classifyseqscommand.cpp

   1 /*
   2  *  classifyseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/2/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "classifyseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "bayesian.h"
  13 #include "phylotree.h"
  14 #include "phylosummary.h"
  15 #include "knn.h"
  16
  17
  18 //**********************************************************************************************************************
  19 vector<string> ClassifySeqsCommand::getValidParameters(){
  20         try {
  21                 string AlignArray[] =  {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
  22                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "ClassifySeqsCommand", "getValidParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 ClassifySeqsCommand::ClassifySeqsCommand(){
  32         try {
  33                 abort = true; calledHelp = true;
  34                 vector<string> tempOutNames;
  35                 outputTypes["taxonomy"] = tempOutNames;
  36                 outputTypes["taxsummary"] = tempOutNames;
  37                 outputTypes["matchdist"] = tempOutNames;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 vector<string> ClassifySeqsCommand::getRequiredParameters(){
  46         try {
  47                 string Array[] =  {"fasta","template","taxonomy"};
  48                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "ClassifySeqsCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> ClassifySeqsCommand::getRequiredFiles(){
  58         try {
  59                 vector<string> myArray;
  60                 return myArray;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "ClassifySeqsCommand", "getRequiredFiles");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
  69         try {
  70                 abort = false; calledHelp = false;
  71
  72                 //allow user to run help
  73                 if(option == "help") { help(); abort = true; calledHelp = true; }
  74
  75                 else {
  76
  77                         //valid paramters for this command
  78                         string AlignArray[] =  {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
  79                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  80
  81                         OptionParser parser(option);
  82                         map<string, string> parameters = parser.getParameters();
  83
  84                         ValidParameters validParameter("classify.seqs");
  85                         map<string, string>::iterator it;
  86
  87                         //check to make sure all parameters are valid for command
  88                         for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["taxonomy"] = tempOutNames;
  95                         outputTypes["taxsummary"] = tempOutNames;
  96                         outputTypes["matchdist"] = tempOutNames;
  97
  98                         //if the user changes the output directory command factory will send this info to us in the output parameter
  99                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 100
 101                         //if the user changes the input directory command factory will send this info to us in the output parameter
 102                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 103                         if (inputDir == "not found"){   inputDir = "";          }
 104                         else {
 105                                 string path;
 106                                 it = parameters.find("template");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
 112                                 }
 113
 114                                 it = parameters.find("taxonomy");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 120                                 }
 121
 122                                 it = parameters.find("group");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 128                                 }
 129                         }
 130
 131                         //check for required parameters
 132                         templateFileName = validParameter.validFile(parameters, "template", true);
 133                         if (templateFileName == "not found") {
 134                                 m->mothurOut("template is a required parameter for the classify.seqs command.");
 135                                 m->mothurOutEndLine();
 136                                 abort = true;
 137                         }
 138                         else if (templateFileName == "not open") { abort = true; }
 139
 140
 141                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 142                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true;  }
 143                         else {
 144                                 m->splitAtDash(fastaFileName, fastaFileNames);
 145
 146                                 //go through files and make sure they are good, if not, then disregard them
 147                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 148                                         if (inputDir != "") {
 149                                                 string path = m->hasPath(fastaFileNames[i]);
 150                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 151                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 152                                         }
 153
 154                                         int ableToOpen;
 155
 156                                         ifstream in;
 157                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 158
 159                                         //if you can't open it, try default location
 160                                         if (ableToOpen == 1) {
 161                                                 if (m->getDefaultPath() != "") { //default path is set
 162                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 163                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 164                                                         ifstream in2;
 165                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 166                                                         in2.close();
 167                                                         fastaFileNames[i] = tryPath;
 168                                                 }
 169                                         }
 170
 171                                         if (ableToOpen == 1) {
 172                                                 if (m->getOutputDir() != "") { //default path is set
 173                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 174                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 175                                                         ifstream in2;
 176                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 177                                                         in2.close();
 178                                                         fastaFileNames[i] = tryPath;
 179                                                 }
 180                                         }
 181
 182                                         in.close();
 183
 184                                         if (ableToOpen == 1) {
 185                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 186                                                 //erase from file list
 187                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 188                                                 i--;
 189                                         }
 190
 191                                 }
 192
