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
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> ClassifySeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
  18                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  20         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  21         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  22                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
  23
  24                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  25                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  26                 CommandParameter pmethod("method", "Multiple", "bayesian-knn", "bayesian", "", "", "",false,false); parameters.push_back(pmethod);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  28                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  29                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  30                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  31                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  32                 //CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  33                 CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
  34                 CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
  35                 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
  36                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  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, group, count, 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 count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
  61                 helpString += "The method parameter allows you to specify classification method to use.  Your options are: bayesian and knn. The default is bayesian.\n";
  62                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n";
  63                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  64 #ifdef USE_MPI
  65                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  66 #endif
  67                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  68                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  69                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  70                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  71                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  72                 helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
  73                 helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
  74                 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";
  75                 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";
  76                 //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
  77                 helpString += "The classify.seqs command should be in the following format: \n";
  78                 helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
  79                 helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
  80                 helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
  81                 helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
  82                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  83                 return helpString;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91 string ClassifySeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  92         try {
  93         string outputFileName = "";
  94                 map<string, vector<string> >::iterator it;
  95
  96         //is this a type this command creates
  97         it = outputTypes.find(type);
  98         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  99         else {
 100             if (type == "taxonomy") {  outputFileName =  "taxonomy"; }
 101             else if (type == "accnos") {  outputFileName =  "flip.accnos"; }
 102             else if (type == "taxsummary") {  outputFileName =  "tax.summary"; }
 103             else if (type == "matchdist") {  outputFileName =  "match.dist"; }
 104             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 105         }
 106         return outputFileName;
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "ClassifySeqsCommand", "getOutputFileNameTag");
 110                 exit(1);
 111         }
 112 }
 113 //**********************************************************************************************************************
 114 ClassifySeqsCommand::ClassifySeqsCommand(){
 115         try {
 116                 abort = true; calledHelp = true;
 117                 setParameters();
 118                 vector<string> tempOutNames;
 119                 outputTypes["taxonomy"] = tempOutNames;
 120                 outputTypes["accnos"] = tempOutNames;
 121                 outputTypes["taxsummary"] = tempOutNames;
 122                 outputTypes["matchdist"] = tempOutNames;
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 126                 exit(1);
 127         }
 128 }
 129 //**********************************************************************************************************************
 130 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 131         try {
 132                 abort = false; calledHelp = false;
 133                 rdb = ReferenceDB::getInstance(); hasName = false; hasCount=false;
 134
 135                 //allow user to run help
 136                 if(option == "help") { help(); abort = true; calledHelp = true; }
 137                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 138
 139                 else {
 140                         vector<string> myArray = setParameters();
 141
 142                         OptionParser parser(option);
 143                         map<string, string> parameters = parser.getParameters();
 144
 145                         ValidParameters validParameter("classify.seqs");
 146                         map<string, string>::iterator it;
 147
 148                         //check to make sure all parameters are valid for command
 149                         for (it = parameters.begin(); it != parameters.end(); it++) {
 150                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 151                         }
 152
 153                         //initialize outputTypes
 154                         vector<string> tempOutNames;
 155                         outputTypes["taxonomy"] = tempOutNames;
 156                         outputTypes["taxsummary"] = tempOutNames;
 157                         outputTypes["matchdist"] = tempOutNames;
 158                         outputTypes["accnos"] = tempOutNames;
 159
 160                         //if the user changes the output directory command factory will send this info to us in the output parameter
 161                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 162
 163                         //if the user changes the input directory command factory will send this info to us in the output parameter
 164                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 165                         if (inputDir == "not found"){   inputDir = "";          }
 166                         else {
 167                                 string path;
 168                                 it = parameters.find("reference");
 169                                 //user has given a template file
 170                                 if(it != parameters.end()){
 171                                         path = m->hasPath(it->second);
 172                                         //if the user has not given a path then, add inputdir. else leave path alone.
 173                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 174                                 }
 175
 176                                 it = parameters.find("taxonomy");
 177                                 //user has given a template file
 178                                 if(it != parameters.end()){
 179                                         path = m->hasPath(it->second);
 180                                         //if the user has not given a path then, add inputdir. else leave path alone.
 181                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 182                                 }
 183
 184                                 it = parameters.find("group");
 185                                 //user has given a template file
 186                                 if(it != parameters.end()){
 187                                         path = m->hasPath(it->second);
 188                                         //if the user has not given a path then, add inputdir. else leave path alone.
