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,true); parameters.push_back(ptaxonomy);
  18                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
  20         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
  21         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
  22                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  23
  24                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
  25                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
  26                 CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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 pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
  33                 CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
  34                 CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
  35                 CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
  36         CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
  37         CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
  38                 CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
  39                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  40                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  41
  42                 vector<string> myArray;
  43                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "ClassifySeqsCommand", "setParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string ClassifySeqsCommand::getHelpString(){
  53         try {
  54                 string helpString = "";
  55                 helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
  56                 helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted, relabund and probs.\n";
  57                 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";
  58                 helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer, blast, align and distance. The default is kmer.\n";
  59                 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";
  60                 helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
  61         helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
  62                 helpString += "The method parameter allows you to specify classification method to use.  Your options are: wang, knn and zap. The default is wang.\n";
  63                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n";
  64                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  65 #ifdef USE_MPI
  66                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  67 #endif
  68                 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.";
  69                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  70                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  71                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  72                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  73                 helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
  74                 helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
  75                 helpString += "The probs parameter shuts off the bootstrapping results for the wang and zap method. The default is true, meaning you want the bootstrapping to be shown.\n";
  76         helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";
  77                 helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the wang method.  The default is 100.\n";
  78                 //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
  79                 helpString += "The classify.seqs command should be in the following format: \n";
  80                 helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
  81                 helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
  82                 helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
  83                 helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
  84                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  85                 return helpString;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
  89                 exit(1);
  90         }
  91 }
  92 //**********************************************************************************************************************
  93 string ClassifySeqsCommand::getOutputPattern(string type) {
  94     try {
  95         string pattern = "";
  96
  97         if (type == "taxonomy") {  pattern = "[filename],[tag],[tag2],taxonomy"; }
  98         else if (type == "taxsummary") {  pattern = "[filename],[tag],[tag2],tax.summary"; }
  99         else if (type == "accnos") {  pattern =  "[filename],[tag],[tag2],flip.accnos"; }
 100         else if (type == "matchdist") {  pattern =  "[filename],[tag],[tag2],match.dist"; }
 101         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 102
 103         return pattern;
 104     }
 105     catch(exception& e) {
 106         m->errorOut(e, "ClassifySeqsCommand", "getOutputPattern");
 107         exit(1);
 108     }
 109 }
 110 //**********************************************************************************************************************
 111 ClassifySeqsCommand::ClassifySeqsCommand(){
 112         try {
 113                 abort = true; calledHelp = true;
 114                 setParameters();
 115                 vector<string> tempOutNames;
 116                 outputTypes["taxonomy"] = tempOutNames;
 117                 outputTypes["accnos"] = tempOutNames;
 118                 outputTypes["taxsummary"] = tempOutNames;
 119                 outputTypes["matchdist"] = tempOutNames;
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127 ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 128         try {
 129                 abort = false; calledHelp = false;
 130                 rdb = ReferenceDB::getInstance(); hasName = false; hasCount=false;
 131
 132                 //allow user to run help
 133                 if(option == "help") { help(); abort = true; calledHelp = true; }
 134                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 135
 136                 else {
 137                         vector<string> myArray = setParameters();
 138
 139                         OptionParser parser(option);
 140                         map<string, string> parameters = parser.getParameters();
 141
 142                         ValidParameters validParameter("classify.seqs");
 143                         map<string, string>::iterator it;
 144
 145                         //check to make sure all parameters are valid for command
 146                         for (it = parameters.begin(); it != parameters.end(); it++) {
 147                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 148                         }
 149
 150                         //initialize outputTypes
 151                         vector<string> tempOutNames;
 152                         outputTypes["taxonomy"] = tempOutNames;
 153                         outputTypes["taxsummary"] = tempOutNames;
 154                         outputTypes["matchdist"] = tempOutNames;
 155                         outputTypes["accnos"] = tempOutNames;
 156
 157                         //if the user changes the output directory command factory will send this info to us in the output parameter
 158                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 159
 160                         //if the user changes the input directory command factory will send this info to us in the output parameter
 161                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 162                         if (inputDir == "not found"){   inputDir = "";          }
 163                         else {
 164                                 string path;
 165                                 it = parameters.find("reference");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 171                                 }
 172
 173                                 it = parameters.find("taxonomy");
 174                                 //user has given a template file
 175                                 if(it != parameters.end()){
 176                                         path = m->hasPath(it->second);
 177                                         //if the user has not given a path then, add inputdir. else leave path alone.
