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"
17 //**********************************************************************************************************************
19 ClassifySeqsCommand::ClassifySeqsCommand(string option) {
23 //allow user to run help
24 if(option == "help") { help(); abort = true; }
28 //valid paramters for this command
29 string AlignArray[] = {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
30 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
32 OptionParser parser(option);
33 map<string, string> parameters = parser.getParameters();
35 ValidParameters validParameter;
36 map<string, string>::iterator it;
38 //check to make sure all parameters are valid for command
39 for (it = parameters.begin(); it != parameters.end(); it++) {
40 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
43 //if the user changes the output directory command factory will send this info to us in the output parameter
44 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
46 //if the user changes the input directory command factory will send this info to us in the output parameter
47 string inputDir = validParameter.validFile(parameters, "inputdir", false);
48 if (inputDir == "not found"){ inputDir = ""; }
51 it = parameters.find("template");
52 //user has given a template file
53 if(it != parameters.end()){
54 path = hasPath(it->second);
55 //if the user has not given a path then, add inputdir. else leave path alone.
56 if (path == "") { parameters["template"] = inputDir + it->second; }
59 it = parameters.find("taxonomy");
60 //user has given a template file
61 if(it != parameters.end()){
62 path = hasPath(it->second);
63 //if the user has not given a path then, add inputdir. else leave path alone.
64 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
67 it = parameters.find("group");
68 //user has given a template file
69 if(it != parameters.end()){
70 path = hasPath(it->second);
71 //if the user has not given a path then, add inputdir. else leave path alone.
72 if (path == "") { parameters["group"] = inputDir + it->second; }
76 //check for required parameters
77 templateFileName = validParameter.validFile(parameters, "template", true);
78 if (templateFileName == "not found") {
79 m->mothurOut("template is a required parameter for the classify.seqs command.");
80 m->mothurOutEndLine();
83 else if (templateFileName == "not open") { abort = true; }
85 groupfile = validParameter.validFile(parameters, "group", false);
86 if (groupfile == "not found") { groupfile = ""; }
88 splitAtDash(groupfile, groupfileNames);
90 //go through files and make sure they are good, if not, then disregard them
91 for (int i = 0; i < groupfileNames.size(); i++) {
93 string path = hasPath(groupfileNames[i]);
94 //if the user has not given a path then, add inputdir. else leave path alone.
95 if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
101 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
102 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
108 ableToOpen = openInputFile(groupfileNames[i], in);
112 for (int j = 1; j < processors; j++) {
113 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
117 MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
121 if (ableToOpen == 1) { m->mothurOut("Unable to match group file with fasta file."); m->mothurOutEndLine(); abort = true; }
126 fastaFileName = validParameter.validFile(parameters, "fasta", false);
127 if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; }
129 splitAtDash(fastaFileName, fastaFileNames);
131 //go through files and make sure they are good, if not, then disregard them
132 for (int i = 0; i < fastaFileNames.size(); i++) {
133 if (inputDir != "") {
134 string path = hasPath(fastaFileNames[i]);
135 //if the user has not given a path then, add inputdir. else leave path alone.
136 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
143 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
144 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
150 ableToOpen = openInputFile(fastaFileNames[i], in);
154 for (int j = 1; j < processors; j++) {
155 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
159 MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
164 if (ableToOpen == 1) {
165 m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
166 //erase from file list
167 fastaFileNames.erase(fastaFileNames.begin()+i);
173 //make sure there is at least one valid file left
174 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
178 taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
179 if (taxonomyFileName == "not found") {
180 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
181 m->mothurOutEndLine();
184 else if (taxonomyFileName == "not open") { abort = true; }
187 namefile = validParameter.validFile(parameters, "name", false);
188 if (namefile == "not found") { namefile = ""; }
191 splitAtDash(namefile, namefileNames);
193 //go through files and make sure they are good, if not, then disregard them
194 for (int i = 0; i < namefileNames.size(); i++) {
195 if (inputDir != "") {
196 string path = hasPath(namefileNames[i]);
197 //if the user has not given a path then, add inputdir. else leave path alone.