 193                                 //make sure there is at least one valid file left
 194                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 195                         }
 196
 197
 198                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 199                         if (taxonomyFileName == "not found") {
 200                                 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
 201                                 m->mothurOutEndLine();
 202                                 abort = true;
 203                         }
 204                         else if (taxonomyFileName == "not open") { abort = true; }
 205
 206
 207                         namefile = validParameter.validFile(parameters, "name", false);
 208                         if (namefile == "not found") { namefile = "";  }
 209
 210                         else {
 211                                 m->splitAtDash(namefile, namefileNames);
 212
 213                                 //go through files and make sure they are good, if not, then disregard them
 214                                 for (int i = 0; i < namefileNames.size(); i++) {
 215                                         if (inputDir != "") {
 216                                                 string path = m->hasPath(namefileNames[i]);
 217                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 218                                                 if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 219                                         }
 220                                         int ableToOpen;
 221
 222                                         ifstream in;
 223                                         ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 224
 225                                         //if you can't open it, try default location
 226                                         if (ableToOpen == 1) {
 227                                                 if (m->getDefaultPath() != "") { //default path is set
 228                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 229                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 230                                                         ifstream in2;
 231                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 232                                                         in2.close();
 233                                                         namefileNames[i] = tryPath;
 234                                                 }
 235                                         }
 236
 237                                         if (ableToOpen == 1) {
 238                                                 if (m->getOutputDir() != "") { //default path is set
 239                                                         string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 240                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 241                                                         ifstream in2;
 242                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 243                                                         in2.close();
 244                                                         namefileNames[i] = tryPath;
 245                                                 }
 246                                         }
 247                                         in.close();
 248
 249                                         if (ableToOpen == 1) {
 250                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 251                                                 //erase from file list
 252                                                 namefileNames.erase(namefileNames.begin()+i);
 253                                                 i--;
 254                                         }
 255
 256                                 }
 257                         }
 258
 259                         if (namefile != "") {
 260                                 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(); }
 261                         }
 262
 263                         groupfile = validParameter.validFile(parameters, "group", false);
 264                         if (groupfile == "not found") { groupfile = "";  }
 265                         else {
 266                                 m->splitAtDash(groupfile, groupfileNames);
 267
 268                                 //go through files and make sure they are good, if not, then disregard them
 269                                 for (int i = 0; i < groupfileNames.size(); i++) {
 270                                         if (inputDir != "") {
 271                                                 string path = m->hasPath(groupfileNames[i]);
 272                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 273                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 274                                         }
 275                                         int ableToOpen;
 276
 277                                         ifstream in;
 278                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 279
 280                                         //if you can't open it, try default location
 281                                         if (ableToOpen == 1) {
 282                                                 if (m->getDefaultPath() != "") { //default path is set
 283                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 284                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 285                                                         ifstream in2;
 286                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 287                                                         in2.close();
 288                                                         groupfileNames[i] = tryPath;
 289                                                 }
 290                                         }
 291
 292                                         if (ableToOpen == 1) {
 293                                                 if (m->getOutputDir() != "") { //default path is set
 294                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 295                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 296                                                         ifstream in2;
 297                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 298                                                         in2.close();
 299                                                         groupfileNames[i] = tryPath;
 300                                                 }
 301                                         }
 302
 303                                         in.close();
 304
 305                                         if (ableToOpen == 1) {
 306                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 307                                                 //erase from file list
 308                                                 groupfileNames.erase(groupfileNames.begin()+i);
 309                                                 i--;
 310                                         }
 311                                 }
 312                         }
 313
 314                         if (groupfile != "") {
 315                                 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(); }
 316                         }else {
 317                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 318                         }
 319
 320                         //check for optional parameter and set defaults
 321                         // ...at some point should added some additional type checking...
