distancecommand.cpp

   1 /*
   2  *  distancecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/7/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "distancecommand.h"
  11 #include "ignoregaps.h"
  12 #include "eachgapdist.h"
  13 #include "eachgapignore.h"
  14 #include "onegapdist.h"
  15 #include "onegapignore.h"
  16
  17 //**********************************************************************************************************************
  18
  19 DistanceCommand::DistanceCommand(string option) {
  20         try {
  21                 abort = false;
  22                 Estimators.clear();
  23
  24                 //allow user to run help
  25                 if(option == "help") { help(); abort = true; }
  26
  27                 else {
  28                         //valid paramters for this command
  29                         string Array[] =  {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
  30
  31                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  32
  33                         OptionParser parser(option);
  34                         map<string, string> parameters = parser.getParameters();
  35
  36                         ValidParameters validParameter("dist.seqs");
  37                         map<string, string>::iterator it2;
  38
  39                         //check to make sure all parameters are valid for command
  40                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  41                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  42                         }
  43
  44                         //if the user changes the input directory command factory will send this info to us in the output parameter
  45                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  46                         if (inputDir == "not found"){   inputDir = "";          }
  47                         else {
  48                                 string path;
  49                                 it2 = parameters.find("fasta");
  50                                 //user has given a template file
  51                                 if(it2 != parameters.end()){
  52                                         path = m->hasPath(it2->second);
  53                                         //if the user has not given a path then, add inputdir. else leave path alone.
  54                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
  55                                 }
  56
  57                                 it2 = parameters.find("oldfasta");
  58                                 //user has given a template file
  59                                 if(it2 != parameters.end()){
  60                                         path = m->hasPath(it2->second);
  61                                         //if the user has not given a path then, add inputdir. else leave path alone.
  62                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
  63                                 }
  64
  65                                 it2 = parameters.find("column");
  66                                 //user has given a template file
  67                                 if(it2 != parameters.end()){
  68                                         path = m->hasPath(it2->second);
  69                                         //if the user has not given a path then, add inputdir. else leave path alone.
  70                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
  71                                 }
  72                         }
  73
  74                         //check for required parameters
  75                         fastafile = validParameter.validFile(parameters, "fasta", true);
  76                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->mothurOutEndLine(); abort = true; }
  77                         else if (fastafile == "not open") { abort = true; }
  78                         else{
  79                                 ifstream inFASTA;
  80                                 m->openInputFile(fastafile, inFASTA);
  81                                 alignDB = SequenceDB(inFASTA);
  82                                 inFASTA.close();
  83                         }
  84
  85                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
  86                         if (oldfastafile == "not found") { oldfastafile = ""; }
  87                         else if (oldfastafile == "not open") { abort = true; }
  88
  89                         column = validParameter.validFile(parameters, "column", true);
  90                         if (column == "not found") { column = ""; }
  91                         else if (column == "not open") { abort = true; }
  92
  93                         //if the user changes the output directory command factory will send this info to us in the output parameter
  94                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  95                                 outputDir = "";
  96                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
  97                         }
  98
  99                         //check for optional parameter and set defaults
 100                         // ...at some point should added some additional type checking...