 178                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 179                                 }
 180             }
 181
 182                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 183                         if (fastaFileName == "not found") {
 184                                 //if there is a current fasta file, use it
 185                                 string filename = m->getFastaFile();
 186                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 187                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 188                         }
 189                         else {
 190                                 m->splitAtDash(fastaFileName, fastaFileNames);
 191
 192                                 //go through files and make sure they are good, if not, then disregard them
 193                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 194
 195                                         bool ignore = false;
 196                                         if (fastaFileNames[i] == "current") {
 197                                                 fastaFileNames[i] = m->getFastaFile();
 198                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 199                                                 else {
 200                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 201                                                         //erase from file list
 202                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 203                                                         i--;
 204                                                 }
 205                                         }
 206
 207                                         if (!ignore) {
 208
 209                                                 if (inputDir != "") {
 210                                                         string path = m->hasPath(fastaFileNames[i]);
 211                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 213                                                 }
 214
 215                                                 int ableToOpen;
 216
 217                                                 ifstream in;
 218                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 219
 220                                                 //if you can't open it, try default location
 221                                                 if (ableToOpen == 1) {
 222                                                         if (m->getDefaultPath() != "") { //default path is set
 223                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 224                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 225                                                                 ifstream in2;
 226                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 227                                                                 in2.close();
 228                                                                 fastaFileNames[i] = tryPath;
 229                                                         }
 230                                                 }
 231
 232                                                 if (ableToOpen == 1) {
 233                                                         if (m->getOutputDir() != "") { //default path is set
 234                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 235                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 236                                                                 ifstream in2;
 237                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 238                                                                 in2.close();
 239                                                                 fastaFileNames[i] = tryPath;
 240                                                         }
 241                                                 }
 242
 243                                                 in.close();
 244
 245                                                 if (ableToOpen == 1) {
 246                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 247                                                         //erase from file list
 248                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 249                                                         i--;
 250                                                 }else {
 251                                                         m->setFastaFile(fastaFileNames[i]);
 252                                                 }
 253                                         }
 254
 255                                 }
 256
 257                                 //make sure there is at least one valid file left
 258                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 259                         }
 260
 261                         namefile = validParameter.validFile(parameters, "name", false);
 262                         if (namefile == "not found") { namefile = "";  }
 263                         else {
 264                                 m->splitAtDash(namefile, namefileNames);
 265
 266                                 //go through files and make sure they are good, if not, then disregard them
 267                                 for (int i = 0; i < namefileNames.size(); i++) {
 268                                         bool ignore = false;
 269                                         if (namefileNames[i] == "current") {
 270                                                 namefileNames[i] = m->getNameFile();
 271                                                 if (namefileNames[i] != "") {  m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 272                                                 else {
 273                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 274                                                         //erase from file list
 275                                                         namefileNames.erase(namefileNames.begin()+i);
 276                                                         i--;
 277                                                 }
 278                                         }
 279
 280                                         if (!ignore) {
 281
 282                                                 if (inputDir != "") {
 283                                                         string path = m->hasPath(namefileNames[i]);
 284                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 285                                                         if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
 286                                                 }
 287                                                 int ableToOpen;
 288
 289                                                 ifstream in;
 290                                                 ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
 291
 292                                                 //if you can't open it, try default location
 293                                                 if (ableToOpen == 1) {
 294                                                         if (m->getDefaultPath() != "") { //default path is set
 295                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 296                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 297                                                                 ifstream in2;
 298                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 299                                                                 in2.close();
 300                                                                 namefileNames[i] = tryPath;
 301                                                         }
 302                                                 }
 303
 304                                                 if (ableToOpen == 1) {
 305                                                         if (m->getOutputDir() != "") { //default path is set
 306                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 307                                                                 m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 308                                                                 ifstream in2;
 309                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 310                                                                 in2.close();
 311                                                                 namefileNames[i] = tryPath;
 312                                                         }
 313                                                 }
 314                                                 in.close();
 315
 316                                                 if (ableToOpen == 1) {
 317                                                         m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
 318                                                         //erase from file list
 319                                                         namefileNames.erase(namefileNames.begin()+i);
 320                                                         i--;
 321                                                 }else {
 322                                                         m->setNameFile(namefileNames[i]);
 323                                                 }
 324                                         }
 325                                 }
 326                         }
 327
 328             if (namefileNames.size() != 0) { hasName = true; }
 329
 330                         if (namefile != "") {
 331                                 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(); }
 332                         }
 333
 334             //check for required parameters
 335                         countfile = validParameter.validFile(parameters, "count", false);
 336                         if (countfile == "not found") {
 337                 countfile = "";
 338                         }else {
 339                                 m->splitAtDash(countfile, countfileNames);