 322                         string temp;
 323                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 324                         convert(temp, kmerSize);
 325
 326                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 327                         convert(temp, processors);
 328
 329                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 330
 331                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 332
 333                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 334                         convert(temp, match);
 335
 336                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 337                         convert(temp, misMatch);
 338
 339                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 340                         convert(temp, gapOpen);
 341
 342                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 343                         convert(temp, gapExtend);
 344
 345                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 346                         convert(temp, numWanted);
 347
 348                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 349                         convert(temp, cutoff);
 350
 351                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 352                         probs = m->isTrue(temp);
 353
 354                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 355                         convert(temp, iters);
 356
 357
 358
 359                         if ((method == "bayesian") && (search != "kmer"))  {
 360                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 361                                 search = "kmer";
 362                         }
 363                 }
 364
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 368                 exit(1);
 369         }
 370 }
 371
 372 //**********************************************************************************************************************
 373
 374 ClassifySeqsCommand::~ClassifySeqsCommand(){
 375
 376         if (abort == false) {
 377                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 378         }
 379 }
 380
 381 //**********************************************************************************************************************
 382
 383 void ClassifySeqsCommand::help(){
 384         try {
 385                 m->mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
 386                 m->mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
 387                 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");
 388                 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");
 389                 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");
 390                 m->mothurOut("The group parameter allows you add a group file so you can have the summary totals broken up by group.\n");
 391                 m->mothurOut("The method parameter allows you to specify classification method to use.  Your options are: bayesian and knn. The default is bayesian.\n");
 392                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 393                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 394                 #ifdef USE_MPI
 395                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 396                 #endif
 397                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 398                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 399                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 400                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 401                 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");
 402                 m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n");
 403                 m->mothurOut("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");
 404                 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");
 405                 m->mothurOut("The classify.seqs command should be in the following format: \n");
 406                 m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
 407                 m->mothurOut("Example classify.seqs(fasta=amazon.fasta, template=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n");
 408                 m->mothurOut("The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n");
 409                 m->mothurOut("The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n");
 410                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 411         }
 412         catch(exception& e) {
 413                 m->errorOut(e, "ClassifySeqsCommand", "help");
 414                 exit(1);
 415         }
 416 }
 417
 418
 419 //**********************************************************************************************************************
 420
 421 int ClassifySeqsCommand::execute(){
 422         try {
 423                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 424
 425                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
 426                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
 427                 else {
 428                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 429                         m->mothurOutEndLine();
 430                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
 431                 }
 432
 433                 if (m->control_pressed) { delete classify; return 0; }
 434
 435
 436                 for (int s = 0; s < fastaFileNames.size(); s++) {
 437
 438                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 439
 440                         string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
 441                         RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 442                         if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
 443                         RippedTaxName +=  ".";
 444
 445                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 446                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 447                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 448                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 449
 450                         if ((method == "knn") && (search == "distance")) {
 451                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
 452                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 453                         }
 454
 455                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 456                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 457
 458                         int start = time(NULL);
 459                         int numFastaSeqs = 0;
 460                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 461
 462 #ifdef USE_MPI
 463                                 int pid, numSeqsPerProcessor;
 464                                 int tag = 2001;
 465                                 vector<unsigned long int> MPIPos;
 466
 467                                 MPI_Status status;
 468                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 469                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 470
 471                                 MPI_File inMPI;
 472                                 MPI_File outMPINewTax;
 473                                 MPI_File outMPITempTax;
 474
 475                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 476                                 int inMode=MPI_MODE_RDONLY;
 477
 478                                 char outNewTax[1024];