198 if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
204 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
205 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
211 ableToOpen = openInputFile(namefileNames[i], in);
215 for (int j = 1; j < processors; j++) {
216 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
220 MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
224 if (ableToOpen == 1) { m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true; }
229 if (namefile != "") {
230 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(); }
233 if (groupfile != "") {
234 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(); }
237 //check for optional parameter and set defaults
238 // ...at some point should added some additional type checking...
240 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
241 convert(temp, kmerSize);
243 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
244 convert(temp, processors);
246 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
248 method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "bayesian"; }
250 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
251 convert(temp, match);
253 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
254 convert(temp, misMatch);
256 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
257 convert(temp, gapOpen);
259 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
260 convert(temp, gapExtend);
262 temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found"){ temp = "10"; }
263 convert(temp, numWanted);
265 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0"; }
266 convert(temp, cutoff);
268 temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
269 probs = isTrue(temp);
271 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
272 convert(temp, iters);
276 if ((method == "bayesian") && (search != "kmer")) {
277 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
283 catch(exception& e) {
284 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
289 //**********************************************************************************************************************
291 ClassifySeqsCommand::~ClassifySeqsCommand(){
293 if (abort == false) {
294 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
298 //**********************************************************************************************************************
300 void ClassifySeqsCommand::help(){
302 m->mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
303 m->mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
304 m->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");
305 m->mothurOut("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");
306 m->mothurOut("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");
307 m->mothurOut("The group parameter allows you add a group file so you can have the summary totals broken up by group.\n");
308 m->mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n");
309 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
310 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
312 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
314 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
315 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
316 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
317 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
318 m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n");
319 m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n");
320 m->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");
321 m->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");
322 m->mothurOut("The classify.seqs command should be in the following format: \n");
323 m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
324 m->mothurOut("Example classify.seqs(fasta=amazon.fasta, template=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n");
325 m->mothurOut("The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n");
326 m->mothurOut("The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n");
327 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
329 catch(exception& e) {
330 m->errorOut(e, "ClassifySeqsCommand", "help");
336 //**********************************************************************************************************************
338 int ClassifySeqsCommand::execute(){
340 if (abort == true) { return 0; }
342 if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
343 else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
345 m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
346 m->mothurOutEndLine();
347 classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
350 if (m->control_pressed) { delete classify; return 0; }
352 vector<string> outputNames;
354 for (int s = 0; s < fastaFileNames.size(); s++) {
356 m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
358 if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
359 string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
360 string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
361 string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
363 outputNames.push_back(newTaxonomyFile);
364 outputNames.push_back(taxSummary);
366 int start = time(NULL);
367 int numFastaSeqs = 0;
368 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
371 int pid, end, numSeqsPerProcessor;
376 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
377 MPI_Comm_size(MPI_COMM_WORLD, &processors);
380 MPI_File outMPINewTax;
381 MPI_File outMPITempTax;