 101                         calc = validParameter.validFile(parameters, "calc", false);
 102                         if (calc == "not found") { calc = "onegap";  }
 103                         else {
 104                                  if (calc == "default")  {  calc = "onegap";  }
 105                         }
 106                         m->splitAtDash(calc, Estimators);
 107
 108                         string temp;
 109                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 110                         convert(temp, countends);
 111
 112                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 113                         convert(temp, cutoff);
 114
 115                         temp = validParameter.validFile(parameters, "processors", false);       if(temp == "not found"){        temp = "1"; }
 116                         convert(temp, processors);
 117
 118                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 119                         convert(temp, compress);
 120
 121                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 122
 123                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 124
 125                         if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
 126
 127                         if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
 128
 129                         ValidCalculators validCalculator;
 130
 131                         if (m->isTrue(countends) == true) {
 132                                 for (int i=0; i<Estimators.size(); i++) {
 133                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 134                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 135                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 136                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 137                                         }
 138                                 }
 139                         }else {
 140                                 for (int i=0; i<Estimators.size(); i++) {
 141                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 142                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 143                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 144                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 145                                         }
 146                                 }
 147                         }
 148
 149                 }
 150
 151         }
 152         catch(exception& e) {
 153                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 154                 exit(1);
 155         }
 156 }
 157
 158 //**********************************************************************************************************************
 159
 160 DistanceCommand::~DistanceCommand(){
 161
 162         for(int i=0;i<lines.size();i++){
 163                 delete lines[i];
 164         }
 165
 166 }
 167
 168 //**********************************************************************************************************************
 169
 170 void DistanceCommand::help(){
 171         try {
 172                 m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
 173                 m->mothurOut("The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors.  \n");
 174                 m->mothurOut("The fasta parameter is required.\n");
 175                 m->mothurOut("The oldfasta and column parameters allow you to append the distances calculated to the column file.\n");
 176                 m->mothurOut("The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
 177                 m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n");
 178                 m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
 179                 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
 180                 m->mothurOut("The processors parameter allows you to specify number of processors to use.  The default is 1.\n");
 181                 m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n");
 182                 m->mothurOut("The dist.seqs command should be in the following format: \n");
 183                 m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
 184                 m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
 185                 m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "DistanceCommand", "help");
 189                 exit(1);
 190         }
 191 }
 192 //**********************************************************************************************************************
 193
 194 int DistanceCommand::execute(){
 195         try {
 196
 197                 if (abort == true) { return 0; }
 198
 199                 int startTime = time(NULL);
 200
 201                 //save number of new sequence
 202                 numNewFasta = alignDB.getNumSeqs();
 203
 204                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 205                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 206
 207                 if (m->control_pressed) { return 0; }
 208
 209                 int numSeqs = alignDB.getNumSeqs();
 210                 cutoff += 0.005;
 211
 212                 string outputFile;
 213
 214                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 215                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
 216                         remove(outputFile.c_str());
 217
 218                         //output numSeqs to phylip formatted dist file
 219                 }else if (output == "column") { //user wants column format
 220                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
 221
 222                         //so we don't accidentally overwrite
 223                         if (outputFile == column) {
 224                                 string tempcolumn = column + ".old";
 225                                 rename(column.c_str(), tempcolumn.c_str());
 226                         }
 227
 228                         remove(outputFile.c_str());
 229                 }else { //assume square
 230                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
 231                         remove(outputFile.c_str());
 232                 }
 233
 234
 235 #ifdef USE_MPI
 236
 237                 int pid, start, end;
 238                 int tag = 2001;
 239
 240                 MPI_Status status;
 241                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 242                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 243
 244                 //each process gets where it should start and stop in the file
 245                 if (output != "square") {
 246                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 247                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 248                 }else{
 249                         start = int ((float(pid)/float(processors)) * numSeqs);
 250                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 251                 }
 252
 253                 if (output == "column") {
 254                         MPI_File outMPI;
 255                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 256
 257                         //char* filename = new char[outputFile.length()];
 258                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 259
 260                         char filename[1024];
 261                         strcpy(filename, outputFile.c_str());
 262
 263                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 264                         //delete filename;
 265
 266                         if (pid == 0) { //you are the root process
 267
 268                                 //do your part
 269                                 string outputMyPart;
 270
 271                                 driverMPI(start, end, outMPI, cutoff);
 272
 273                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 274
 275                                 //wait on chidren
 276                                 for(int i = 1; i < processors; i++) {
 277                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 278
 279                                         char buf[5];
 280                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 281                                 }
 282                         }else { //you are a child process
 283                                 //do your part
 284                                 driverMPI(start, end, outMPI, cutoff);
 285
 286                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 287
 288                                 char buf[5];
 289                                 strcpy(buf, "done");
 290                                 //tell parent you are done.