 479                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 480
 481                                 char outTempTax[1024];
 482                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 483
 484                                 char inFileName[1024];
 485                                 strcpy(inFileName, fastaFileNames[s].c_str());
 486
 487                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 488                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 489                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 490
 491                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 492
 493                                 if (pid == 0) { //you are the root process
 494
 495                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 496
 497                                         //send file positions to all processes
 498                                         for(int i = 1; i < processors; i++) {
 499                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 500                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 501                                         }
 502
 503                                         //figure out how many sequences you have to align
 504                                         numSeqsPerProcessor = numFastaSeqs / processors;
 505                                         int startIndex =  pid * numSeqsPerProcessor;
 506                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 507
 508
 509                                         //align your part
 510                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 511
 512                                         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;  }
 513
 514                                         for (int i = 1; i < processors; i++) {
 515                                                 int done;
 516                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 517                                         }
 518                                 }else{ //you are a child process
 519                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 520                                         MPIPos.resize(numFastaSeqs+1);
 521                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 522
 523                                         //figure out how many sequences you have to align
 524                                         numSeqsPerProcessor = numFastaSeqs / processors;
 525                                         int startIndex =  pid * numSeqsPerProcessor;
 526                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 527
 528
 529                                         //align your part
 530                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 531
 532                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 533
 534                                         int done = 0;
 535                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 536                                 }
 537
 538                                 //close files
 539                                 MPI_File_close(&inMPI);
 540                                 MPI_File_close(&outMPINewTax);
 541                                 MPI_File_close(&outMPITempTax);
 542                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 543
 544 #else
 545
 546                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 547
 548                         for (int i = 0; i < (positions.size()-1); i++) {
 549                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 550                         }
 551
 552                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 553                         if(processors == 1){
 554                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 555                         }
 556                         else{
 557                                 processIDS.resize(0);
 558
 559                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 560
 561                         }
 562         #else
 563                         numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 564         #endif
 565 #endif
 566
 567                 m->mothurOutEndLine();
 568                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 569                 start = time(NULL);
 570
 571
 572                 #ifdef USE_MPI
 573                         if (pid == 0) {  //this part does not need to be paralellized
 574
 575                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 576                 #else
 577                         //read namefile
 578                         if(namefile != "") {
 579
 580                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 581
 582                                 nameMap.clear(); //remove old names
 583
 584                                 ifstream inNames;
 585                                 m->openInputFile(namefileNames[s], inNames);
 586
 587                                 string firstCol, secondCol;
 588                                 while(!inNames.eof()) {
 589                                         inNames >> firstCol >> secondCol; m->gobble(inNames);
 590
 591                                         vector<string> temp;
 592                                         m->splitAtComma(secondCol, temp);
 593
 594                                         nameMap[firstCol] = temp;
 595                                 }
 596                                 inNames.close();
 597
 598                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 599                         }
 600                 #endif
 601
 602                         string group = "";
 603                         if (groupfile != "") {  group = groupfileNames[s]; }
 604
 605                         PhyloSummary taxaSum(taxonomyFileName, group);
 606
 607                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 608
 609                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 610                         else {
 611                                 ifstream in;
 612                                 m->openInputFile(tempTaxonomyFile, in);
 613
 614                                 //read in users taxonomy file and add sequences to tree
 615                                 string name, taxon;
 616
 617                                 while(!in.eof()){
 618                                         in >> name >> taxon; m->gobble(in);
 619
 620                                         itNames = nameMap.find(name);
 621
 622                                         if (itNames == nameMap.end()) {
 623                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 624                                         }else{
 625                                                 for (int i = 0; i < itNames->second.size(); i++) {
 626                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 627                                                 }
 628                                                 itNames->second.clear();
 629                                                 nameMap.erase(itNames->first);
 630                                         }
 631                                 }
 632                                 in.close();
 633                         }
 634                         remove(tempTaxonomyFile.c_str());
 635
 636                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 637
 638                         //print summary file
 639                         ofstream outTaxTree;