 340
 341                                 //go through files and make sure they are good, if not, then disregard them
 342                                 for (int i = 0; i < countfileNames.size(); i++) {
 343
 344                                         bool ignore = false;
 345                                         if (countfileNames[i] == "current") {
 346                                                 countfileNames[i] = m->getCountTableFile();
 347                                                 if (countfileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
 348                                                 else {
 349                                                         m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
 350                                                         //erase from file list
 351                                                         countfileNames.erase(countfileNames.begin()+i);
 352                                                         i--;
 353                                                 }
 354                                         }
 355
 356                                         if (!ignore) {
 357
 358                                                 if (inputDir != "") {
 359                                                         string path = m->hasPath(countfileNames[i]);
 360                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 361                                                         if (path == "") {       countfileNames[i] = inputDir + countfileNames[i];               }
 362                                                 }
 363
 364                                                 int ableToOpen;
 365                                                 ifstream in;
 366
 367                                                 ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
 368
 369                                                 //if you can't open it, try default location
 370                                                 if (ableToOpen == 1) {
 371                                                         if (m->getDefaultPath() != "") { //default path is set
 372                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
 373                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 374                                                                 ifstream in2;
 375                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 376                                                                 in2.close();
 377                                                                 countfileNames[i] = tryPath;
 378                                                         }
 379                                                 }
 380
 381                                                 if (ableToOpen == 1) {
 382                                                         if (m->getOutputDir() != "") { //default path is set
 383                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
 384                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 385                                                                 ifstream in2;
 386                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 387                                                                 in2.close();
 388                                                                 countfileNames[i] = tryPath;
 389                                                         }
 390                                                 }
 391
 392                                                 in.close();
 393
 394                                                 if (ableToOpen == 1) {
 395                                                         m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 396                                                         //erase from file list
 397                                                         countfileNames.erase(countfileNames.begin()+i);
 398                                                         i--;
 399                                                 }else {
 400                                                         m->setCountTableFile(countfileNames[i]);
 401                                                 }
 402                                         }
 403                                 }
 404                         }
 405
 406             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(); } }
 407
 408                         //make sure there is at least one valid file left
 409             if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 410
 411                         groupfile = validParameter.validFile(parameters, "group", false);
 412                         if (groupfile == "not found") { groupfile = "";  }
 413                         else {
 414                                 m->splitAtDash(groupfile, groupfileNames);
 415
 416                                 //go through files and make sure they are good, if not, then disregard them
 417                                 for (int i = 0; i < groupfileNames.size(); i++) {
 418
 419                                         bool ignore = false;
 420                                         if (groupfileNames[i] == "current") {
 421                                                 groupfileNames[i] = m->getGroupFile();
 422                                                 if (groupfileNames[i] != "") {  m->mothurOut("Using " + groupfileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
 423                                                 else {
 424                                                         m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
 425                                                         //erase from file list
 426                                                         groupfileNames.erase(groupfileNames.begin()+i);
 427                                                         i--;
 428                                                 }
 429                                         }
 430
 431                                         if (!ignore) {
 432
 433                                                 if (inputDir != "") {
 434                                                         string path = m->hasPath(groupfileNames[i]);
 435                             cout << path << '\t' << inputDir << endl;
 436                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 437                                                         if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
 438                                                 }
 439
 440                                                 int ableToOpen;
 441
 442                                                 ifstream in;
 443                                                 ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
 444
 445                                                 //if you can't open it, try default location
 446                                                 if (ableToOpen == 1) {
 447                                                         if (m->getDefaultPath() != "") { //default path is set
 448                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 449                                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 450                                                                 ifstream in2;
 451                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 452                                                                 in2.close();
 453                                                                 groupfileNames[i] = tryPath;
 454                                                         }
 455                                                 }
 456
 457                                                 if (ableToOpen == 1) {
 458                                                         if (m->getOutputDir() != "") { //default path is set
 459                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 460                                                                 m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 461                                                                 ifstream in2;
 462                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 463                                                                 in2.close();
 464                                                                 groupfileNames[i] = tryPath;
 465                                                         }
 466                                                 }
 467
 468                                                 in.close();
 469
 470                                                 if (ableToOpen == 1) {
 471                                                         m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 472                                                         //erase from file list
 473                                                         groupfileNames.erase(groupfileNames.begin()+i);
 474                                                         i--;
 475                                                 }else {
 476                                                         m->setGroupFile(groupfileNames[i]);
 477                                                 }
 478                                         }
 479
 480                                 }
 481                         }
 482
 483                         if (groupfile != "") {
 484                                 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(); }
 485                 if (hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
 486                         }else {
 487                                 for (int i = 0; i < fastaFileNames.size(); i++) {  groupfileNames.push_back("");  }
 488                         }
 489
 490                         //check for optional parameter and set defaults
 491                         // ...at some point should added some additional type checking...
