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::setParameters(){
  20         try {
  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);
  40
  41                 vector<string> myArray;
  42                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ClassifySeqsCommand", "setParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 string ClassifySeqsCommand::getHelpString(){
  52         try {
  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";
  63 #ifdef USE_MPI
  64                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  65 #endif
  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";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 ClassifySeqsCommand::ClassifySeqsCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  92                 vector<string> tempOutNames;
  93                 outputTypes["taxonomy"] = tempOutNames;
  94                 outputTypes["taxsummary"] = tempOutNames;
  95                 outputTypes["matchdist"] = tempOutNames;
  96         }
  97         catch(exception& e) {
  98                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
  99                 exit(1);
 100         }
 101 }
 102 //**********************************************************************************************************************
 103 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 104         try {
 105                 abort = false; calledHelp = false;
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; calledHelp = true; }
 109
 110                 else {
 111                         vector<string> myArray = setParameters();
 112
 113                         OptionParser parser(option);
 114                         map<string, string> parameters = parser.getParameters();
 115
 116                         ValidParameters validParameter("classify.seqs");
 117                         map<string, string>::iterator it;
 118
 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;  }
 122                         }
 123
 124                         //initialize outputTypes
 125                         vector<string> tempOutNames;
 126                         outputTypes["taxonomy"] = tempOutNames;
 127                         outputTypes["taxsummary"] = tempOutNames;
 128                         outputTypes["matchdist"] = tempOutNames;
 129
 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 = "";         }
 132
 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 = "";          }
 136                         else {
 137                                 string path;
 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;                }
 144                                 }
 145
 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;         }
 152                                 }
 153
 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;            }
 160                                 }
 161                         }
 162
 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();
 168                                 abort = true;
 169                         }
 170                         else if (templateFileName == "not open") { abort = true; }
 171
 172
 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; }
 179                         }
 180                         else {
 181                                 m->splitAtDash(fastaFileName, fastaFileNames);
 182
 183                                 //go through files and make sure they are good, if not, then disregard them
 184                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 185                                         if (inputDir != "") {
 186                                                 string path = m->hasPath(fastaFileNames[i]);
 187                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 188                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 189                                         }
 190
 191                                         int ableToOpen;
 192
 193                                         ifstream in;
 194                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 195
 196                                         //if you can't open it, try default location
 197                                         if (ableToOpen == 1) {
 198                                                 if (m->getDefaultPath() != "") { //default path is set
 199                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 200                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 201                                                         ifstream in2;
 202                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 203                                                         in2.close();
 204                                                         fastaFileNames[i] = tryPath;
 205                                                 }
 206                                         }
 207
 208                                         if (ableToOpen == 1) {
 209                                                 if (m->getOutputDir() != "") { //default path is set
 210                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 211                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 212                                                         ifstream in2;
 213                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 214                                                         in2.close();
 215                                                         fastaFileNames[i] = tryPath;
 216                                                 }
 217                                         }
 218
 219                                         in.close();
 220
 221                                         if (ableToOpen == 1) {
 222                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 223                                                 //erase from file list
 224                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 225                                                 i--;
 226                                         }
 227
 228                                 }
 229
 230                                 //make sure there is at least one valid file left
 231                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 232                         }
 233
 234
 235                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 236                         if (taxonomyFileName == "not found") {
 237                                 m->mothurOut("taxonomy is a required parameter for the classify.seqs command.");
 238                                 m->mothurOutEndLine();
 239                                 abort = true;
 240                         }
 241                         else if (taxonomyFileName == "not open") { abort = true; }
 242
 243
 244                         namefile = validParameter.validFile(parameters, "name", false);
 245                         if (namefile == "not found") { namefile = "";  }
 246
 247                         else {
 248                                 m->splitAtDash(namefile, namefileNames);
 249
 250                                 //go through files and make sure they are good, if not, then disregard them
 251                                 for (int i = 0; i < namefileNames.size(); i++) {
 252                                         if (inputDir != "") {
 253                                                 string path = m->hasPath(namefileNames[i]);
 254                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 255                                                 if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 256                                         }
 257                                         int ableToOpen;
 258
 259                                         ifstream in;
 260                                         ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 261
 262                                         //if you can't open it, try default location
 263                                         if (ableToOpen == 1) {
 264                                                 if (m->getDefaultPath() != "") { //default path is set
 265                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 266                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 267                                                         ifstream in2;
