->readNames(namefileNames[s], nameMap);
+ m->mothurOut(" Done."); m->mothurOutEndLine();
}
- in.close();
-
- taxaBrowser.assignHeirarchyIDs(0);
+ #endif
- taxaBrowser.binUnclassified();
+ string group = "";
+ GroupMap* groupMap = NULL;
+ CountTable* ct = NULL;
+ PhyloSummary* taxaSum;
+ if (hasCount) {
+ ct = new CountTable();
+ ct->readTable(countfileNames[s], true, false);
+ taxaSum = new PhyloSummary(taxonomyFileName, ct);
+ taxaSum->summarize(tempTaxonomyFile);
+ }else {
+ if (groupfile != "") { group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
+
+ taxaSum = new PhyloSummary(taxonomyFileName, groupMap);
+
+ if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
+
+ 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()){
+ if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
+
+ in >> name >> taxon; m->gobble(in);
+
+ itNames = nameMap.find(name);
+
+ 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);
- remove(tempTaxonomyFile.c_str());
+ if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
//print summary file
ofstream outTaxTree;
- openOutputFile(taxSummary, outTaxTree);
- taxaBrowser.print(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 = taxaBrowser.getMaxLevel();
-
- //read taxfile - this reading and rewriting is done to preserve the confidence sscores.
+ int maxLevel = taxaSum->getMaxLevel();
+
+ //read taxfile - this reading and rewriting is done to preserve the confidence scores.
+ string name, taxon;
while (!inTax.eof()) {
- inTax >> name >> taxon; gobble(inTax);
+ if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; 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);
inTax.close();
outTax.close();
- remove(newTaxonomyFile.c_str());
+ if (ct != NULL) { delete ct; }
+ if (groupMap != NULL) { delete groupMap; } delete taxaSum;
+ m->mothurRemove(newTaxonomyFile);
rename(unclass.c_str(), newTaxonomyFile.c_str());
- mothurOutEndLine();
- mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); mothurOutEndLine(); mothurOutEndLine();
+ 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
+ }
+ delete classify;
+
+ 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();
+
+ //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); }
}
- delete classify;
+ current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
+
+
return 0;
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "execute");
+ m->errorOut(e, "ClassifySeqsCommand", "execute");
exit(1);
}
}
return newTax;
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
+ m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
exit(1);
}
}
/**************************************************************************************************/
-void 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 = 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", filename);
+ 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
- }
- catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
- try{
- ofstream output;
- ifstream input;
- openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ 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, writeShortcuts);
+ 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);
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
}
- input.close();
- output.close();
+ #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++){
+ 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"));
+ }
+
+ //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;
+
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
+ m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
exit(1);
}
}
-
//**********************************************************************************************************************
-int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName, string filename){
+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(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
+
+ string taxonomy;
- inFASTA.seekg(line->start);
+ inFASTA.seekg(filePos->start);
+
+ 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() != "") {
+
+ 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 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->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n"); }
+
+ }
+ //report progress
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); }
+
+ 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<line->numSeqs;i++){
+ 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);
- Sequence* candidateSeq = new Sequence(inFASTA);
+ 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 != "bad seq") {
- //output confidence scores or not
- if (probs) {
- outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
- }else{
- outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
- cout << 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) {
+ 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);
- outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
+ MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
+ delete buf3;
}
+
}
delete candidateSeq;
- if((i+1) % 100 == 0){
- mothurOut("Classifying sequence " + toString(i+1)); mothurOutEndLine();
- }
+ if((i+1) % 100 == 0){ cout << "Classifying sequence " << (i+1) << endl; }
}
- inFASTA.close();
- outTax.close();
- outTaxSimple.close();
+ 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
/**************************************************************************************************/
projects / mothur.git / blobdiff