 291                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 292                         }
 293
 294                         MPI_File_close(&outMPI);
 295
 296                 }else { //lower triangle format
 297                         if (pid == 0) { //you are the root process
 298
 299                                 //do your part
 300                                 string outputMyPart;
 301                                 unsigned long int mySize;
 302
 303                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 304                                 else { driverMPI(start, end, outputFile, mySize, output); }
 305
 306                                 if (m->control_pressed) {  delete distCalculator;  return 0; }
 307
 308                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 309                                 MPI_File outMPI;
 310                                 MPI_File inMPI;
 311
 312                                 //char* filename = new char[outputFile.length()];
 313                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 314
 315                                 char filename[1024];
 316                                 strcpy(filename, outputFile.c_str());
 317
 318                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 319                                 //delete filename;
 320
 321                                 //wait on chidren
 322                                 for(int b = 1; b < processors; b++) {
 323                                         unsigned long int fileSize;
 324
 325                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 326
 327                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 328
 329                                         string outTemp = outputFile + toString(b) + ".temp";
 330
 331                                         char* buf = new char[outTemp.length()];
 332                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 333
 334                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 335                                         delete buf;
 336
 337                                         int count = 0;
 338                                         while (count < fileSize) {
 339                                                 char buf2[1];
 340                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 341                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 342                                                 count += 1;
 343                                         }
 344
 345                                         MPI_File_close(&inMPI); //deleted on close
 346                                 }
 347
 348                                 MPI_File_close(&outMPI);
 349                         }else { //you are a child process
 350                                 //do your part
 351                                 unsigned long int size;
 352                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 353                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 354
 355                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 356
 357                                 //tell parent you are done.
 358                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 359                         }
 360                 }
 361                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 362 #else
 363
 364         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 365                 //if you don't need to fork anything
 366                 if(processors == 1){
 367                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 368                         else { driver(0, numSeqs, outputFile, "square");  }
 369                 }else{ //you have multiple processors
 370
 371                         for (int i = 0; i < processors; i++) {
 372                                 lines.push_back(new linePair());
 373                                 if (output != "square") {
 374                                         lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
 375                                         lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 376                                 }else{
 377                                         lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
 378                                         lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
 379                                 }
 380                         }
 381
 382                         createProcesses(outputFile);
 383
 384                         map<int, int>::iterator it = processIDS.begin();
 385                         rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
 386                         it++;
 387
 388                         //append and remove temp files
 389                         for (; it != processIDS.end(); it++) {
 390                                 m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
 391                                 remove((outputFile + toString(it->second) + ".temp").c_str());
 392                         }
 393                 }
 394         #else
 395                 //ifstream inFASTA;
 396                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 397                 else { driver(0, numSeqs, outputFile, "square");  }
 398         #endif
 399
 400 #endif
 401                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 402
 403                 #ifdef USE_MPI
 404                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 405
 406                         if (pid == 0) { //only one process should output to screen
 407                 #endif
 408
 409                 //if (output == "square") {  convertMatrix(outputFile); }
 410
 411                 ifstream fileHandle;
 412                 fileHandle.open(outputFile.c_str());
 413                 if(fileHandle) {
 414                         m->gobble(fileHandle);
 415                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 416                 }
 417
 418                 //append the old column file to the new one
 419                 if ((oldfastafile != "") && (column != ""))  {
 420                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 421                         if (outputFile == column) {
 422                                 string tempcolumn = column + ".old";
 423                                 m->appendFiles(tempcolumn, outputFile);
 424                                 remove(tempcolumn.c_str());
 425                         }else{
 426                                 m->appendFiles(outputFile, column);
 427                                 remove(outputFile.c_str());