 492                         string temp;
 493                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 494                         m->setProcessors(temp);
 495                         m->mothurConvert(temp, processors);
 496
 497                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 498                         save = m->isTrue(temp);
 499                         rdb->save = save;
 500                         if (save) { //clear out old references
 501                                 rdb->clearMemory();
 502                         }
 503
 504                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 505                         templateFileName = validParameter.validFile(parameters, "reference", true);
 506                         if (templateFileName == "not found") {
 507                                 //check for saved reference sequences
 508                                 if (rdb->referenceSeqs.size() != 0) {
 509                                         templateFileName = "saved";
 510                                 }else {
 511                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
 512                                         m->mothurOutEndLine();
 513                                         abort = true;
 514                                 }
 515                         }else if (templateFileName == "not open") { abort = true; }
 516                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 517
 518                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 519                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 520                         if (taxonomyFileName == "not found") {
 521                                 //check for saved reference sequences
 522                                 if (rdb->wordGenusProb.size() != 0) {
 523                                         taxonomyFileName = "saved";
 524                                 }else {
 525                                         m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
 526                                         m->mothurOutEndLine();
 527                                         abort = true;
 528                                 }
 529                         }else if (taxonomyFileName == "not open") { abort = true; }
 530                         else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
 531
 532                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 533
 534                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "wang";        }
 535
 536             temp = validParameter.validFile(parameters, "ksize", false);                if (temp == "not found"){
 537                 temp = "8";
 538                 if (method == "zap") { temp = "7"; }
 539             }
 540                         m->mothurConvert(temp, kmerSize);
 541
 542                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 543                         m->mothurConvert(temp, match);
 544
 545                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 546                         m->mothurConvert(temp, misMatch);
 547
 548                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 549                         m->mothurConvert(temp, gapOpen);
 550
 551                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 552                         m->mothurConvert(temp, gapExtend);
 553
 554                         temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
 555                         m->mothurConvert(temp, numWanted);
 556
 557                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
 558                         m->mothurConvert(temp, cutoff);
 559
 560                         temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
 561                         probs = m->isTrue(temp);
 562
 563             temp = validParameter.validFile(parameters, "relabund", false);             if (temp == "not found"){       temp = "false";                 }
 564                         relabund = m->isTrue(temp);
 565
 566             temp = validParameter.validFile(parameters, "shortcuts", false);    if (temp == "not found"){       temp = "true";                  }
 567                         writeShortcuts = m->isTrue(temp);
 568
 569                         //temp = validParameter.validFile(parameters, "flip", false);                   if (temp == "not found"){       temp = "T";                             }
 570                         //flip = m->isTrue(temp);
 571                         flip = true;
 572
 573                         temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
 574                         m->mothurConvert(temp, iters);
 575
 576
 577                         if ((method == "wang") && (search != "kmer"))  {
 578                                 m->mothurOut("The wang method requires the kmer search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
 579                                 search = "kmer";
 580                         }
 581
 582             if ((method == "zap") && ((search != "kmer") && (search != "align")))  {
 583                                 m->mothurOut("The zap method requires the kmer or align search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
 584                                 search = "kmer";
 585                         }
 586
 587             if (!abort) {
 588                 if (!hasCount) {
 589                     if (namefileNames.size() == 0){
 590                         if (fastaFileNames.size() != 0) {
 591                             vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
 592                             parser.getNameFile(files);
 593                         }
 594                     }
 595                 }
 596             }
 597         }
 598         }
 599         catch(exception& e) {
 600                 m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
 601                 exit(1);
 602         }
 603 }
 604
 605 //**********************************************************************************************************************
 606 ClassifySeqsCommand::~ClassifySeqsCommand(){
 607         if (abort == false) {
 608                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 609         }
 610 }
 611 //**********************************************************************************************************************
 612
 613 int ClassifySeqsCommand::execute(){
 614         try {
 615                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 616
 617         string outputMethodTag = method;
 618                 if(method == "wang"){   classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);     }
 619                 else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
 620         else if(method == "zap"){
 621             outputMethodTag = search + "_" + outputMethodTag;
 622             if (search == "kmer") {   classify = new KmerTree(templateFileName, taxonomyFileName, kmerSize, cutoff); }
 623             else {  classify = new AlignTree(templateFileName, taxonomyFileName, cutoff);  }
 624         }
 625                 else {
 626                         m->mothurOut(search + " is not a valid method option. I will run the command using wang.");
 627                         m->mothurOutEndLine();
 628                         classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);
 629                 }
 630
 631                 if (m->control_pressed) { delete classify; return 0; }
 632
 633                 for (int s = 0; s < fastaFileNames.size(); s++) {
 634
 635                         m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 636
 637                         string baseTName = m->getSimpleName(taxonomyFileName);
 638                         if (taxonomyFileName == "saved") {  baseTName = rdb->getSavedTaxonomy();        }
 639
 640             //set rippedTaxName to
 641                         string RippedTaxName = "";
 642             bool foundDot = false;
 643             for (int i = baseTName.length()-1; i >= 0; i--) {
 644                 if (foundDot && (baseTName[i] != '.')) {  RippedTaxName = baseTName[i] + RippedTaxName; }
 645                 else if (foundDot && (baseTName[i] == '.')) {  break; }
 646                 else if (!foundDot && (baseTName[i] == '.')) {  foundDot = true; }
 647             }
 648             //if (RippedTaxName != "") { RippedTaxName +=  "."; }
 649
 650                         if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 651             map<string, string> variables;
 652             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
 653             variables["[tag]"] = RippedTaxName;
 654             variables["[tag2]"] = outputMethodTag;
 655                         string newTaxonomyFile = getOutputFileName("taxonomy", variables);
 656                         string newaccnosFile = getOutputFileName("accnos", variables);