 268                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 269                                                         in2.close();
 270                                                         namefileNames[i] = tryPath;
 271                                                 }
 272                                         }
 273
 274                                         if (ableToOpen == 1) {
 275                                                 if (m->getOutputDir() != "") { //default path is set
 276                                                         string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 277                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 278                                                         ifstream in2;
 279                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 280                                                         in2.close();
 281                                                         namefileNames[i] = tryPath;
 282                                                 }
 283                                         }
 284                                         in.close();
 285
 286                                         if (ableToOpen == 1) {
 287                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 288                                                 //erase from file list
 289                                                 namefileNames.erase(namefileNames.begin()+i);
 290                                                 i--;
 291                                         }
 292
 293                                 }
 294                         }
 295
 296                         if (namefile != "") {
 297                                 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(); }
 298                         }
 299
 300                         groupfile = validParameter.validFile(parameters, "group", false);
 301                         if (groupfile == "not found") { groupfile = "";  }
 302                         else {
 303                                 m->splitAtDash(groupfile, groupfileNames);
 304
 305                                 //go through files and make sure they are good, if not, then disregard them
 306                                 for (int i = 0; i < groupfileNames.size(); i++) {
 307                                         if (inputDir != "") {
 308                                                 string path = m->hasPath(groupfileNames[i]);
 309                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 310                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 311                                         }
 312                                         int ableToOpen;
 313
 314                                         ifstream in;
 315                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 316
 317                                         //if you can't open it, try default location
 318                                         if (ableToOpen == 1) {
 319                                                 if (m->getDefaultPath() != "") { //default path is set
 320                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 321                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 322                                                         ifstream in2;
 323                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 324                                                         in2.close();
 325                                                         groupfileNames[i] = tryPath;
 326                                                 }
 327                                         }
 328
 329                                         if (ableToOpen == 1) {
 330                                                 if (m->getOutputDir() != "") { //default path is set
 331                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 332                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 333                                                         ifstream in2;
 334                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 335                                                         in2.close();
 336                                                         groupfileNames[i] = tryPath;
 337                                                 }
 338                                         }
 339
 340                                         in.close();
 341
 342                                         if (ableToOpen == 1) {
 343                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 344                                                 //erase from file list
 345                                                 groupfileNames.erase(groupfileNames.begin()+i);
 346                                                 i--;
 347                                         }
 348                                 }
 349                         }
 350
 351                         if (groupfile != "") {
 352                                 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(); }
 353                         }else {
 354                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 355                         }
 356
 357                         //check for optional parameter and set defaults
 358                         // ...at some point should added some additional type checking...
 359                         string temp;
 360                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 361                         convert(temp, kmerSize);
 362
 363                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 364                         m->setProcessors(temp);
 365                         convert(temp, processors);
 366
 367                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 368
 369                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 370
 371                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 372                         convert(temp, match);
 373
 374                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 375                         convert(temp, misMatch);
 376
 377                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 378                         convert(temp, gapOpen);
 379
 380                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 381                         convert(temp, gapExtend);
 382
 383                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 384                         convert(temp, numWanted);
 385
 386                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 387                         convert(temp, cutoff);
 388
 389                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 390                         probs = m->isTrue(temp);
 391
 392                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 393                         convert(temp, iters);
 394
 395
 396
 397                         if ((method == "bayesian") && (search != "kmer"))  {
 398                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 399                                 search = "kmer";
 400                         }
 401                 }
 402
 403         }
 404         catch(exception& e) {
 405                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 406                 exit(1);
 407         }
 408 }
 409
 410 //**********************************************************************************************************************
 411 ClassifySeqsCommand::~ClassifySeqsCommand(){
 412         if (abort == false) {
 413                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 414         }
 415 }
 416 //**********************************************************************************************************************
 417
 418 int ClassifySeqsCommand::execute(){
 419         try {
 420                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 421
 422                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
 423                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
 424                 else {
 425                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 426                         m->mothurOutEndLine();
 427                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
 428                 }
 429
 430                 if (m->control_pressed) { delete classify; return 0; }
 431
 432