 428                                 outputFile = column;
 429                         }
 430
 431                         if (outputDir != "") {
 432                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 433                                 rename(outputFile.c_str(), newOutputName.c_str());
 434                                 remove(outputFile.c_str());
 435                                 outputFile = newOutputName;
 436                         }
 437                 }
 438
 439
 440                 #ifdef USE_MPI
 441                         }
 442                 #endif
 443
 444                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 445
 446                 delete distCalculator;
 447
 448                 m->mothurOutEndLine();
 449                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 450                 m->mothurOut(outputFile); m->mothurOutEndLine();
 451                 m->mothurOutEndLine();
 452                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 453
 454
 455                 if (m->isTrue(compress)) {
 456                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 457                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 458                         system(("gzip -v " + outputFile).c_str());
 459                 }
 460
 461                 return 0;
 462
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "DistanceCommand", "execute");
 466                 exit(1);
 467         }
 468 }
 469 /**************************************************************************************************/
 470 void DistanceCommand::createProcesses(string filename) {
 471         try {
 472 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 473                 int process = 0;
 474                 processIDS.clear();
 475
 476                 //loop through and create all the processes you want
 477                 while (process != processors) {
 478                         int pid = fork();
 479
 480                         if (pid > 0) {
 481                                 processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 482                                 process++;
 483                         }else if (pid == 0){
 484                                 if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
 485                                 else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
 486                                 exit(0);
 487                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 488                 }
 489
 490                 //force parent to wait until all the processes are done
 491                 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
 492                         int temp = it->second;
 493                         wait(&temp);
 494                 }
 495 #endif
 496         }
 497         catch(exception& e) {
 498                 m->errorOut(e, "DistanceCommand", "createProcesses");
 499                 exit(1);
 500         }
 501 }
 502
 503 /**************************************************************************************************/
 504 /////// need to fix to work with calcs and sequencedb
 505 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 506         try {
 507
 508                 int startTime = time(NULL);
 509
 510                 //column file
 511                 ofstream outFile(dFileName.c_str(), ios::trunc);
 512                 outFile.setf(ios::fixed, ios::showpoint);
 513                 outFile << setprecision(4);
 514
 515                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 516
 517                 for(int i=startLine;i<endLine;i++){
 518                         if(output == "lt")      {
 519                                 string name = alignDB.get(i).getName();
 520                                 if (name.length() < 10) { //pad with spaces to make compatible
 521                                         while (name.length() < 10) {  name += " ";  }
 522                                 }
 523                                 outFile << name << '\t';
 524                         }
 525                         for(int j=0;j<i;j++){
 526
 527                                 if (m->control_pressed) { outFile.close(); return 0;  }
 528
 529                                 //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 530                                 //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
 531                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 532
 533                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 534                                 double dist = distCalculator->getDist();
 535
 536                                 if(dist <= cutoff){
 537                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 538                                 }
 539                                 if (output == "lt") {  outFile << dist << '\t'; }
 540                         }
 541
 542                         if (output == "lt") { outFile << endl; }
 543
 544                         if(i % 100 == 0){
 545                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 546                         }
 547
 548                 }
 549                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 550
 551                 outFile.close();
 552
 553                 return 1;
 554         }
 555         catch(exception& e) {
 556                 m->errorOut(e, "DistanceCommand", "driver");
 557                 exit(1);
 558         }
 559 }
 560 /**************************************************************************************************/
 561 /////// need to fix to work with calcs and sequencedb
 562 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 563         try {
 564
 565                 int startTime = time(NULL);
 566
 567                 //column file
 568                 ofstream outFile(dFileName.c_str(), ios::trunc);
 569                 outFile.setf(ios::fixed, ios::showpoint);
 570                 outFile << setprecision(4);
 571
 572                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 573
 574                 for(int i=startLine;i<endLine;i++){
 575
 576                         string name = alignDB.get(i).getName();
 577                         //pad with spaces to make compatible
 578                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 579
 580                         outFile << name << '\t';
 581
 582                         for(int j=0;j<alignDB.getNumSeqs();j++){
 583
 584                                 if (m->control_pressed) { outFile.close(); return 0;  }
 585