 640                         m->openOutputFile(taxSummary, outTaxTree);
 641                         taxaSum.print(outTaxTree);
 642                         outTaxTree.close();
 643
 644                         //output taxonomy with the unclassified bins added
 645                         ifstream inTax;
 646                         m->openInputFile(newTaxonomyFile, inTax);
 647
 648                         ofstream outTax;
 649                         string unclass = newTaxonomyFile + ".unclass.temp";
 650                         m->openOutputFile(unclass, outTax);
 651
 652                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 653                         int maxLevel = taxaSum.getMaxLevel();
 654
 655                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 656                         string name, taxon;
 657                         while (!inTax.eof()) {
 658                                 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; }
 659
 660                                 inTax >> name >> taxon; m->gobble(inTax);
 661
 662                                 string newTax = addUnclassifieds(taxon, maxLevel);
 663
 664                                 outTax << name << '\t' << newTax << endl;
 665                         }
 666                         inTax.close();
 667                         outTax.close();
 668
 669                         remove(newTaxonomyFile.c_str());
 670                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 671
 672                         m->mothurOutEndLine();
 673                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 674
 675                         #ifdef USE_MPI
 676                                 }
 677                         #endif
 678
 679                         m->mothurOutEndLine();
 680                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 681                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 682                         m->mothurOutEndLine();
 683                 }
 684
 685                 delete classify;
 686                 return 0;
 687         }
 688         catch(exception& e) {
 689                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 690                 exit(1);
 691         }
 692 }
 693
 694 /**************************************************************************************************/
 695 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 696         try{
 697                 string newTax, taxon;
 698                 int level = 0;
 699
 700                 //keep what you have counting the levels
 701                 while (tax.find_first_of(';') != -1) {
 702                         //get taxon
 703                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 704                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 705                         newTax += taxon;
 706                         level++;
 707                 }
 708
 709                 //add "unclassified" until you reach maxLevel
 710                 while (level < maxlevel) {
 711                         newTax += "unclassified;";
 712                         level++;
 713                 }
 714
 715                 return newTax;
 716         }
 717         catch(exception& e) {
 718                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 719                 exit(1);
 720         }
 721 }
 722
 723 /**************************************************************************************************/
 724
 725 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 726         try {
 727 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 728                 int process = 1;
 729                 int num = 0;
 730
 731                 //loop through and create all the processes you want
 732                 while (process != processors) {
 733                         int pid = fork();
 734
 735                         if (pid > 0) {
 736                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 737                                 process++;
 738                         }else if (pid == 0){
 739                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
 740
 741                                 //pass numSeqs to parent
 742                                 ofstream out;
 743                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 744                                 m->openOutputFile(tempFile, out);
 745                                 out << num << endl;
 746                                 out.close();
 747
 748                                 exit(0);
 749                         }else {
 750                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 751                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 752                                 exit(0);
 753                         }
 754                 }
 755
 756                 //parent does its part
 757                 num = driver(lines[0], taxFileName, tempTaxFile, filename);
 758
 759                 //force parent to wait until all the processes are done
 760                 for (int i=0;i<processIDS.size();i++) {
 761                         int temp = processIDS[i];
 762                         wait(&temp);
 763                 }
 764
 765                 for (int i = 0; i < processIDS.size(); i++) {
 766                         ifstream in;
 767                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 768                         m->openInputFile(tempFile, in);
 769                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 770                         in.close(); remove(tempFile.c_str());
 771                 }
 772
 773                 for(int i=0;i<processIDS.size();i++){
 774                         appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 775                         appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 776                         remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
 777                         remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
 778                 }
 779
 780                 return num;
 781 #endif
 782         }
 783         catch(exception& e) {
 784                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 785                 exit(1);
 786         }
 787 }
 788 /**************************************************************************************************/
 789
 790 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 791         try{
 792
 793                 ofstream output;
 794                 ifstream input;
 795                 m->openOutputFileAppend(filename, output);
 796                 m->openInputFile(temp, input);
 797
 798                 while(char c = input.get()){
 799                         if(input.eof())         {       break;                  }
 800                         else                            {       output << c;    }
 801                 }
 802
 803                 input.close();
 804                 output.close();
 805         }
 806         catch(exception& e) {
 807                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 808                 exit(1);
 809         }
 810 }
 811
 812 //**********************************************************************************************************************
 813
 814 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
 815         try {
 816                 ofstream outTax;
 817                 m->openOutputFile(taxFName, outTax);
 818
 819                 ofstream outTaxSimple;
 820                 m->openOutputFile(tempTFName, outTaxSimple);
 821
