2 * classifyseqscommand.cpp
5 * Created by westcott on 11/2/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "classifyseqscommand.h"
11 #include "sequence.hpp"
13 #include "phylotree.h"
14 #include "phylosummary.h"
18 //**********************************************************************************************************************
19 vector<string> ClassifySeqsCommand::setParameters(){
21 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
22 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
23 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
24 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
25 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
26 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance", "kmer", "", "", "",false,false); parameters.push_back(psearch);
27 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
28 CommandParameter pmethod("method", "Multiple", "bayesian-knn", "bayesian", "", "", "",false,false); parameters.push_back(pmethod);
29 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
30 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
31 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
32 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
33 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
34 CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
35 CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
36 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
37 CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
38 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
39 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
41 vector<string> myArray;
42 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
46 m->errorOut(e, "ClassifySeqsCommand", "setParameters");
50 //**********************************************************************************************************************
51 string ClassifySeqsCommand::getHelpString(){
53 string helpString = "";
54 helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
55 helpString += "The classify.seqs command parameters are reference, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
56 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";
57 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";
58 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";
59 helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
60 helpString += "The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n";
61 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n";
62 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
64 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
66 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
67 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
68 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
69 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
70 helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n";
71 helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n";
72 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";
73 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";
74 helpString += "The classify.seqs command should be in the following format: \n";
75 helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
76 helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
77 helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
78 helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
79 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
83 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
87 //**********************************************************************************************************************
88 ClassifySeqsCommand::ClassifySeqsCommand(){
90 abort = true; calledHelp = true;
92 vector<string> tempOutNames;
93 outputTypes["taxonomy"] = tempOutNames;
94 outputTypes["taxsummary"] = tempOutNames;
95 outputTypes["matchdist"] = tempOutNames;
98 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
102 //**********************************************************************************************************************
103 ClassifySeqsCommand::ClassifySeqsCommand(string option) {
105 abort = false; calledHelp = false;
107 //allow user to run help
108 if(option == "help") { help(); abort = true; calledHelp = true; }
111 vector<string> myArray = setParameters();
113 OptionParser parser(option);
114 map<string, string> parameters = parser.getParameters();
116 ValidParameters validParameter("classify.seqs");
117 map<string, string>::iterator it;
119 //check to make sure all parameters are valid for command
120 for (it = parameters.begin(); it != parameters.end(); it++) {
121 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
124 //initialize outputTypes
125 vector<string> tempOutNames;
126 outputTypes["taxonomy"] = tempOutNames;
127 outputTypes["taxsummary"] = tempOutNames;
128 outputTypes["matchdist"] = tempOutNames;
130 //if the user changes the output directory command factory will send this info to us in the output parameter
131 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
133 //if the user changes the input directory command factory will send this info to us in the output parameter
134 string inputDir = validParameter.validFile(parameters, "inputdir", false);
135 if (inputDir == "not found"){ inputDir = ""; }
138 it = parameters.find("reference");
139 //user has given a template file
140 if(it != parameters.end()){
141 path = m->hasPath(it->second);
142 //if the user has not given a path then, add inputdir. else leave path alone.
143 if (path == "") { parameters["reference"] = inputDir + it->second; }
146 it = parameters.find("taxonomy");
147 //user has given a template file
148 if(it != parameters.end()){
149 path = m->hasPath(it->second);
150 //if the user has not given a path then, add inputdir. else leave path alone.
151 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
154 it = parameters.find("group");
155 //user has given a template file
156 if(it != parameters.end()){
157 path = m->hasPath(it->second);
158 //if the user has not given a path then, add inputdir. else leave path alone.
159 if (path == "") { parameters["group"] = inputDir + it->second; }
163 //check for required parameters
164 templateFileName = validParameter.validFile(parameters, "reference", true);
165 if (templateFileName == "not found") {
166 m->mothurOut("reference is a required parameter for the classify.seqs command.");
167 m->mothurOutEndLine();
170 else if (templateFileName == "not open") { abort = true; }
173 fastaFileName = validParameter.validFile(parameters, "fasta", false);
174 if (fastaFileName == "not found") {
175 //if there is a current fasta file, use it
176 string filename = m->getFastaFile();
177 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
178 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
181 m->splitAtDash(fastaFileName, fastaFileNames);
183 //go through files and make sure they are good, if not, then disregard them
184 for (int i = 0; i < fastaFileNames.size(); i++) {
187 if (fastaFileNames[i] == "current") {
188 fastaFileNames[i] = m->getFastaFile();
189 if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
191 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
192 //erase from file list
193 fastaFileNames.erase(fastaFileNames.begin()+i);
200 if (inputDir != "") {
201 string path = m->hasPath(fastaFileNames[i]);
202 //if the user has not given a path then, add inputdir. else leave path alone.