 586                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 587                                 double dist = distCalculator->getDist();
 588
 589                                 outFile << dist << '\t';
 590                         }
 591
 592                         outFile << endl;
 593
 594                         if(i % 100 == 0){
 595                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 596                         }
 597
 598                 }
 599                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 600
 601                 outFile.close();
 602
 603                 return 1;
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "DistanceCommand", "driver");
 607                 exit(1);
 608         }
 609 }
 610 #ifdef USE_MPI
 611 /**************************************************************************************************/
 612 /////// need to fix to work with calcs and sequencedb
 613 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 614         try {
 615                 MPI_Status status;
 616                 int startTime = time(NULL);
 617
 618                 string outputString = "";
 619
 620                 for(int i=startLine;i<endLine;i++){
 621
 622                         for(int j=0;j<i;j++){
 623
 624                                 if (m->control_pressed) {  return 0;  }
 625
 626                                 //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 627                                 //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
 628                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 629
 630                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 631                                 double dist = distCalculator->getDist();
 632
 633                                 if(dist <= cutoff){
 634                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 635                                 }
 636                         }
 637
 638                         if(i % 100 == 0){
 639                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 640                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 641                         }
 642
 643
 644                         //send results to parent
 645                         int length = outputString.length();
 646
 647                         char* buf = new char[length];
 648                         memcpy(buf, outputString.c_str(), length);
 649
 650                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 651                         outputString = "";
 652                         delete buf;
 653
 654                 }
 655
 656                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 657                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 658                 return 1;
 659         }
 660         catch(exception& e) {
 661                 m->errorOut(e, "DistanceCommand", "driverMPI");
 662                 exit(1);
 663         }
 664 }
 665 /**************************************************************************************************/
 666 /////// need to fix to work with calcs and sequencedb
 667 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 668         try {
 669                 MPI_Status status;
 670
 671                 MPI_File outMPI;
 672                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 673
 674                 //char* filename = new char[file.length()];
 675                 //memcpy(filename, file.c_str(), file.length());
 676
 677                 char filename[1024];
 678                 strcpy(filename, file.c_str());
 679
 680                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 681                 //delete filename;
 682
 683                 int startTime = time(NULL);
 684
 685                 string outputString = "";
 686                 size = 0;
 687
 688                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 689
 690                 for(int i=startLine;i<endLine;i++){
 691
 692                         string name = alignDB.get(i).getName();
 693                         if (name.length() < 10) { //pad with spaces to make compatible
 694                                 while (name.length() < 10) {  name += " ";  }
 695                         }
 696                         outputString += name + "\t";
 697
 698                         for(int j=0;j<i;j++){
 699
 700                                 if (m->control_pressed) {  return 0;  }
 701
 702                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 703                                 double dist = distCalculator->getDist();
 704
 705                                 outputString += toString(dist) + "\t";
 706                         }
 707
 708                         outputString += "\n";
 709
 710
 711                         if(i % 100 == 0){
 712                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 713                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 714                         }
 715
 716
 717                         //send results to parent
 718                         int length = outputString.length();
 719                         char* buf = new char[length];
 720                         memcpy(buf, outputString.c_str(), length);
 721
 722                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 723                         size += outputString.length();
 724                         outputString = "";
 725                         delete buf;
 726                 }
 727
 728                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 729                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 730                 MPI_File_close(&outMPI);
 731
 732                 return 1;
 733         }
 734         catch(exception& e) {
 735                 m->errorOut(e, "DistanceCommand", "driverMPI");
 736                 exit(1);
 737         }
 738 }
 739 /**************************************************************************************************/
 740 /////// need to fix to work with calcs and sequencedb
 741 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 742         try {
 743                 MPI_Status status;
 744
 745                 MPI_File outMPI;
 746                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 747
 748                 //char* filename = new char[file.length()];
 749                 //memcpy(filename, file.c_str(), file.length());
 750
 751                 char filename[1024];
 752                 strcpy(filename, file.c_str());
 753
 754                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 755                 //delete filename;
 756
 757                 int startTime = time(NULL);
 758
 759                 string outputString = "";