 189                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 190                                 }
 191
 192                 it = parameters.find("count");
 193                                 //user has given a template file
 194                                 if(it != parameters.end()){
 195                                         path = m->hasPath(it->second);
 196                                         //if the user has not given a path then, add inputdir. else leave path alone.
 197                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 198                                 }
 199                         }
 200
 201                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 202                         if (fastaFileName == "not found") {
 203                                 //if there is a current fasta file, use it
 204                                 string filename = m->getFastaFile();
 205                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 206                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 207                         }
 208                         else {
 209                                 m->splitAtDash(fastaFileName, fastaFileNames);
 210
 211                                 //go through files and make sure they are good, if not, then disregard them
 212                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 213
 214                                         bool ignore = false;
 215                                         if (fastaFileNames[i] == "current") {
 216                                                 fastaFileNames[i] = m->getFastaFile();
 217                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 218                                                 else {
 219                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 220                                                         //erase from file list
 221                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 222                                                         i--;
 223                                                 }
 224                                         }
 225
 226                                         if (!ignore) {
 227
 228                                                 if (inputDir != "") {
 229                                                         string path = m->hasPath(fastaFileNames[i]);
 230                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 231                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 232                                                 }
 233
 234                                                 int ableToOpen;
 235
 236                                                 ifstream in;
 237                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 238
 239                                                 //if you can't open it, try default location
 240                                                 if (ableToOpen == 1) {
 241                                                         if (m->getDefaultPath() != "") { //default path is set
 242                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 243                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 244                                                                 ifstream in2;
 245                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 246                                                                 in2.close();
 247                                                                 fastaFileNames[i] = tryPath;
 248                                                         }
 249                                                 }
 250
 251                                                 if (ableToOpen == 1) {
 252                                                         if (m->getOutputDir() != "") { //default path is set
 253                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 254                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 255                                                                 ifstream in2;
 256                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 257                                                                 in2.close();
 258                                                                 fastaFileNames[i] = tryPath;
 259                                                         }
 260                                                 }
 261
 262                                                 in.close();
 263
 264                                                 if (ableToOpen == 1) {
 265                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 266                                                         //erase from file list
 267                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 268                                                         i--;
 269                                                 }else {
 270                                                         m->setFastaFile(fastaFileNames[i]);
 271                                                 }
 272                                         }
 273
 274                                 }
 275
 276                                 //make sure there is at least one valid file left
 277                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 278                         }
 279
 280                         namefile = validParameter.validFile(parameters, "name", false);
 281                         if (namefile == "not found") { namefile = "";  }
 282
 283                         else {
 284                                 m->splitAtDash(namefile, namefileNames);
 285
 286                                 //go through files and make sure they are good, if not, then disregard them
 287                                 for (int i = 0; i < namefileNames.size(); i++) {
 288                                         bool ignore = false;
 289                                         if (namefileNames[i] == "current") {
 290                                                 namefileNames[i] = m->getNameFile();
 291                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 292                                                 else {
 293                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 294                                                         //erase from file list
 295                                                         namefileNames.erase(namefileNames.begin()+i);
 296                                                         i--;
 297                                                 }
 298                                         }
 299
 300                                         if (!ignore) {
 301
 302                                                 if (inputDir != "") {
 303                                                         string path = m->hasPath(namefileNames[i]);
 304                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 305                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 306                                                 }
 307                                                 int ableToOpen;
 308
 309                                                 ifstream in;
 310                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 311
 312                                                 //if you can't open it, try default location
 313                                                 if (ableToOpen == 1) {
 314                                                         if (m->getDefaultPath() != "") { //default path is set
 315                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 316                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 317                                                                 ifstream in2;
 318                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 319                                                                 in2.close();
 320                                                                 namefileNames[i] = tryPath;
 321                                                         }
 322                                                 }
 323
 324                                                 if (ableToOpen == 1) {
 325                                                         if (m->getOutputDir() != "") { //default path is set
 326                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 327                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 328                                                                 ifstream in2;
 329                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 330                                                                 in2.close();
 331                                                                 namefileNames[i] = tryPath;
 332                                                         }
 333                                                 }
 334                                                 in.close();
 335
 336                                                 if (ableToOpen == 1) {
 337                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 338                                                         //erase from file list
 339                                                         namefileNames.erase(namefileNames.begin()+i);
 340                                                         i--;
 341                                                 }else {