 433                 for (int s = 0; s < fastaFileNames.size(); s++) {
 434
 435                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 436
 437                         string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName));
 438                         RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
 439                         if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
 440                         RippedTaxName +=  ".";
 441
 442                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 443                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 444                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 445                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 446
 447                         if ((method == "knn") && (search == "distance")) {
 448                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist";
 449                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 450                         }
 451
 452                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 453                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 454
 455                         int start = time(NULL);
 456                         int numFastaSeqs = 0;
 457                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 458
 459 #ifdef USE_MPI
 460                                 int pid, numSeqsPerProcessor;
 461                                 int tag = 2001;
 462                                 vector<unsigned long int> MPIPos;
 463
 464                                 MPI_Status status;
 465                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 466                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 467
 468                                 MPI_File inMPI;
 469                                 MPI_File outMPINewTax;
 470                                 MPI_File outMPITempTax;
 471
 472                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 473                                 int inMode=MPI_MODE_RDONLY;
 474
 475                                 char outNewTax[1024];
 476                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 477
 478                                 char outTempTax[1024];
 479                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 480
 481                                 char inFileName[1024];
 482                                 strcpy(inFileName, fastaFileNames[s].c_str());
 483
 484                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 485                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 486                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 487
 488                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 489
 490                                 if (pid == 0) { //you are the root process
 491
 492                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 493
 494                                         //send file positions to all processes
 495                                         for(int i = 1; i < processors; i++) {
 496                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 497                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 498                                         }
 499
 500                                         //figure out how many sequences you have to align
 501                                         numSeqsPerProcessor = numFastaSeqs / processors;
 502                                         int startIndex =  pid * numSeqsPerProcessor;
 503                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 504
 505
 506                                         //align your part
 507                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 508
 509                                         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;  }
 510
 511                                         for (int i = 1; i < processors; i++) {
 512                                                 int done;
 513                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 514                                         }
 515                                 }else{ //you are a child process
 516                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 517                                         MPIPos.resize(numFastaSeqs+1);
 518                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 519
 520                                         //figure out how many sequences you have to align
 521                                         numSeqsPerProcessor = numFastaSeqs / processors;
 522                                         int startIndex =  pid * numSeqsPerProcessor;
 523                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 524
 525
 526                                         //align your part
 527                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
 528
 529                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 530
 531                                         int done = 0;
 532                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 533                                 }
 534
 535                                 //close files
 536                                 MPI_File_close(&inMPI);
 537                                 MPI_File_close(&outMPINewTax);
 538                                 MPI_File_close(&outMPITempTax);
 539                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 540
 541 #else
 542
 543                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 544
 545                         for (int i = 0; i < (positions.size()-1); i++) {
 546                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 547                         }
 548
 549                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 550                         if(processors == 1){
 551                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 552                         }
 553                         else{
 554                                 processIDS.resize(0);
 555
 556                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 557
 558                         }
 559         #else
 560                         numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 561         #endif
 562 #endif
 563
 564                 m->mothurOutEndLine();
 565                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 566                 start = time(NULL);
 567
 568
 569                 #ifdef USE_MPI
 570                         if (pid == 0) {  //this part does not need to be paralellized
 571
 572                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 573                 #else
 574                         //read namefile
 575                         if(namefile != "") {
 576
 577                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 578
 579                                 nameMap.clear(); //remove old names
 580
 581                                 ifstream inNames;
 582                                 m->openInputFile(namefileNames[s], inNames);
 583
 584                                 string firstCol, secondCol;
 585                                 while(!inNames.eof()) {
 586                                         inNames >> firstCol >> secondCol; m->gobble(inNames);
 587
 588                                         vector<string> temp;
 589                                         m->splitAtComma(secondCol, temp);
 590
 591                                         nameMap[firstCol] = temp;
 592                                 }
 593                                 inNames.close();
 594
 595                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 596                         }
 597                 #endif
 598
 599                         string group = "";
 600                         if (groupfile != "") {  group = groupfileNames[s]; }
 601
 602                         PhyloSummary taxaSum(taxonomyFileName, group);
 603
 604                         if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 605
 606                         if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
 607                         else {
 608                                 ifstream in;
 609                                 m->openInputFile(tempTaxonomyFile, in);
 610
 611                                 //read in users taxonomy file and add sequences to tree