 760                 size = 0;
 761
 762                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 763
 764                 for(int i=startLine;i<endLine;i++){
 765
 766                         string name = alignDB.get(i).getName();
 767                         if (name.length() < 10) { //pad with spaces to make compatible
 768                                 while (name.length() < 10) {  name += " ";  }
 769                         }
 770                         outputString += name + "\t";
 771
 772                         for(int j=0;j<alignDB.getNumSeqs();j++){
 773
 774                                 if (m->control_pressed) {  return 0;  }
 775
 776                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 777                                 double dist = distCalculator->getDist();
 778
 779                                 outputString += toString(dist) + "\t";
 780                         }
 781
 782                         outputString += "\n";
 783
 784
 785                         if(i % 100 == 0){
 786                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 787                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 788                         }
 789
 790
 791                         //send results to parent
 792                         int length = outputString.length();
 793                         char* buf = new char[length];
 794                         memcpy(buf, outputString.c_str(), length);
 795
 796                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 797                         size += outputString.length();
 798                         outputString = "";
 799                         delete buf;
 800                 }
 801
 802                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 803                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 804                 MPI_File_close(&outMPI);
 805
 806                 return 1;
 807         }
 808         catch(exception& e) {
 809                 m->errorOut(e, "DistanceCommand", "driverMPI");
 810                 exit(1);
 811         }
 812 }
 813 #endif
 814 /**************************************************************************************************
 815 int DistanceCommand::convertMatrix(string outputFile) {
 816         try{
 817
 818                 //sort file by first column so the distances for each row are together
 819                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 820
 821                 //use the unix sort
 822                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 823                         string command = "sort -n " + outputFile + " -o " + outfile;
 824                         system(command.c_str());
 825                 #else //sort using windows sort
 826                         string command = "sort " + outputFile + " /O " + outfile;
 827                         system(command.c_str());
 828                 #endif
 829
 830
 831                 //output to new file distance for each row and save positions in file where new row begins
 832                 ifstream in;
 833                 m->openInputFile(outfile, in);
 834
 835                 ofstream out;
 836                 m->openOutputFile(outputFile, out);
 837
 838                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 839
 840                 out << alignDB.getNumSeqs() << endl;
 841
 842                 //get first currentRow
 843                 string first, currentRow, second;
 844                 float dist;
 845                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 846                 map<string, float>::iterator it;
 847
 848                 in >> first;
 849                 currentRow = first;
 850
 851                 rowDists[first] = 0.00; //distance to yourself is 0.0
 852
 853                 in.seekg(0);
 854                 //m->openInputFile(outfile, in);
 855
 856                 while(!in.eof()) {
 857                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 858
 859                         in >> first >> second >> dist; m->gobble(in);
 860
 861                         if (first != currentRow) {
 862                                 //print out last row
 863                                 out << currentRow << '\t'; //print name
 864
 865                                 //print dists
 866                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 867                                         out << it->second << '\t';
 868                                 }
 869                                 out << endl;
 870
 871                                 //start new row
 872                                 currentRow = first;
 873                                 rowDists.clear();
 874                                 rowDists[first] = 0.00;
 875                                 rowDists[second] = dist;
 876                         }else{
 877                                 rowDists[second] = dist;
 878                         }
 879                 }
 880                 //print out last row
 881                 out << currentRow << '\t'; //print name
 882
 883                 //print dists
 884                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 885                         out << it->second << '\t';
 886                 }
 887                 out << endl;
 888
 889                 in.close();
 890                 out.close();
 891
 892                 remove(outfile.c_str());
 893
 894                 return 1;
 895
 896         }
 897         catch(exception& e) {
 898                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 899                 exit(1);
 900         }
 901 }
 902 /**************************************************************************************************
 903 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 904         try{
 905
 906                 //sort file by first column so the distances for each row are together
 907                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 908
 909                 //use the unix sort
 910                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 911                         string command = "sort -n " + outputFile + " -o " + outfile;
 912                         system(command.c_str());
 913                 #else //sort using windows sort
 914                         string command = "sort " + outputFile + " /O " + outfile;
 915                         system(command.c_str());
 916                 #endif
 917
 918
 919                 //output to new file distance for each row and save positions in file where new row begins
 920                 ifstream in;
 921                 m->openInputFile(outfile, in);