 657                         string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
 658                         string taxSummary = getOutputFileName("taxsummary", variables);
 659
 660                         if ((method == "knn") && (search == "distance")) {
 661                                 string DistName = getOutputFileName("matchdist", variables);
 662                                 classify->setDistName(DistName);  outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
 663                         }
 664
 665                         outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
 666                         outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
 667
 668                         int start = time(NULL);
 669                         int numFastaSeqs = 0;
 670                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 671
 672 #ifdef USE_MPI
 673                                 int pid, numSeqsPerProcessor;
 674                                 int tag = 2001;
 675                                 vector<unsigned long long> MPIPos;
 676
 677                                 MPI_Status status;
 678                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 679                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 680
 681                                 MPI_File inMPI;
 682                                 MPI_File outMPINewTax;
 683                                 MPI_File outMPITempTax;
 684                                 MPI_File outMPIAcc;
 685
 686                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 687                                 int inMode=MPI_MODE_RDONLY;
 688
 689                                 char outNewTax[1024];
 690                                 strcpy(outNewTax, newTaxonomyFile.c_str());
 691
 692                                 char outTempTax[1024];
 693                                 strcpy(outTempTax, tempTaxonomyFile.c_str());
 694
 695                                 char outAcc[1024];
 696                                 strcpy(outAcc, newaccnosFile.c_str());
 697
 698                                 char inFileName[1024];
 699                                 strcpy(inFileName, fastaFileNames[s].c_str());
 700
 701                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 702                                 MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
 703                                 MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
 704                                 MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
 705
 706                                 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;  }
 707
 708                                 if (pid == 0) { //you are the root process
 709
 710                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 711
 712                                         //send file positions to all processes
 713                                         for(int i = 1; i < processors; i++) {
 714                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 715                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 716                                         }
 717
 718                                         //figure out how many sequences you have to align
 719                                         numSeqsPerProcessor = numFastaSeqs / processors;
 720                                         int startIndex =  pid * numSeqsPerProcessor;
 721                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 722
 723
 724                                         //align your part
 725                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 726
 727                                         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;  }
 728
 729                                         for (int i = 1; i < processors; i++) {
 730                                                 int done;
 731                                                 MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 732                                         }
 733                                 }else{ //you are a child process
 734                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 735                                         MPIPos.resize(numFastaSeqs+1);
 736                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 737
 738                                         //figure out how many sequences you have to align
 739                                         numSeqsPerProcessor = numFastaSeqs / processors;
 740                                         int startIndex =  pid * numSeqsPerProcessor;
 741                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 742
 743
 744                                         //align your part
 745                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
 746
 747                                         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;  }
 748
 749                                         int done = 0;
 750                                         MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 751                                 }
 752
 753                                 //close files
 754                                 MPI_File_close(&inMPI);
 755                                 MPI_File_close(&outMPINewTax);
 756                                 MPI_File_close(&outMPITempTax);
 757                                 MPI_File_close(&outMPIAcc);
 758                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 759
 760 #else
 761
 762                         vector<unsigned long long> positions;
 763 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 764                         positions = m->divideFile(fastaFileNames[s], processors);
 765                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 766 #else
 767                         if (processors == 1) {
 768                                 lines.push_back(new linePair(0, 1000));
 769                         }else {
 770                                 positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
 771                 if (positions.size() < processors) { processors = positions.size(); }
 772
 773                                 //figure out how many sequences you have to process
 774                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 775                                 for (int i = 0; i < processors; i++) {
 776                                         int startIndex =  i * numSeqsPerProcessor;
 777                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 778                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 779                                 }
 780                         }
 781 #endif
 782                         if(processors == 1){
 783                                 numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 784                         }else{
 785                                 numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
 786                         }
 787 #endif
 788
 789                         if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification.  If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
 790                 outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
 791             }else { m->mothurRemove(newaccnosFile); }
 792
 793                 m->mothurOutEndLine();
 794                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 795                 start = time(NULL);
 796
 797
 798
 799                 #ifdef USE_MPI
 800                         if (pid == 0) {  //this part does not need to be paralellized
 801
 802                                 if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
 803                 #else
 804                         //read namefile
 805                         if(namefile != "") {
 806
 807                             m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
 808                                 nameMap.clear(); //remove old names
 809                                 m->readNames(namefileNames[s], nameMap);
 810                                 m->mothurOut("  Done."); m->mothurOutEndLine();
 811                         }
 812                 #endif
 813
 814                 string group = "";
 815                 GroupMap* groupMap = NULL;
 816                 CountTable* ct = NULL;
 817                 PhyloSummary* taxaSum;
 818                 if (hasCount) {
 819                     ct = new CountTable();
 820                     ct->readTable(countfileNames[s], true, false);
 821                     taxaSum = new PhyloSummary(taxonomyFileName, ct, relabund);
 822                     taxaSum->summarize(tempTaxonomyFile);
 823                 }else {
 824                     if (groupfile != "") {  group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