 822                 ifstream inFASTA;
 823                 m->openInputFile(filename, inFASTA);
 824
 825                 string taxonomy;
 826
 827                 inFASTA.seekg(filePos->start);
 828
 829                 bool done = false;
 830                 int count = 0;
 831
 832                 while (!done) {
 833                         if (m->control_pressed) { return 0; }
 834
 835                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
 836
 837                         if (candidateSeq->getName() != "") {
 838
 839                                 taxonomy = classify->getTaxonomy(candidateSeq);
 840
 841                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 842
 843                                 if (taxonomy != "bad seq") {
 844                                         //output confidence scores or not
 845                                         if (probs) {
 846                                                 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 847                                         }else{
 848                                                 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 849                                         }
 850
 851                                         outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 852                                 }
 853                                 count++;
 854                         }
 855                         delete candidateSeq;
 856
 857                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 858                                 unsigned long int pos = inFASTA.tellg();
 859                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 860                         #else
 861                                 if (inFASTA.eof()) { break; }
 862                         #endif
 863
 864                         //report progress
 865                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 866
 867                 }
 868                 //report progress
 869                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 870
 871                 inFASTA.close();
 872                 outTax.close();
 873                 outTaxSimple.close();
 874
 875                 return count;
 876         }
 877         catch(exception& e) {
 878                 m->errorOut(e, "ClassifySeqsCommand", "driver");
 879                 exit(1);
 880         }
 881 }
 882 //**********************************************************************************************************************
 883 #ifdef USE_MPI
 884 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
 885         try {
 886                 MPI_Status statusNew;
 887                 MPI_Status statusTemp;
 888                 MPI_Status status;
 889
 890                 int pid;
 891                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 892
 893                 string taxonomy;
 894                 string outputString;
 895
 896                 for(int i=0;i<num;i++){
 897
 898                         if (m->control_pressed) { return 0; }
 899
 900                         //read next sequence
 901                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 902                         char* buf4 = new char[length];
 903                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 904
 905                         string tempBuf = buf4;
 906                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 907                         istringstream iss (tempBuf,istringstream::in);
 908                         delete buf4;
 909
 910                         Sequence* candidateSeq = new Sequence(iss);
 911
 912                         if (candidateSeq->getName() != "") {
 913                                 taxonomy = classify->getTaxonomy(candidateSeq);
 914
 915                                 if (taxonomy != "bad seq") {
 916                                         //output confidence scores or not
 917                                         if (probs) {
 918                                                 outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
 919                                         }else{
 920                                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 921                                         }
 922
 923                                         int length = outputString.length();
 924                                         char* buf2 = new char[length];
 925                                         memcpy(buf2, outputString.c_str(), length);
 926
 927                                         MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
 928                                         delete buf2;
 929
 930                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 931                                         length = outputString.length();
 932                                         char* buf = new char[length];
 933                                         memcpy(buf, outputString.c_str(), length);
 934
 935                                         MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
 936                                         delete buf;
 937                                 }
 938                         }
 939                         delete candidateSeq;
 940
 941                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
 942                 }
 943
 944                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
 945
 946
 947                 return 1;
 948         }
 949         catch(exception& e) {
 950                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
 951                 exit(1);
 952         }
 953 }
 954
 955 //**********************************************************************************************************************
 956 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
 957         try {
 958
 959                 nameMap.clear(); //remove old names
 960
 961                 MPI_File inMPI;
 962                 MPI_Offset size;
 963                 MPI_Status status;
 964
 965                 //char* inFileName = new char[nameFilename.length()];
 966                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
 967
 968                 char inFileName[1024];
 969                 strcpy(inFileName, nameFilename.c_str());
 970
 971                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 972                 MPI_File_get_size(inMPI, &size);
 973                 //delete inFileName;
 974
 975                 char* buffer = new char[size];
 976                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 977
 978                 string tempBuf = buffer;
 979                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 980                 istringstream iss (tempBuf,istringstream::in);
 981                 delete buffer;
 982
 983                 string firstCol, secondCol;
 984                 while(!iss.eof()) {
 985                         iss >> firstCol >> secondCol; m->gobble(iss);
 986
 987                         vector<string> temp;
 988                         m->splitAtComma(secondCol, temp);
 989
 990                         nameMap[firstCol] = temp;
 991                 }
 992
 993                 MPI_File_close(&inMPI);
 994
 995                 return 1;
 996         }
 997         catch(exception& e) {
 998                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
 999                 exit(1);
1000         }
1001 }
1002 #endif
1003 /**************************************************************************************************/