 612                                 string name, taxon;
 613
 614                                 while(!in.eof()){
 615                                         in >> name >> taxon; m->gobble(in);
 616
 617                                         itNames = nameMap.find(name);
 618
 619                                         if (itNames == nameMap.end()) {
 620                                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 621                                         }else{
 622                                                 for (int i = 0; i < itNames->second.size(); i++) {
 623                                                         taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 624                                                 }
 625                                                 itNames->second.clear();
 626                                                 nameMap.erase(itNames->first);
 627                                         }
 628                                 }
 629                                 in.close();
 630                         }
 631                         remove(tempTaxonomyFile.c_str());
 632
 633                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
 634
 635                         //print summary file
 636                         ofstream outTaxTree;
 637                         m->openOutputFile(taxSummary, outTaxTree);
 638                         taxaSum.print(outTaxTree);
 639                         outTaxTree.close();
 640
 641                         //output taxonomy with the unclassified bins added
 642                         ifstream inTax;
 643                         m->openInputFile(newTaxonomyFile, inTax);
 644
 645                         ofstream outTax;
 646                         string unclass = newTaxonomyFile + ".unclass.temp";
 647                         m->openOutputFile(unclass, outTax);
 648
 649                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 650                         int maxLevel = taxaSum.getMaxLevel();
 651
 652                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 653                         string name, taxon;
 654                         while (!inTax.eof()) {
 655                                 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; }
 656
 657                                 inTax >> name >> taxon; m->gobble(inTax);
 658
 659                                 string newTax = addUnclassifieds(taxon, maxLevel);
 660
 661                                 outTax << name << '\t' << newTax << endl;
 662                         }
 663                         inTax.close();
 664                         outTax.close();
 665
 666                         remove(newTaxonomyFile.c_str());
 667                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 668
 669                         m->mothurOutEndLine();
 670                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 671
 672                         #ifdef USE_MPI
 673                                 }
 674                         #endif
 675
 676                         m->mothurOutEndLine();
 677                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 678                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 679                         m->mothurOutEndLine();
 680                 }
 681
 682                 //set taxonomy file as new current taxonomyfile
 683                 string current = "";
 684                 itTypes = outputTypes.find("taxonomy");
 685                 if (itTypes != outputTypes.end()) {
 686                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 687                 }
 688
 689                 delete classify;
 690                 return 0;
 691         }
 692         catch(exception& e) {
 693                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 694                 exit(1);
 695         }
 696 }
 697
 698 /**************************************************************************************************/
 699 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 700         try{
 701                 string newTax, taxon;
 702                 int level = 0;
 703
 704                 //keep what you have counting the levels
 705                 while (tax.find_first_of(';') != -1) {
 706                         //get taxon
 707                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 708                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 709                         newTax += taxon;
 710                         level++;
 711                 }
 712
 713                 //add "unclassified" until you reach maxLevel
 714                 while (level < maxlevel) {
 715                         newTax += "unclassified;";
 716                         level++;
 717                 }
 718
 719                 return newTax;
 720         }
 721         catch(exception& e) {
 722                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 723                 exit(1);
 724         }
 725 }
 726
 727 /**************************************************************************************************/
 728
 729 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 730         try {
 731 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 732                 int process = 1;
 733                 int num = 0;
 734
 735                 //loop through and create all the processes you want
 736                 while (process != processors) {
 737                         int pid = fork();
 738
 739                         if (pid > 0) {
 740                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 741                                 process++;
 742                         }else if (pid == 0){
 743                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
 744
 745                                 //pass numSeqs to parent
 746                                 ofstream out;
 747                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 748                                 m->openOutputFile(tempFile, out);
 749                                 out << num << endl;
 750                                 out.close();
 751
 752                                 exit(0);
 753                         }else {
 754                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 755                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 756                                 exit(0);
 757                         }
 758                 }
 759
 760                 //parent does its part
 761                 num = driver(lines[0], taxFileName, tempTaxFile, filename);
 762
 763                 //force parent to wait until all the processes are done
 764                 for (int i=0;i<processIDS.size();i++) {
 765                         int temp = processIDS[i];
 766                         wait(&temp);
 767                 }
 768
 769                 for (int i = 0; i < processIDS.size(); i++) {
 770                         ifstream in;
 771                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 772                         m->openInputFile(tempFile, in);
 773                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 774                         in.close(); remove(tempFile.c_str());
 775                 }
 776
 777                 for(int i=0;i<processIDS.size();i++){
 778                         appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 779                         appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
 780                         remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
 781                         remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
 782                 }
 783
 784                 return num;
 785 #endif
 786         }
 787         catch(exception& e) {
 788                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
 789                 exit(1);
 790         }
 791 }
 792 /**************************************************************************************************/
 793
 794 void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
 795         try{
 796
 797                 ofstream output;
 798                 ifstream input;
 799                 m->openOutputFileAppend(filename, output);
 800                 m->openInputFile(temp, input);
 801
 802                 while(char c = input.get()){
 803                         if(input.eof())         {       break;                  }