 825
 826                     taxaSum = new PhyloSummary(taxonomyFileName, groupMap, relabund);
 827
 828                     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; }
 829
 830                     if (namefile == "") {  taxaSum->summarize(tempTaxonomyFile);  }
 831                     else {
 832                         ifstream in;
 833                         m->openInputFile(tempTaxonomyFile, in);
 834
 835                         //read in users taxonomy file and add sequences to tree
 836                         string name, taxon;
 837
 838                         while(!in.eof()){
 839                             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; }
 840
 841                             in >> name >> taxon; m->gobble(in);
 842
 843                             itNames = nameMap.find(name);
 844
 845                             if (itNames == nameMap.end()) {
 846                                 m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
 847                             }else{
 848                                 for (int i = 0; i < itNames->second.size(); i++) {
 849                                     taxaSum->addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
 850                                 }
 851                                 itNames->second.clear();
 852                                 nameMap.erase(itNames->first);
 853                             }
 854                         }
 855                         in.close();
 856                     }
 857                 }
 858                         m->mothurRemove(tempTaxonomyFile);
 859
 860                         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; }
 861
 862                         //print summary file
 863                         ofstream outTaxTree;
 864                         m->openOutputFile(taxSummary, outTaxTree);
 865                         taxaSum->print(outTaxTree);
 866                         outTaxTree.close();
 867
 868                         //output taxonomy with the unclassified bins added
 869                         ifstream inTax;
 870                         m->openInputFile(newTaxonomyFile, inTax);
 871
 872                         ofstream outTax;
 873                         string unclass = newTaxonomyFile + ".unclass.temp";
 874                         m->openOutputFile(unclass, outTax);
 875
 876                         //get maxLevel from phylotree so you know how many 'unclassified's to add
 877                         int maxLevel = taxaSum->getMaxLevel();
 878
 879                         //read taxfile - this reading and rewriting is done to preserve the confidence scores.
 880                         string name, taxon;
 881                         while (!inTax.eof()) {
 882                                 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; }
 883
 884                                 inTax >> name >> taxon; m->gobble(inTax);
 885
 886                                 string newTax = addUnclassifieds(taxon, maxLevel);
 887
 888                                 outTax << name << '\t' << newTax << endl;
 889                         }
 890                         inTax.close();
 891                         outTax.close();
 892
 893             if (ct != NULL) { delete ct; }
 894             if (groupMap != NULL) { delete groupMap; } delete taxaSum;
 895                         m->mothurRemove(newTaxonomyFile);
 896                         rename(unclass.c_str(), newTaxonomyFile.c_str());
 897
 898                         m->mothurOutEndLine();
 899                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 900
 901                         #ifdef USE_MPI
 902                                 }
 903                         #endif
 904                 }
 905         delete classify;
 906
 907         m->mothurOutEndLine();
 908         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 909         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 910         m->mothurOutEndLine();
 911
 912                 //set taxonomy file as new current taxonomyfile
 913                 string current = "";
 914                 itTypes = outputTypes.find("taxonomy");
 915                 if (itTypes != outputTypes.end()) {
 916                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 917                 }
 918
 919                 current = "";
 920                 itTypes = outputTypes.find("accnos");
 921                 if (itTypes != outputTypes.end()) {
 922                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 923                 }
 924
 925
 926
 927                 return 0;
 928         }
 929         catch(exception& e) {
 930                 m->errorOut(e, "ClassifySeqsCommand", "execute");
 931                 exit(1);
 932         }
 933 }
 934
 935 /**************************************************************************************************/
 936 string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 937         try{
 938                 string newTax, taxon;
 939                 int level = 0;
 940
 941                 //keep what you have counting the levels
 942                 while (tax.find_first_of(';') != -1) {
 943                         //get taxon
 944                         taxon = tax.substr(0,tax.find_first_of(';'))+';';
 945                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
 946                         newTax += taxon;
 947                         level++;
 948                 }
 949
 950                 //add "unclassified" until you reach maxLevel
 951                 while (level < maxlevel) {
 952                         newTax += "unclassified;";
 953                         level++;
 954                 }
 955
 956                 return newTax;
 957         }
 958         catch(exception& e) {
 959                 m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
 960                 exit(1);
 961         }
 962 }
 963
 964 /**************************************************************************************************/
 965
 966 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
 967         try {
 968
 969                 int num = 0;
 970                 processIDS.clear();
 971
 972 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 973                 int process = 1;
 974
 975                 //loop through and create all the processes you want
 976                 while (process != processors) {
 977                         int pid = fork();
 978
 979                         if (pid > 0) {
 980                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 981                                 process++;
 982                         }else if (pid == 0){
 983                                 num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
 984
 985                                 //pass numSeqs to parent
 986                                 ofstream out;
 987                                 string tempFile = filename + toString(getpid()) + ".num.temp";
 988                                 m->openOutputFile(tempFile, out);
 989                                 out << num << endl;
 990                                 out.close();
 991
 992                                 exit(0);
 993                         }else {
 994                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 995                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 996                                 exit(0);
 997                         }
 998                 }
 999
1000                 //parent does its part
1001                 num = driver(lines[0], taxFileName, tempTaxFile, accnos, filename);
1002
1003                 //force parent to wait until all the processes are done
1004                 for (int i=0;i<processIDS.size();i++) {
1005                         int temp = processIDS[i];
1006                         wait(&temp);
1007                 }
1008
1009                 for (int i = 0; i < processIDS.size(); i++) {
1010                         ifstream in;
1011                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1012                         m->openInputFile(tempFile, in);
1013                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1014                         in.close(); m->mothurRemove(m->getFullPathName(tempFile));
1015                 }
1016 #else
1017                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1018                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
1019                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1020                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1021
1022                 vector<classifyData*> pDataArray;
1023                 DWORD   dwThreadIdArray[processors-1];
1024                 HANDLE  hThreadArray[processors-1];
1025
1026                 //Create processor worker threads.