203 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
209 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
211 //if you can't open it, try default location
212 if (ableToOpen == 1) {
213 if (m->getDefaultPath() != "") { //default path is set
214 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
215 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
217 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
219 fastaFileNames[i] = tryPath;
223 if (ableToOpen == 1) {
224 if (m->getOutputDir() != "") { //default path is set
225 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
226 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
228 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
230 fastaFileNames[i] = tryPath;
236 if (ableToOpen == 1) {
237 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
238 //erase from file list
239 fastaFileNames.erase(fastaFileNames.begin()+i);
246 //make sure there is at least one valid file left
247 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
251 taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
252 if (taxonomyFileName == "not found") {
253 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
254 m->mothurOutEndLine();
257 else if (taxonomyFileName == "not open") { abort = true; }
260 namefile = validParameter.validFile(parameters, "name", false);
261 if (namefile == "not found") { namefile = ""; }
264 m->splitAtDash(namefile, namefileNames);
266 //go through files and make sure they are good, if not, then disregard them
267 for (int i = 0; i < namefileNames.size(); i++) {
269 if (namefileNames[i] == "current") {
270 namefileNames[i] = m->getNameFile();
271 if (namefileNames[i] != "") { m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
273 m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
274 //erase from file list
275 namefileNames.erase(namefileNames.begin()+i);
282 if (inputDir != "") {
283 string path = m->hasPath(namefileNames[i]);
284 //if the user has not given a path then, add inputdir. else leave path alone.
285 if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
290 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
292 //if you can't open it, try default location
293 if (ableToOpen == 1) {
294 if (m->getDefaultPath() != "") { //default path is set
295 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
296 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
298 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
300 namefileNames[i] = tryPath;
304 if (ableToOpen == 1) {
305 if (m->getOutputDir() != "") { //default path is set
306 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
307 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
309 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
311 namefileNames[i] = tryPath;
316 if (ableToOpen == 1) {
317 m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
318 //erase from file list
319 namefileNames.erase(namefileNames.begin()+i);
326 if (namefile != "") {
327 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(); }
330 groupfile = validParameter.validFile(parameters, "group", false);
331 if (groupfile == "not found") { groupfile = ""; }
333 m->splitAtDash(groupfile, groupfileNames);
335 //go through files and make sure they are good, if not, then disregard them
336 for (int i = 0; i < groupfileNames.size(); i++) {
337 if (inputDir != "") {
338 string path = m->hasPath(groupfileNames[i]);
339 //if the user has not given a path then, add inputdir. else leave path alone.
340 if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
345 ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
347 //if you can't open it, try default location
348 if (ableToOpen == 1) {
349 if (m->getDefaultPath() != "") { //default path is set
350 string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
351 m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
353 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
355 groupfileNames[i] = tryPath;
359 if (ableToOpen == 1) {
360 if (m->getOutputDir() != "") { //default path is set
361 string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
362 m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
364 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
366 groupfileNames[i] = tryPath;
372 if (ableToOpen == 1) {
373 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
374 //erase from file list
375 groupfileNames.erase(groupfileNames.begin()+i);
381 if (groupfile != "") {
382 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(); }
384 for (int i = 0; i < fastaFileNames.size(); i++) { groupfileNames.push_back(""); }
387 //check for optional parameter and set defaults
388 // ...at some point should added some additional type checking...