 342                                                         m->setNameFile(namefileNames[i]);
 343                                                 }
 344                                         }
 345                                 }
 346                         }
 347
 348             if (namefileNames.size() != 0) { hasName = true; }
 349
 350                         if (namefile != "") {
 351                                 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(); }
 352                         }
 353
 354             //check for required parameters
 355                         countfile = validParameter.validFile(parameters, "count", false);
 356                         if (countfile == "not found") {
 357                 countfile = "";
 358                         }else {
 359                                 m->splitAtDash(countfile, countfileNames);
 360
 361                                 //go through files and make sure they are good, if not, then disregard them
 362                                 for (int i = 0; i < countfileNames.size(); i++) {
 363
 364                                         bool ignore = false;
 365                                         if (countfileNames[i] == "current") {
 366                                                 countfileNames[i] = m->getCountTableFile();
 367                                                 if (countfileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
 368                                                 else {
 369                                                         m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
 370                                                         //erase from file list
 371                                                         countfileNames.erase(countfileNames.begin()+i);
 372                                                         i--;
 373                                                 }
 374                                         }
 375
 376                                         if (!ignore) {
 377
 378                                                 if (inputDir != "") {
 379                                                         string path = m->hasPath(countfileNames[i]);
 380                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 381                                                         if (path == "") {       countfileNames[i] = inputDir + countfileNames[i];               }
 382                                                 }
 383
 384                                                 int ableToOpen;
 385                                                 ifstream in;
 386
 387                                                 ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
 388
 389                                                 //if you can't open it, try default location
 390                                                 if (ableToOpen == 1) {
 391                                                         if (m->getDefaultPath() != "") { //default path is set
 392                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
 393                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 394                                                                 ifstream in2;
 395                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 396                                                                 in2.close();
 397                                                                 countfileNames[i] = tryPath;
 398                                                         }
 399                                                 }
 400
 401                                                 if (ableToOpen == 1) {
 402                                                         if (m->getOutputDir() != "") { //default path is set
 403                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
 404                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 405                                                                 ifstream in2;
 406                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 407                                                                 in2.close();
 408                                                                 countfileNames[i] = tryPath;
 409                                                         }
 410                                                 }
 411
 412                                                 in.close();
 413
 414                                                 if (ableToOpen == 1) {
 415                                                         m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 416                                                         //erase from file list
 417                                                         countfileNames.erase(countfileNames.begin()+i);
 418                                                         i--;
 419                                                 }else {
 420                                                         m->setCountTableFile(countfileNames[i]);
 421                                                 }
 422                                         }
 423                                 }
 424                         }
 425
 426             if (countfileNames.size() != 0) { hasCount = true; if (countfileNames.size() != fastaFileNames.size()) {m->mothurOut("If you provide a count file, you must have one for each fasta file."); m->mothurOutEndLine(); } }
 427
 428                         //make sure there is at least one valid file left
 429             if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 430
 431                         groupfile = validParameter.validFile(parameters, "group", false);
 432                         if (groupfile == "not found") { groupfile = "";  }
 433                         else {
 434                                 m->splitAtDash(groupfile, groupfileNames);
 435
 436                                 //go through files and make sure they are good, if not, then disregard them
 437                                 for (int i = 0; i < groupfileNames.size(); i++) {
 438                                         if (inputDir != "") {
 439                                                 string path = m->hasPath(groupfileNames[i]);
 440                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 441                                                 if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 442                                         }
 443                                         int ableToOpen;
 444
 445                                         ifstream in;
 446                                         ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 447
 448                                         //if you can't open it, try default location
 449                                         if (ableToOpen == 1) {
 450                                                 if (m->getDefaultPath() != "") { //default path is set
 451                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 452                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 453                                                         ifstream in2;
 454                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 455                                                         in2.close();
 456                                                         groupfileNames[i] = tryPath;
 457                                                 }
 458                                         }
 459
 460                                         if (ableToOpen == 1) {
 461                                                 if (m->getOutputDir() != "") { //default path is set
 462                                                         string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 463                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 464                                                         ifstream in2;
 465                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 466                                                         in2.close();
 467                                                         groupfileNames[i] = tryPath;
 468                                                 }
 469                                         }
 470
 471                                         in.close();
 472
 473                                         if (ableToOpen == 1) {
 474                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
 475                                                 //erase from file list
 476                                                 groupfileNames.erase(groupfileNames.begin()+i);
 477                                                 i--;
 478                                         }else {
 479                                                 m->setGroupFile(groupfileNames[i]);
 480                                         }
 481                                 }
 482                         }
 483
 484                         if (groupfile != "") {
 485                                 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(); }
 486                 if (hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
 487                         }else {
 488                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 489                         }
 490
 491                         //check for optional parameter and set defaults
 492                         // ...at some point should added some additional type checking...