1027                 for( int i=0; i<processors-1; i++ ){
1028                         // Allocate memory for thread data.
1029                         string extension = "";
1030                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
1031
1032                         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, writeShortcuts);
1033                         pDataArray.push_back(tempclass);
1034
1035                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
1036                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1037                         hThreadArray[i] = CreateThread(NULL, 0, MyClassThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1038
1039                 }
1040
1041                 //parent does its part
1042                 num = driver(lines[processors-1], taxFileName + toString(processors-1) + ".temp", tempTaxFile + toString(processors-1) + ".temp", accnos + toString(processors-1) + ".temp", filename);
1043                 processIDS.push_back((processors-1));
1044
1045                 //Wait until all threads have terminated.
1046                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1047
1048                 //Close all thread handles and free memory allocations.
1049                 for(int i=0; i < pDataArray.size(); i++){
1050                         num += pDataArray[i]->count;
1051             if (pDataArray[i]->count != pDataArray[i]->end) {
1052                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
1053             }
1054                         CloseHandle(hThreadArray[i]);
1055                         delete pDataArray[i];
1056                 }
1057
1058         #endif
1059         vector<string> nonBlankAccnosFiles;
1060                 if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
1061                 else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
1062
1063                 for(int i=0;i<processIDS.size();i++){
1064                         m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
1065                         m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
1066             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
1067                                 nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
1068                         }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
1069
1070                         m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
1071                         m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
1072                 }
1073
1074         //append accnos files
1075                 if (nonBlankAccnosFiles.size() != 0) {
1076                         rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
1077
1078                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
1079                                 m->appendFiles(nonBlankAccnosFiles[h], accnos);
1080                                 m->mothurRemove(nonBlankAccnosFiles[h]);
1081                         }
1082                 }else { //recreate the accnosfile if needed
1083                         ofstream out;
1084                         m->openOutputFile(accnos, out);
1085                         out.close();
1086                 }
1087
1088                 return num;
1089
1090         }
1091         catch(exception& e) {
1092                 m->errorOut(e, "ClassifySeqsCommand", "createProcesses");
1093                 exit(1);
1094         }
1095 }
1096 //**********************************************************************************************************************
1097
1098 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){
1099         try {
1100                 ofstream outTax;
1101                 m->openOutputFile(taxFName, outTax);
1102
1103                 ofstream outTaxSimple;
1104                 m->openOutputFile(tempTFName, outTaxSimple);
1105
1106                 ofstream outAcc;
1107                 m->openOutputFile(accnos, outAcc);
1108
1109                 ifstream inFASTA;
1110                 m->openInputFile(filename, inFASTA);
1111
1112                 string taxonomy;
1113
1114                 inFASTA.seekg(filePos->start);
1115
1116                 bool done = false;
1117                 int count = 0;
1118
1119                 while (!done) {
1120                         if (m->control_pressed) {
1121                                 inFASTA.close();
1122                                 outTax.close();
1123                                 outTaxSimple.close();
1124                                 outAcc.close(); return 0; }
1125
1126                         Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
1127
1128                         if (candidateSeq->getName() != "") {
1129
1130                                 taxonomy = classify->getTaxonomy(candidateSeq);
1131
1132                                 if (m->control_pressed) { delete candidateSeq; return 0; }
1133
1134                                 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(); }
1135
1136                                 //output confidence scores or not
1137                                 if (probs) {
1138                                         outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
1139                                 }else{
1140                                         outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1141                                 }
1142
1143                                 if (classify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
1144
1145                                 outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
1146
1147                                 count++;
1148                         }
1149                         delete candidateSeq;
1150
1151                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1152                                 unsigned long long pos = inFASTA.tellg();
1153                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1154                         #else
1155                                 if (inFASTA.eof()) { break; }
1156                         #endif
1157
1158                         //report progress
1159                         if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n");              }
1160
1161                 }
1162                 //report progress