390 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
391 convert(temp, kmerSize);
393 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
394 m->setProcessors(temp);
395 convert(temp, processors);
397 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
399 method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "bayesian"; }
401 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
402 convert(temp, match);
404 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
405 convert(temp, misMatch);
407 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
408 convert(temp, gapOpen);
410 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
411 convert(temp, gapExtend);
413 temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found"){ temp = "10"; }
414 convert(temp, numWanted);
416 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0"; }
417 convert(temp, cutoff);
419 temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
420 probs = m->isTrue(temp);
422 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
423 convert(temp, iters);
427 if ((method == "bayesian") && (search != "kmer")) {
428 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
434 catch(exception& e) {
435 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
440 //**********************************************************************************************************************
441 ClassifySeqsCommand::~ClassifySeqsCommand(){
442 if (abort == false) {
443 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
446 //**********************************************************************************************************************
448 int ClassifySeqsCommand::execute(){
450 if (abort == true) { if (calledHelp) { return 0; } return 2; }
452 if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
453 else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
455 m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
456 m->mothurOutEndLine();
457 classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
460 if (m->control_pressed) { delete classify; return 0; }
463 for (int s = 0; s < fastaFileNames.size(); s++) {
465 m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
467 string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
468 RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
469 if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
470 RippedTaxName += ".";
472 if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
473 string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
474 string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
475 string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
477 if ((method == "knn") && (search == "distance")) {
478 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
479 classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
482 outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
483 outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary);
485 int start = time(NULL);
486 int numFastaSeqs = 0;
487 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
490 int pid, numSeqsPerProcessor;
492 vector<unsigned long int> MPIPos;
495 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
496 MPI_Comm_size(MPI_COMM_WORLD, &processors);
499 MPI_File outMPINewTax;
500 MPI_File outMPITempTax;
502 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
503 int inMode=MPI_MODE_RDONLY;
505 char outNewTax[1024];
506 strcpy(outNewTax, newTaxonomyFile.c_str());
508 char outTempTax[1024];
509 strcpy(outTempTax, tempTaxonomyFile.c_str());
511 char inFileName[1024];
512 strcpy(inFileName, fastaFileNames[s].c_str());
514 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
515 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
516 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
518 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
520 if (pid == 0) { //you are the root process
522 MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
524 //send file positions to all processes
525 for(int i = 1; i < processors; i++) {
526 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
527 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
530 //figure out how many sequences you have to align
531 numSeqsPerProcessor = numFastaSeqs / processors;
532 int startIndex = pid * numSeqsPerProcessor;
533 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
537 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
539 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
541 for (int i = 1; i < processors; i++) {
543 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
545 }else{ //you are a child process
546 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
547 MPIPos.resize(numFastaSeqs+1);
548 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
550 //figure out how many sequences you have to align
551 numSeqsPerProcessor = numFastaSeqs / processors;
552 int startIndex = pid * numSeqsPerProcessor;
553 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
557 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
559 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
562 MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
566 MPI_File_close(&inMPI);
567 MPI_File_close(&outMPINewTax);
568 MPI_File_close(&outMPITempTax);
569 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
573 vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
575 for (int i = 0; i < (positions.size()-1); i++) {
576 lines.push_back(new linePair(positions[i], positions[(i+1)]));
579 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
581 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
584 processIDS.resize(0);
586 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
590 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
594 m->mothurOutEndLine();
595 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
600 if (pid == 0) { //this part does not need to be paralellized
602 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush(); MPIReadNamesFile(namefileNames[s]); m->mothurOut(" Done."); m->mothurOutEndLine(); }
607 m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
609 nameMap.clear(); //remove old names
612 m->openInputFile(namefileNames[s], inNames);
614 string firstCol, secondCol;
615 while(!inNames.eof()) {
616 inNames >> firstCol >> secondCol; m->gobble(inNames);
619 m->splitAtComma(secondCol, temp);
621 nameMap[firstCol] = temp;
625 m->mothurOut(" Done."); m->mothurOutEndLine();
630 if (groupfile != "") { group = groupfileNames[s]; }
632 PhyloSummary taxaSum(taxonomyFileName, group);
634 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
636 if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
639 m->openInputFile(tempTaxonomyFile, in);
641 //read in users taxonomy file and add sequences to tree
645 in >> name >> taxon; m->gobble(in);
647 itNames = nameMap.find(name);
649 if (itNames == nameMap.end()) {
650 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
652 for (int i = 0; i < itNames->second.size(); i++) {
653 taxaSum.addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
655 itNames->second.clear();
656 nameMap.erase(itNames->first);
661 remove(tempTaxonomyFile.c_str());
663 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
667 m->openOutputFile(taxSummary, outTaxTree);
668 taxaSum.print(outTaxTree);
671 //output taxonomy with the unclassified bins added
673 m->openInputFile(newTaxonomyFile, inTax);
676 string unclass = newTaxonomyFile + ".unclass.temp";
677 m->openOutputFile(unclass, outTax);
679 //get maxLevel from phylotree so you know how many 'unclassified's to add
680 int maxLevel = taxaSum.getMaxLevel();
682 //read taxfile - this reading and rewriting is done to preserve the confidence scores.