 493                         string temp;
 494                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 495                         m->mothurConvert(temp, kmerSize);
 496
 497                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 498                         m->setProcessors(temp);
 499                         m->mothurConvert(temp, processors);
 500
 501                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 502                         save = m->isTrue(temp);
 503                         rdb->save = save;
 504                         if (save) { //clear out old references
 505                                 rdb->clearMemory();
 506                         }
 507
 508                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 509                         templateFileName = validParameter.validFile(parameters, "reference", true);
 510                         if (templateFileName == "not found") {
 511                                 //check for saved reference sequences
 512                                 if (rdb->referenceSeqs.size() != 0) {
 513                                         templateFileName = "saved";
 514                                 }else {
 515                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
 516                                         m->mothurOutEndLine();
 517                                         abort = true;
 518                                 }
 519                         }else if (templateFileName == "not open") { abort = true; }
 520                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 521
 522                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 523                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 524                         if (taxonomyFileName == "not found") {
 525                                 //check for saved reference sequences
 526                                 if (rdb->wordGenusProb.size() != 0) {
 527                                         taxonomyFileName = "saved";
 528                                 }else {
 529                                         m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
 530                                         m->mothurOutEndLine();
 531                                         abort = true;
 532                                 }
 533                         }else if (taxonomyFileName == "not open") { abort = true; }
 534                         else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
 535
 536                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 537
 538                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
 539
 540                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 541                         m->mothurConvert(temp, match);
 542
 543                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 544                         m->mothurConvert(temp, misMatch);
 545
 546                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 547                         m->mothurConvert(temp, gapOpen);
 548
 549                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 550                         m->mothurConvert(temp, gapExtend);
 551
 552                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 553                         m->mothurConvert(temp, numWanted);
 554
 555                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 556                         m->mothurConvert(temp, cutoff);
 557
 558                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 559                         probs = m->isTrue(temp);
 560
 561                         //temp = validParameter.validFile(parameters, "flip", false);                   if (temp == "not found"){       temp = "T";                             }
 562                         //flip = m->isTrue(temp);
 563                         flip = true;
 564
 565                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 566                         m->mothurConvert(temp, iters);
 567
 568
 569                         if ((method == "bayesian") && (search != "kmer"))  {
 570                                 m->mothurOut("The bayesian method requires the kmer search." + search + "will be disregarded." ); m->mothurOutEndLine();
 571                                 search = "kmer";
 572                         }
 573
 574             if (!abort) {
 575                 if (!hasCount) {
 576                     if (namefileNames.size() == 0){
 577                         if (fastaFileNames.size() != 0) {
 578                             vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
 579                             parser.getNameFile(files);
 580                         }
 581                     }
 582                 }
 583             }
 584         }
 585         }
 586         catch(exception& e) {
 587                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 588                 exit(1);
 589         }
 590 }
 591
 592 //**********************************************************************************************************************
 593 ClassifySeqsCommand::~ClassifySeqsCommand(){
 594         if (abort == false) {
 595                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 596         }
 597 }
 598 //**********************************************************************************************************************
 599
 600 int ClassifySeqsCommand::execute(){
 601         try {
 602                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 603
 604                 if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);             }
 605                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
 606                 else {
 607                         m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
 608                         m->mothurOutEndLine();
 609                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);
 610                 }
 611
 612                 if (m->control_pressed) { delete classify; return 0; }
 613
 614                 for (int s = 0; s < fastaFileNames.size(); s++) {
 615
 616                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 617
 618                         string baseTName = taxonomyFileName;
 619                         if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy();  }
 620
 621             //set rippedTaxName to
 622                         string RippedTaxName = "";
 623             bool foundDot = false;
 624             for (int i = baseTName.length()-1; i >= 0; i--) {
 625                 if (foundDot && (baseTName[i] != '.')) {  RippedTaxName = baseTName[i] + RippedTaxName; }
 626                 else if (foundDot && (baseTName[i] == '.')) {  break; }
 627                 else if (!foundDot && (baseTName[i] == '.')) {  foundDot = true; }
 628             }
 629             if (RippedTaxName != "") { RippedTaxName +=  "."; }
 630
 631                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 632                         string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxonomy");
 633                         string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("accnos");
 634                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 635                         string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + getOutputFileNameTag("taxsummary");
 636
 637                         if ((method == "knn") && (search == "distance")) {
 638                                 string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("matchdist");
 639                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 640                         }
 641
 642                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 643                         outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
 644                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 645
 646                         int start = time(NULL);
 647                         int numFastaSeqs = 0;
 648                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 649
 650 #ifdef USE_MPI
 651                                 int pid, numSeqsPerProcessor;
 652                                 int tag = 2001;