1163                 if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
1164
1165                 inFASTA.close();
1166                 outTax.close();
1167                 outTaxSimple.close();
1168                 outAcc.close();
1169
1170                 return count;
1171         }
1172         catch(exception& e) {
1173                 m->errorOut(e, "ClassifySeqsCommand", "driver");
1174                 exit(1);
1175         }
1176 }
1177 //**********************************************************************************************************************
1178 #ifdef USE_MPI
1179 int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, MPI_File& accFile, vector<unsigned long long>& MPIPos){
1180         try {
1181                 MPI_Status statusNew;
1182                 MPI_Status statusTemp;
1183                 MPI_Status statusAcc;
1184                 MPI_Status status;
1185
1186                 int pid;
1187                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1188
1189                 string taxonomy;
1190                 string outputString;
1191
1192                 for(int i=0;i<num;i++){
1193
1194                         if (m->control_pressed) { return 0; }
1195
1196                         //read next sequence
1197                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1198                         char* buf4 = new char[length];
1199                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1200
1201                         string tempBuf = buf4;
1202                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1203                         istringstream iss (tempBuf,istringstream::in);
1204                         delete buf4;
1205
1206                         Sequence* candidateSeq = new Sequence(iss);
1207
1208                         if (candidateSeq->getName() != "") {
1209                                 taxonomy = classify->getTaxonomy(candidateSeq);
1210
1211                                 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(); }
1212
1213                                 //output confidence scores or not
1214                                 if (probs) {
1215                                         outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
1216                                 }else{
1217                                         outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1218                                 }
1219
1220                                 int length = outputString.length();
1221                                 char* buf2 = new char[length];
1222                                 memcpy(buf2, outputString.c_str(), length);
1223
1224                                 MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew);
1225                                 delete buf2;
1226
1227                                 outputString =  candidateSeq->getName() + "\t" + classify->getSimpleTax() + "\n";
1228                                 length = outputString.length();
1229                                 char* buf = new char[length];
1230                                 memcpy(buf, outputString.c_str(), length);
1231
1232                                 MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
1233                                 delete buf;
1234
1235                                 if (classify->getFlipped()) {
1236                                         outputString =  candidateSeq->getName() + "\n";
1237                                         length = outputString.length();
1238                                         char* buf3 = new char[length];
1239                                         memcpy(buf3, outputString.c_str(), length);
1240
1241                                         MPI_File_write_shared(accFile, buf3, length, MPI_CHAR, &statusAcc);
1242                                         delete buf3;
1243                                 }
1244
1245                         }
1246                         delete candidateSeq;
1247
1248                         if((i+1) % 100 == 0){   cout << "Classifying sequence " << (i+1) << endl;       }
1249                 }
1250
1251                 if(num % 100 != 0){     cout << "Classifying sequence " << (num) << endl;       }
1252
1253
1254                 return 1;
1255         }
1256         catch(exception& e) {
1257                 m->errorOut(e, "ClassifySeqsCommand", "driverMPI");
1258                 exit(1);
1259         }
1260 }
1261
1262 //**********************************************************************************************************************
1263 int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
1264         try {
1265
1266                 nameMap.clear(); //remove old names
1267
1268                 MPI_File inMPI;
1269                 MPI_Offset size;
1270                 MPI_Status status;
1271
1272                 //char* inFileName = new char[nameFilename.length()];
1273                 //memcpy(inFileName, nameFilename.c_str(), nameFilename.length());
1274
1275                 char inFileName[1024];
1276                 strcpy(inFileName, nameFilename.c_str());
1277
1278                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
1279                 MPI_File_get_size(inMPI, &size);
1280                 //delete inFileName;
1281
1282                 char* buffer = new char[size];
1283                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
1284
1285                 string tempBuf = buffer;
1286                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
1287                 istringstream iss (tempBuf,istringstream::in);
1288                 delete buffer;
1289
1290                 string firstCol, secondCol;
1291                 while(!iss.eof()) {
1292                         iss >> firstCol >> secondCol; m->gobble(iss);
1293
1294                         vector<string> temp;
1295                         m->splitAtComma(secondCol, temp);
1296
1297                         nameMap[firstCol] = temp;
1298                 }
1299
1300                 MPI_File_close(&inMPI);
1301
1302                 return 1;
1303         }
1304         catch(exception& e) {
1305                 m->errorOut(e, "ClassifySeqsCommand", "MPIReadNamesFile");
1306                 exit(1);
1307         }
1308 }
1309 #endif
1310 /**************************************************************************************************/