 922
 923                 ofstream out;
 924                 m->openOutputFile(outputFile, out);
 925
 926                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 927
 928                 out << alignDB.getNumSeqs() << endl;
 929
 930                 //get first currentRow
 931                 string first, currentRow, second;
 932                 float dist;
 933                 int i, j;
 934                 i = 0; j = 0;
 935                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 936                 map<string, float>::iterator it;
 937
 938                 in >> first;
 939                 currentRow = first;
 940
 941                 rowDists[first] = 0.00; //distance to yourself is 0.0
 942
 943                 in.seekg(0);
 944                 //m->openInputFile(outfile, in);
 945
 946                 while(!in.eof()) {
 947                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 948
 949                         in >> first >> second >> dist; m->gobble(in);
 950
 951                         if (first != currentRow) {
 952                                 //print out last row
 953                                 out << currentRow << '\t'; //print name
 954
 955                                 //print dists
 956                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 957                                         if (j >= i) { break; }
 958                                         out << it->second << '\t';
 959                                         j++;
 960                                 }
 961                                 out << endl;
 962
 963                                 //start new row
 964                                 currentRow = first;
 965                                 rowDists.clear();
 966                                 rowDists[first] = 0.00;
 967                                 rowDists[second] = dist;
 968                                 j = 0;
 969                                 i++;
 970                         }else{
 971                                 rowDists[second] = dist;
 972                         }
 973                 }
 974                 //print out last row
 975                 out << currentRow << '\t'; //print name
 976
 977                 //print dists
 978                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 979                         out << it->second << '\t';
 980                 }
 981                 out << endl;
 982
 983                 in.close();
 984                 out.close();
 985
 986                 remove(outfile.c_str());
 987
 988                 return 1;
 989
 990         }
 991         catch(exception& e) {
 992                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
 993                 exit(1);
 994         }
 995 }
 996 /**************************************************************************************************/
 997 //its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
 998 //but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
 999 //also check to make sure the 2 files have the same alignment length.
1000 bool DistanceCommand::sanityCheck() {
1001         try{
1002                 bool good = true;
1003
1004                 //make sure the 2 fasta files have the same alignment length
1005                 ifstream in;
1006                 m->openInputFile(fastafile, in);
1007                 int fastaAlignLength = 0;
1008                 if (in) {
1009                         Sequence tempIn(in);
1010                         fastaAlignLength = tempIn.getAligned().length();
1011                 }
1012                 in.close();
1013
1014                 ifstream in2;
1015                 m->openInputFile(oldfastafile, in2);
1016                 int oldfastaAlignLength = 0;
1017                 if (in2) {
1018                         Sequence tempIn2(in2);
1019                         oldfastaAlignLength = tempIn2.getAligned().length();
1020                 }
1021                 in2.close();
1022
1023                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1024
1025                 //read fasta file and save names as well as adding them to the alignDB
1026                 set<string> namesOldFasta;
1027
1028                 ifstream inFasta;
1029                 m->openInputFile(oldfastafile, inFasta);
1030
1031                 while (!inFasta.eof()) {
1032                         if (m->control_pressed) {  inFasta.close(); return good;  }
1033
1034                         Sequence temp(inFasta);
1035
1036                         if (temp.getName() != "") {
1037                                 namesOldFasta.insert(temp.getName());  //save name
1038                                 alignDB.push_back(temp);  //add to DB
1039                         }
1040
1041                         m->gobble(inFasta);
1042                 }
1043
1044                 inFasta.close();
1045
1046                 //read through the column file checking names and removing distances above the cutoff
1047                 ifstream inDist;
1048                 m->openInputFile(column, inDist);
1049
1050                 ofstream outDist;
1051                 string outputFile = column + ".temp";
1052                 m->openOutputFile(outputFile, outDist);
1053
1054                 string name1, name2;
1055                 float dist;
1056                 while (!inDist.eof()) {
1057                         if (m->control_pressed) {  inDist.close(); outDist.close(); remove(outputFile.c_str()); return good;  }
1058
1059                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1060
1061                         //both names are in fasta file and distance is below cutoff
1062                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1063                         else{
1064                                 if (dist <= cutoff) {
1065                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1066                                 }
1067                         }
1068                 }
1069
1070                 inDist.close();
1071                 outDist.close();
1072
1073                 if (good) {
1074                         remove(column.c_str());
1075                         rename(outputFile.c_str(), column.c_str());
1076                 }else{
1077                         remove(outputFile.c_str()); //temp file is bad because file mismatch above
1078                 }
1079
1080         }
1081         catch(exception& e) {
1082                 m->errorOut(e, "DistanceCommand", "m->appendFiles");
1083                 exit(1);
1084         }
1085 }
1086 /**************************************************************************************************/
1087
1088
1089
1090