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