383 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
384 int inMode=MPI_MODE_RDONLY;
386 //char* outNewTax = new char[newTaxonomyFile.length()];
387 //memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length());
389 char outNewTax[1024];
390 strcpy(outNewTax, newTaxonomyFile.c_str());
392 //char* outTempTax = new char[tempTaxonomyFile.length()];
393 //memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length());
395 char outTempTax[1024];
396 strcpy(outTempTax, tempTaxonomyFile.c_str());
398 //char* inFileName = new char[fastaFileNames[s].length()];
399 //memcpy(inFileName, fastaFileNames[s].c_str(), fastaFileNames[s].length());
401 char inFileName[1024];
402 strcpy(inFileName, fastaFileNames[s].c_str());
404 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
405 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
406 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
412 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
414 if(namefile != "") { MPIReadNamesFile(namefileNames[s]); }
416 if (pid == 0) { //you are the root process
418 MPIPos = setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
420 //send file positions to all processes
421 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
422 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
424 //figure out how many sequences you have to align
425 numSeqsPerProcessor = numFastaSeqs / processors;
426 int startIndex = pid * numSeqsPerProcessor;
427 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
431 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
433 if (m->control_pressed) { 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; }
435 for (int i = 1; i < processors; i++) {
437 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
439 }else{ //you are a child process
440 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
441 MPIPos.resize(numFastaSeqs+1);
442 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
444 //figure out how many sequences you have to align
445 numSeqsPerProcessor = numFastaSeqs / processors;
446 int startIndex = pid * numSeqsPerProcessor;
447 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
451 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
453 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
456 MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
460 MPI_File_close(&inMPI);
461 MPI_File_close(&outMPINewTax);
462 MPI_File_close(&outMPITempTax);
467 nameMap.clear(); //remove old names
470 openInputFile(namefileNames[s], inNames);
472 string firstCol, secondCol;
473 while(!inNames.eof()) {
474 inNames >> firstCol >> secondCol; gobble(inNames);
475 nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
480 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
483 openInputFile(fastaFileNames[s], inFASTA);
484 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
487 lines.push_back(new linePair(0, numFastaSeqs));
489 driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
492 vector<int> positions;
493 processIDS.resize(0);
496 openInputFile(fastaFileNames[s], inFASTA);
499 while(!inFASTA.eof()){
500 input = getline(inFASTA);
501 if (input.length() != 0) {
502 if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
507 numFastaSeqs = positions.size();
509 int numSeqsPerProcessor = numFastaSeqs / processors;
511 for (int i = 0; i < processors; i++) {
512 int startPos = positions[ i * numSeqsPerProcessor ];
513 if(i == processors - 1){
514 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
516 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
518 createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
520 rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
521 rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
523 for(int i=1;i<processors;i++){
524 appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
525 appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
526 remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
527 remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
533 openInputFile(fastaFileNames[s], inFASTA);
534 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
537 lines.push_back(new linePair(0, numFastaSeqs));
539 driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
544 if (pid == 0) { //this part does not need to be paralellized
547 m->mothurOutEndLine();
548 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
551 PhyloSummary taxaSum(taxonomyFileName, groupfileNames[s]);
553 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
555 if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
558 openInputFile(tempTaxonomyFile, in);
560 //read in users taxonomy file and add sequences to tree
563 in >> name >> taxon; gobble(in);
565 itNames = nameMap.find(name);
567 if (itNames == nameMap.end()) {
568 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
570 for (int i = 0; i < itNames->second; i++) {
571 taxaSum.addSeqToTree(name, taxon); //add it as many times as there are identical seqs
577 remove(tempTaxonomyFile.c_str());
579 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
583 openOutputFile(taxSummary, outTaxTree);
584 taxaSum.print(outTaxTree);
587 //output taxonomy with the unclassified bins added
589 openInputFile(newTaxonomyFile, inTax);
592 string unclass = newTaxonomyFile + ".unclass.temp";
593 openOutputFile(unclass, outTax);
595 //get maxLevel from phylotree so you know how many 'unclassified's to add
596 int maxLevel = taxaSum.getMaxLevel();
598 //read taxfile - this reading and rewriting is done to preserve the confidence scores.