 653                                 vector<unsigned long long> MPIPos;
 654
 655                                 MPI_Status status;
 656                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 657                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 658
 659                                 MPI_File inMPI;
 660                                 MPI_File outMPINewTax;
 661                                 MPI_File outMPITempTax;
 662                                 MPI_File outMPIAcc;
 663
 664                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 665                                 int inMode=MPI_MODE_RDONLY;
 666
 667                                 char outNewTax[1024];
 668                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 669
 670                                 char outTempTax[1024];
 671                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 672
 673                                 char outAcc[1024];
 674                                 strcpy(outAcc, newaccnosFile.c_str());
 675
 676                                 char inFileName[1024];
 677                                 strcpy(inFileName, fastaFileNames[s].c_str());
 678
 679                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 680                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 681                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 682                                 MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
 683
 684                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  delete classify;  return 0;  }
 685
 686                                 if (pid == 0) { //you are the root process
 687
 688                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 689
 690                                         //send file positions to all processes
 691                                         for(int i = 1; i < processors; i++) {
 692                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 693                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 694                                         }
 695
 696                                         //figure out how many sequences you have to align
 697                                         numSeqsPerProcessor = numFastaSeqs / processors;
 698                                         int startIndex =  pid * numSeqsPerProcessor;
 699                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 700
 701
 702                                         //align your part
 703                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 704
 705                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc);   MPI_File_close(&outMPITempTax);  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } delete classify; return 0;  }
 706
 707                                         for (int i = 1; i < processors; i++) {
 708                                                 int done;
 709                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 710                                         }
 711                                 }else{ //you are a child process
 712                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 713                                         MPIPos.resize(numFastaSeqs+1);
 714                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 715
 716                                         //figure out how many sequences you have to align
 717                                         numSeqsPerProcessor = numFastaSeqs / processors;
 718                                         int startIndex =  pid * numSeqsPerProcessor;
 719                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 720
 721
 722                                         //align your part
 723                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 724
 725                                         if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);  MPI_File_close(&outMPIAcc);  MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
 726
 727                                         int done = 0;
 728                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 729                                 }
 730
 731                                 //close files
 732                                 MPI_File_close(&inMPI);
 733                                 MPI_File_close(&outMPINewTax);
 734                                 MPI_File_close(&outMPITempTax);
 735                                 MPI_File_close(&outMPIAcc);
 736                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 737
 738 #else
 739
 740                         vector<unsigned long long> positions;
 741 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 742                         positions = m->divideFile(fastaFileNames[s], processors);
 743                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 744 #else
 745                         if (processors == 1) {
 746                                 lines.push_back(new linePair(0, 1000));
 747                         }else {
 748                                 positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
 749                 if (positions.size() < processors) { processors = positions.size(); }
 750
 751                                 //figure out how many sequences you have to process
 752                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 753                                 for (int i = 0; i < processors; i++) {
 754                                         int startIndex =  i * numSeqsPerProcessor;
 755                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 756                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 757                                 }
 758                         }
 759 #endif
 760                         if(processors == 1){
 761                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 762                         }else{
 763                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 764                         }
 765 #endif
 766
 767                         if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
 768
 769                 m->mothurOutEndLine();
 770                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 771                 start = time(NULL);
 772
 773
 774
 775                 #ifdef USE_MPI
 776                         if (pid == 0) {  //this part does not need to be paralellized
 777
 778                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 779                 #else
 780                         //read namefile
 781                         if(namefile != "") {
 782
 783                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 784                                 nameMap.clear(); //remove old names
 785                                 m->readNames(namefileNames[s], nameMap);
 786                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 787                         }
 788                 #endif
 789
 790                 string group = "";
 791                 GroupMap* groupMap = NULL;
 792                 CountTable* ct = NULL;
 793                 PhyloSummary* taxaSum;
 794                 if (hasCount) {
 795                     ct = new CountTable();
 796                     ct->readTable(countfileNames[s]);
 797                     taxaSum = new PhyloSummary(baseTName, ct);
 798                     taxaSum->summarize(tempTaxonomyFile);
 799                 }else {
 800                     if (groupfile != "") {  group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
 801
 802                     taxaSum = new PhyloSummary(baseTName, groupMap);
 803
 804                     if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; }  if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 805
 806                     if (namefile == "") {  taxaSum->summarize(tempTaxonomyFile);  }
 807                     else {
 808                         ifstream in;
 809                         m->openInputFile(tempTaxonomyFile, in);
 810
 811                         //read in users taxonomy file and add sequences to tree
 812                         string name, taxon;
 813
 814                         while(!in.eof()){