684 while (!inTax.eof()) {
685 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
687 inTax >> name >> taxon; m->gobble(inTax);
689 string newTax = addUnclassifieds(taxon, maxLevel);
691 outTax << name << '\t' << newTax << endl;
696 remove(newTaxonomyFile.c_str());
697 rename(unclass.c_str(), newTaxonomyFile.c_str());
699 m->mothurOutEndLine();
700 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
706 m->mothurOutEndLine();
707 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
708 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
709 m->mothurOutEndLine();
712 //set taxonomy file as new current taxonomyfile
714 itTypes = outputTypes.find("taxonomy");
715 if (itTypes != outputTypes.end()) {
716 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
722 catch(exception& e) {
723 m->errorOut(e, "ClassifySeqsCommand", "execute");
728 /**************************************************************************************************/
729 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
731 string newTax, taxon;
734 //keep what you have counting the levels
735 while (tax.find_first_of(';') != -1) {
737 taxon = tax.substr(0,tax.find_first_of(';'))+';';
738 tax = tax.substr(tax.find_first_of(';')+1, tax.length());
743 //add "unclassified" until you reach maxLevel
744 while (level < maxlevel) {
745 newTax += "unclassified;";
751 catch(exception& e) {
752 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
757 /**************************************************************************************************/
759 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
761 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
765 //loop through and create all the processes you want
766 while (process != processors) {
770 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
773 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
775 //pass numSeqs to parent
777 string tempFile = filename + toString(getpid()) + ".num.temp";
778 m->openOutputFile(tempFile, out);
784 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
785 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
790 //parent does its part
791 num = driver(lines[0], taxFileName, tempTaxFile, filename);
793 //force parent to wait until all the processes are done
794 for (int i=0;i<processIDS.size();i++) {
795 int temp = processIDS[i];
799 for (int i = 0; i < processIDS.size(); i++) {
801 string tempFile = filename + toString(processIDS[i]) + ".num.temp";
802 m->openInputFile(tempFile, in);
803 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
804 in.close(); remove(tempFile.c_str());
807 for(int i=0;i<processIDS.size();i++){
808 appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
809 appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
810 remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
811 remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
817 catch(exception& e) {
818 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
822 /**************************************************************************************************/
824 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
829 m->openOutputFileAppend(filename, output);
830 m->openInputFile(temp, input);
832 while(char c = input.get()){
833 if(input.eof()) { break; }
834 else { output << c; }
840 catch(exception& e) {
841 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
846 //**********************************************************************************************************************
848 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
851 m->openOutputFile(taxFName, outTax);
853 ofstream outTaxSimple;
854 m->openOutputFile(tempTFName, outTaxSimple);
857 m->openInputFile(filename, inFASTA);
861 inFASTA.seekg(filePos->start);
867 if (m->control_pressed) { return 0; }
869 Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
871 if (candidateSeq->getName() != "") {
873 taxonomy = classify->getTaxonomy(candidateSeq);
875 if (m->control_pressed) { delete candidateSeq; return 0; }
877 if (taxonomy != "bad seq") {
878 //output confidence scores or not
880 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
882 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
885 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
891 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
892 unsigned long int pos = inFASTA.tellg();
893 if ((pos == -1) || (pos >= filePos->end)) { break; }
895 if (inFASTA.eof()) { break; }
899 if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
903 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
907 outTaxSimple.close();
911 catch(exception& e) {
912 m->errorOut(e, "ClassifySeqsCommand", "driver");
916 //**********************************************************************************************************************
918 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
920 MPI_Status statusNew;
921 MPI_Status statusTemp;
925 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
930 for(int i=0;i<num;i++){
932 if (m->control_pressed) { return 0; }
935 int length = MPIPos[start+i+1] - MPIPos[start+i];
936 char* buf4 = new char[length];
937 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
939 string tempBuf = buf4;
940 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
941 istringstream iss (tempBuf,istringstream::in);
944 Sequence* candidateSeq = new Sequence(iss);
946 if (candidateSeq->getName() != "") {
947 taxonomy = classify->getTaxonomy(candidateSeq);
949 if (taxonomy != "bad seq") {
950 //output confidence scores or not
952 outputString = candidateSeq->getName() + "\t" + taxonomy + "\n";
954 outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
957 int length = outputString.length();
958 char* buf2 = new char[length];
959 memcpy(buf2, outputString.c_str(), length);
961 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
964 outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
965 length = outputString.length();
966 char* buf = new char[length];
967 memcpy(buf, outputString.c_str(), length);
969 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
975 if((i+1) % 100 == 0){ cout << "Classifying sequence " << (i+1) << endl; }
978 if(num % 100 != 0){ cout << "Classifying sequence " << (num) << endl; }
983 catch(exception& e) {
984 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
989 //**********************************************************************************************************************
990 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
993 nameMap.clear(); //remove old names
999 //char* inFileName = new char[nameFilename.length()];
1000 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1002 char inFileName[1024];
1003 strcpy(inFileName, nameFilename.c_str());
1005 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1006 MPI_File_get_size(inMPI, &size);
1007 //delete inFileName;
1009 char* buffer = new char[size];
1010 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1012 string tempBuf = buffer;
1013 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
1014 istringstream iss (tempBuf,istringstream::in);
1017 string firstCol, secondCol;
1019 iss >> firstCol >> secondCol; m->gobble(iss);
1021 vector<string> temp;
1022 m->splitAtComma(secondCol, temp);
1024 nameMap[firstCol] = temp;
1027 MPI_File_close(&inMPI);
1031 catch(exception& e) {
1032 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1037 /**************************************************************************************************/