600 while (!inTax.eof()) {
601 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
603 inTax >> name >> taxon; gobble(inTax);
605 string newTax = addUnclassifieds(taxon, maxLevel);
607 outTax << name << '\t' << newTax << endl;
612 remove(newTaxonomyFile.c_str());
613 rename(unclass.c_str(), newTaxonomyFile.c_str());
615 m->mothurOutEndLine();
616 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
622 m->mothurOutEndLine();
623 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
624 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
625 m->mothurOutEndLine();
631 catch(exception& e) {
632 m->errorOut(e, "ClassifySeqsCommand", "execute");
637 /**************************************************************************************************/
638 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
640 string newTax, taxon;
643 //keep what you have counting the levels
644 while (tax.find_first_of(';') != -1) {
646 taxon = tax.substr(0,tax.find_first_of(';'))+';';
647 tax = tax.substr(tax.find_first_of(';')+1, tax.length());
652 //add "unclassified" until you reach maxLevel
653 while (level < maxlevel) {
654 newTax += "unclassified;";
660 catch(exception& e) {
661 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
666 /**************************************************************************************************/
668 void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
670 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
672 // processIDS.resize(0);
674 //loop through and create all the processes you want
675 while (process != processors) {
679 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
682 driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
684 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
687 //force parent to wait until all the processes are done
688 for (int i=0;i<processors;i++) {
689 int temp = processIDS[i];
694 catch(exception& e) {
695 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
699 /**************************************************************************************************/
701 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
706 openOutputFileAppend(filename, output);
707 openInputFile(temp, input);
709 while(char c = input.get()){
710 if(input.eof()) { break; }
711 else { output << c; }
717 catch(exception& e) {
718 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
723 //**********************************************************************************************************************
725 int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName, string filename){
728 openOutputFile(taxFName, outTax);
730 ofstream outTaxSimple;
731 openOutputFile(tempTFName, outTaxSimple);
734 openInputFile(filename, inFASTA);
736 inFASTA.seekg(line->start);
740 for(int i=0;i<line->numSeqs;i++){
741 if (m->control_pressed) { return 0; }
743 Sequence* candidateSeq = new Sequence(inFASTA);
745 if (candidateSeq->getName() != "") {
746 taxonomy = classify->getTaxonomy(candidateSeq);
748 if (m->control_pressed) { delete candidateSeq; return 0; }
750 if (taxonomy != "bad seq") {
751 //output confidence scores or not
753 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
755 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
758 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
763 if((i+1) % 100 == 0){
764 m->mothurOut("Classifying sequence " + toString(i+1)); m->mothurOutEndLine();
770 outTaxSimple.close();
774 catch(exception& e) {
775 m->errorOut(e, "ClassifySeqsCommand", "driver");
779 //**********************************************************************************************************************
781 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<long>& MPIPos){
783 MPI_Status statusNew;
784 MPI_Status statusTemp;
788 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
793 for(int i=0;i<num;i++){
795 if (m->control_pressed) { return 0; }
798 int length = MPIPos[start+i+1] - MPIPos[start+i];
799 char* buf4 = new char[length];
800 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
802 string tempBuf = buf4;
803 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
804 istringstream iss (tempBuf,istringstream::in);
807 Sequence* candidateSeq = new Sequence(iss);
809 if (candidateSeq->getName() != "") {
810 taxonomy = classify->getTaxonomy(candidateSeq);
812 if (taxonomy != "bad seq") {
813 //output confidence scores or not
815 outputString = candidateSeq->getName() + "\t" + taxonomy + "\n";
817 outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
820 int length = outputString.length();
821 char* buf2 = new char[length];
822 memcpy(buf2, outputString.c_str(), length);
824 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
827 outputString = candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
828 length = outputString.length();
829 char* buf = new char[length];
830 memcpy(buf, outputString.c_str(), length);
832 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
838 if((i+1) % 100 == 0){ cout << "Classifying sequence " << (i+1) << endl; }
841 if(num % 100 != 0){ cout << "Classifying sequence " << (num) << endl; }
846 catch(exception& e) {
847 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
852 //**********************************************************************************************************************
853 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
856 nameMap.clear(); //remove old names
862 //char* inFileName = new char[nameFilename.length()];
863 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
865 char inFileName[1024];
866 strcpy(inFileName, nameFilename.c_str());
868 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
869 MPI_File_get_size(inMPI, &size);
872 char* buffer = new char[size];
873 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
875 string tempBuf = buffer;
876 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
877 istringstream iss (tempBuf,istringstream::in);
880 string firstCol, secondCol;
882 iss >> firstCol >> secondCol; gobble(iss);
883 nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
886 MPI_File_close(&inMPI);
890 catch(exception& e) {
891 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
896 /**************************************************************************************************/