 815                             if (m->control_pressed) { outputTypes.clear();  if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 816
 817                             in >> name >> taxon; m->gobble(in);
 818
 819                             itNames = nameMap.find(name);
 820
 821                             if (itNames == nameMap.end()) {
 822                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 823                             }else{
 824                                 for (int i = 0; i < itNames->second.size(); i++) {
 825                                     taxaSum->addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 826                                 }
 827                                 itNames->second.clear();
 828                                 nameMap.erase(itNames->first);
 829                             }
 830                         }
 831                         in.close();
 832                     }
 833                 }
 834                         m->mothurRemove(tempTaxonomyFile);
 835
 836                         if (m->control_pressed) {  outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
 837
 838                         //print summary file
 839                         ofstream outTaxTree;
 840                         m->openOutputFile(taxSummary, outTaxTree);
 841                         taxaSum->print(outTaxTree);
 842                         outTaxTree.close();
 843
 844                         //output taxonomy with the unclassified bins added
 845                         ifstream inTax;
 846                         m->openInputFile(newTaxonomyFile, inTax);
 847
 848                         ofstream outTax;
 849                         string unclass = newTaxonomyFile + ".unclass.temp";
 850                         m->openOutputFile(unclass, outTax);
 851
 852                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 853                         int maxLevel = taxaSum->getMaxLevel();
 854
 855                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 856                         string name, taxon;
 857                         while (!inTax.eof()) {
 858                                 if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; }  if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } m->mothurRemove(unclass); delete classify; return 0; }
 859
 860                                 inTax >> name >> taxon; m->gobble(inTax);
 861
 862                                 string newTax = addUnclassifieds(taxon, maxLevel);
 863
 864                                 outTax << name << '\t' << newTax << endl;
 865                         }
 866                         inTax.close();
 867                         outTax.close();
 868
 869             if (ct != NULL) { delete ct; }
 870             if (groupMap != NULL) { delete groupMap; } delete taxaSum;
 871                         m->mothurRemove(newTaxonomyFile);
 872                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 873
 874                         m->mothurOutEndLine();
 875                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 876
 877                         #ifdef USE_MPI
 878                                 }
 879                         #endif
 880
 881                         m->mothurOutEndLine();
 882                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 883                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 884                         m->mothurOutEndLine();
 885                 }
 886
 887                 //set taxonomy file as new current taxonomyfile
 888                 string current = "";
 889                 itTypes = outputTypes.find("taxonomy");
 890                 if (itTypes != outputTypes.end()) {
 891                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 892                 }
 893
 894                 current = "";
 895                 itTypes = outputTypes.find("accnos");
 896                 if (itTypes != outputTypes.end()) {
 897                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 898                 }
 899
 900                 delete classify;
 901
 902                 return 0;
 903         }
 904         catch(exception& e) {
 905                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 906                 exit(1);
 907         }
 908 }
 909
 910 /**************************************************************************************************/
 911 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 912         try{
 913                 string newTax, taxon;
 914                 int level = 0;
 915
 916                 //keep what you have counting the levels
 917                 while (tax.find_first_of(';') != -1) {
 918                         //get taxon
 919                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 920                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 921                         newTax += taxon;
 922                         level++;
 923                 }
 924
 925                 //add "unclassified" until you reach maxLevel
 926                 while (level < maxlevel) {
 927                         newTax += "unclassified;";
 928                         level++;
 929                 }
 930
 931                 return newTax;
 932         }
 933         catch(exception& e) {
 934                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 935                 exit(1);
 936         }
 937 }
 938
 939 /**************************************************************************************************/
 940
 941 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
 942         try {
 943
 944                 int num = 0;
 945                 processIDS.clear();
 946
 947 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 948                 int process = 1;
 949
 950                 //loop through and create all the processes you want
 951                 while (process != processors) {
 952                         int pid = fork();
 953
 954                         if (pid > 0) {
 955                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 956                                 process++;
 957                         }else if (pid == 0){
 958                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
 959
 960                                 //pass numSeqs to parent
 961                                 ofstream out;
 962                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 963                                 m->openOutputFile(tempFile, out);
 964                                 out << num << endl;
 965                                 out.close();
 966
 967                                 exit(0);
 968                         }else {
 969                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 970                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 971                                 exit(0);
 972                         }
 973                 }
 974
 975                 //parent does its part
 976                 num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
 977
 978                 //force parent to wait until all the processes are done
 979                 for (int i=0;i<processIDS.size();i++) {
 980                         int temp = processIDS[i];
 981                         wait(&temp);
 982                 }
 983
 984                 for (int i = 0; i < processIDS.size(); i++) {
 985                         ifstream in;
 986                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 987                         m->openInputFile(tempFile, in);
 988                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 989                         in.close(); m->mothurRemove(m->getFullPathName(tempFile));
 990                 }
 991 #else
 992                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 993                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 994                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 995                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 996
 997                 vector<classifyData*> pDataArray;
 998                 DWORD   dwThreadIdArray[processors-1];
 999                 HANDLE  hThreadArray[processors-1];
1000
1001                 //Create processor worker threads.