 804                         else                            {       output << c;    }
 805                 }
 806
 807                 input.close();
 808                 output.close();
 809         }
 810         catch(exception& e) {
 811                 m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
 812                 exit(1);
 813         }
 814 }
 815
 816 //**********************************************************************************************************************
 817
 818 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){
 819         try {
 820                 ofstream outTax;
 821                 m->openOutputFile(taxFName, outTax);
 822
 823                 ofstream outTaxSimple;
 824                 m->openOutputFile(tempTFName, outTaxSimple);
 825
 826                 ifstream inFASTA;
 827                 m->openInputFile(filename, inFASTA);
 828
 829                 string taxonomy;
 830
 831                 inFASTA.seekg(filePos->start);
 832
 833                 bool done = false;
 834                 int count = 0;
 835
 836                 while (!done) {
 837                         if (m->control_pressed) { return 0; }
 838
 839                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
 840
 841                         if (candidateSeq->getName() != "") {
 842
 843                                 taxonomy = classify->getTaxonomy(candidateSeq);
 844
 845                                 if (m->control_pressed) { delete candidateSeq; return 0; }
 846
 847                                 if (taxonomy != "bad seq") {
 848                                         //output confidence scores or not
 849                                         if (probs) {
 850                                                 outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 851                                         }else{
 852                                                 outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 853                                         }
 854
 855                                         outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
 856                                 }
 857                                 count++;
 858                         }
 859                         delete candidateSeq;
 860
 861                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 862                                 unsigned long int pos = inFASTA.tellg();
 863                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 864                         #else
 865                                 if (inFASTA.eof()) { break; }
 866                         #endif
 867
 868                         //report progress
 869                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 870
 871                 }
 872                 //report progress
 873                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 874
 875                 inFASTA.close();
 876                 outTax.close();
 877                 outTaxSimple.close();
 878
 879                 return count;
 880         }
 881         catch(exception& e) {
 882                 m->errorOut(e, "ClassifySeqsCommand", "driver");
 883                 exit(1);
 884         }
 885 }
 886 //**********************************************************************************************************************
 887 #ifdef USE_MPI
 888 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
 889         try {
 890                 MPI_Status statusNew;
 891                 MPI_Status statusTemp;
 892                 MPI_Status status;
 893
 894                 int pid;
 895                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 896
 897                 string taxonomy;
 898                 string outputString;
 899
 900                 for(int i=0;i<num;i++){
 901
 902                         if (m->control_pressed) { return 0; }
 903
 904                         //read next sequence
 905                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 906                         char* buf4 = new char[length];
 907                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 908
 909                         string tempBuf = buf4;
 910                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 911                         istringstream iss (tempBuf,istringstream::in);
 912                         delete buf4;
 913
 914                         Sequence* candidateSeq = new Sequence(iss);
 915
 916                         if (candidateSeq->getName() != "") {
 917                                 taxonomy = classify->getTaxonomy(candidateSeq);
 918
 919                                 if (taxonomy != "bad seq") {
 920                                         //output confidence scores or not
 921                                         if (probs) {
 922                                                 outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
 923                                         }else{
 924                                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 925                                         }
 926
 927                                         int length = outputString.length();
 928                                         char* buf2 = new char[length];
 929                                         memcpy(buf2, outputString.c_str(), length);
 930
 931                                         MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
 932                                         delete buf2;
 933
 934                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
 935                                         length = outputString.length();
 936                                         char* buf = new char[length];
 937                                         memcpy(buf, outputString.c_str(), length);
 938
 939                                         MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
 940                                         delete buf;
 941                                 }
 942                         }
 943                         delete candidateSeq;
 944
 945                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
 946                 }
 947
 948                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
 949
 950
 951                 return 1;
 952         }
 953         catch(exception& e) {
 954                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
 955                 exit(1);
 956         }
 957 }
 958
 959 //**********************************************************************************************************************
 960 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
 961         try {
 962
 963                 nameMap.clear(); //remove old names
 964
 965                 MPI_File inMPI;
 966                 MPI_Offset size;
 967                 MPI_Status status;
 968
 969                 //char* inFileName = new char[nameFilename.length()];
 970                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
 971
 972                 char inFileName[1024];
 973                 strcpy(inFileName, nameFilename.c_str());
 974
 975                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 976                 MPI_File_get_size(inMPI, &size);
 977                 //delete inFileName;
 978
 979                 char* buffer = new char[size];
 980                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 981
 982                 string tempBuf = buffer;
 983                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 984                 istringstream iss (tempBuf,istringstream::in);
 985                 delete buffer;
 986
 987                 string firstCol, secondCol;
 988                 while(!iss.eof()) {
 989                         iss >> firstCol >> secondCol; m->gobble(iss);
 990
 991                         vector<string> temp;
 992                         m->splitAtComma(secondCol, temp);
 993
 994                         nameMap[firstCol] = temp;
 995                 }
 996
 997                 MPI_File_close(&inMPI);
 998
 999                 return 1;
1000         }
1001         catch(exception& e) {
1002                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1003                 exit(1);
1004         }
1005 }
1006 #endif
1007 /**************************************************************************************************/