1002                 for( int i=0; i<processors-1; i++ ){
1003                         // Allocate memory for thread data.
1004                         string extension = "";
1005                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
1006
1007                         classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip);
1008                         pDataArray.push_back(tempclass);
1009
1010                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
1011                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1012                         hThreadArray[i] = CreateThread(NULL, 0, MyClassThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1013
1014                 }
1015
1016                 //parent does its part
1017                 num = driver(lines[processors-1], taxFileName + toString(processors-1) + ".temp", tempTaxFile + toString(processors-1) + ".temp", accnos + toString(processors-1) + ".temp", filename);
1018                 processIDS.push_back((processors-1));
1019
1020                 //Wait until all threads have terminated.
1021                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1022
1023                 //Close all thread handles and free memory allocations.
1024                 for(int i=0; i < pDataArray.size(); i++){
1025                         num += pDataArray[i]->count;
1026                         CloseHandle(hThreadArray[i]);
1027                         delete pDataArray[i];
1028                 }
1029
1030         #endif
1031         vector<string> nonBlankAccnosFiles;
1032                 if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
1033                 else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
1034
1035                 for(int i=0;i<processIDS.size();i++){
1036                         m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
1037                         m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
1038             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
1039                                 nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
1040                         }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
1041
1042                         m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
1043                         m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
1044                 }
1045
1046         //append accnos files
1047                 if (nonBlankAccnosFiles.size() != 0) {
1048                         rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
1049
1050                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
1051                                 m->appendFiles(nonBlankAccnosFiles[h], accnos);
1052                                 m->mothurRemove(nonBlankAccnosFiles[h]);
1053                         }
1054                 }else { //recreate the accnosfile if needed
1055                         ofstream out;
1056                         m->openOutputFile(accnos, out);
1057                         out.close();
1058                 }
1059
1060                 return num;
1061
1062         }
1063         catch(exception& e) {
1064                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
1065                 exit(1);
1066         }
1067 }
1068 //**********************************************************************************************************************
1069
1070 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
1071         try {
1072                 ofstream outTax;
1073                 m->openOutputFile(taxFName, outTax);
1074
1075                 ofstream outTaxSimple;
1076                 m->openOutputFile(tempTFName, outTaxSimple);
1077
1078                 ofstream outAcc;
1079                 m->openOutputFile(accnos, outAcc);
1080
1081                 ifstream inFASTA;
1082                 m->openInputFile(filename, inFASTA);
1083
1084                 string taxonomy;
1085
1086                 inFASTA.seekg(filePos->start);
1087
1088                 bool done = false;
1089                 int count = 0;
1090
1091                 while (!done) {
1092                         if (m->control_pressed) {
1093                                 inFASTA.close();
1094                                 outTax.close();
1095                                 outTaxSimple.close();
1096                                 outAcc.close(); return 0; }
1097
1098                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
1099
1100                         if (candidateSeq->getName() != "") {
1101
1102                                 taxonomy = classify->getTaxonomy(candidateSeq);
1103
1104                                 if (m->control_pressed) { delete candidateSeq; return 0; }
1105
1106                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1107
1108                                 //output confidence scores or not
1109                                 if (probs) {
1110                                         outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
1111                                 }else{
1112                                         outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1113                                 }
1114
1115                                 if (classify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
1116
1117                                 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1118
1119                                 count++;
1120                         }
1121                         delete candidateSeq;
1122
1123                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1124                                 unsigned long long pos = inFASTA.tellg();
1125                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1126                         #else
1127                                 if (inFASTA.eof()) { break; }
1128                         #endif
1129
1130                         //report progress
1131                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1132
1133                 }
1134                 //report progress
1135                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1136
1137                 inFASTA.close();
1138                 outTax.close();
1139                 outTaxSimple.close();
1140                 outAcc.close();
1141
1142                 return count;
1143         }
1144         catch(exception& e) {
1145                 m->errorOut(e, "ClassifySeqsCommand", "driver");
1146                 exit(1);
1147         }
1148 }
1149 //**********************************************************************************************************************
1150 #ifdef USE_MPI
1151 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, MPI_File& accFile, vector<unsigned long long>& MPIPos){
1152         try {
1153                 MPI_Status statusNew;
1154                 MPI_Status statusTemp;
1155                 MPI_Status statusAcc;
1156                 MPI_Status status;
1157
1158                 int pid;
1159                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1160
1161                 string taxonomy;
1162                 string outputString;
1163
1164                 for(int i=0;i<num;i++){
1165
1166                         if (m->control_pressed) { return 0; }
1167
1168                         //read next sequence
1169                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1170                         char* buf4 = new char[length];
1171                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1172
1173                         string tempBuf = buf4;
1174                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1175                         istringstream iss (tempBuf,istringstream::in);
1176                         delete buf4;
1177
1178                         Sequence* candidateSeq = new Sequence(iss);
1179
1180                         if (candidateSeq->getName() != "") {
1181                                 taxonomy = classify->getTaxonomy(candidateSeq);
1182
1183                                 if (taxonomy == "unknown;") { m->mothurOut("[WARNING]: " + candidateSeq->getName() + " could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences."); m->mothurOutEndLine(); }
1184
1185                                 //output confidence scores or not
1186                                 if (probs) {
1187                                         outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
1188                                 }else{
1189                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1190                                 }
1191
1192                                 int length = outputString.length();
1193                                 char* buf2 = new char[length];
1194                                 memcpy(buf2, outputString.c_str(), length);
1195
1196                                 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
1197                                 delete buf2;
1198
1199                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1200                                 length = outputString.length();
1201                                 char* buf = new char[length];
1202                                 memcpy(buf, outputString.c_str(), length);
1203
1204                                 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
1205                                 delete buf;
1206
1207                                 if (classify->getFlipped()) {
1208                                         outputString =  candidateSeq->getName() + "\n";
1209                                         length = outputString.length();
1210                                         char* buf3 = new char[length];
1211                                         memcpy(buf3, outputString.c_str(), length);
1212
1213                                         MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
1214                                         delete buf3;
1215                                 }
1216
1217                         }
1218                         delete candidateSeq;
1219
1220                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
1221                 }
1222
1223                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
1224
1225
1226                 return 1;
1227         }
1228         catch(exception& e) {
1229                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
1230                 exit(1);
1231         }
1232 }
1233
1234 //**********************************************************************************************************************
1235 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
1236         try {
1237
1238                 nameMap.clear(); //remove old names
1239
1240                 MPI_File inMPI;
1241                 MPI_Offset size;
1242                 MPI_Status status;
1243
1244                 //char* inFileName = new char[nameFilename.length()];
1245                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1246
1247                 char inFileName[1024];
1248                 strcpy(inFileName, nameFilename.c_str());
1249
1250                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1251                 MPI_File_get_size(inMPI, &size);
1252                 //delete inFileName;
1253
1254                 char* buffer = new char[size];
1255                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1256
1257                 string tempBuf = buffer;
1258                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1259                 istringstream iss (tempBuf,istringstream::in);
1260                 delete buffer;
1261
1262                 string firstCol, secondCol;
1263                 while(!iss.eof()) {
1264                         iss >> firstCol >> secondCol; m->gobble(iss);
1265
1266                         vector<string> temp;
1267                         m->splitAtComma(secondCol, temp);
1268
1269                         nameMap[firstCol] = temp;
1270                 }
1271
1272                 MPI_File_close(&inMPI);
1273
1274                 return 1;
1275         }
1276         catch(exception& e) {
1277                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1278                 exit(1);
1279         }
1280 }
1281 #endif
1282 /**************************************************************************************************/