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 vector<string> DistanceCommand::setParameters(){
  19         try {
  20                 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
  21                 CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
  22                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  23                 CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
  24                 CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
  25                 CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
  26                 CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  28                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "DistanceCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string DistanceCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
  46                 helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors.  \n";
  47                 helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
  48                 helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
  49                 helpString += "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";
  50                 helpString += "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";
  51                 helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
  52                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
  53                 helpString += "The processors parameter allows you to specify number of processors to use.  The default is 1.\n";
  54                 helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
  55                 helpString += "The dist.seqs command should be in the following format: \n";
  56                 helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
  57                 helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
  58                 helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n";
  59                 return helpString;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "DistanceCommand", "getHelpString");
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67 DistanceCommand::DistanceCommand(){
  68         try {
  69                 abort = true; calledHelp = true;
  70                 setParameters();
  71                 vector<string> tempOutNames;
  72                 outputTypes["phylip"] = tempOutNames;
  73                 outputTypes["column"] = tempOutNames;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 DistanceCommand::DistanceCommand(string option) {
  82         try {
  83                 abort = false; calledHelp = false;
  84                 Estimators.clear();
  85
  86                 //allow user to run help
  87                 if(option == "help") { help(); abort = true; calledHelp = true; }
  88
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string, string> parameters = parser.getParameters();
  94
  95                         ValidParameters validParameter("dist.seqs");
  96                         map<string, string>::iterator it2;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 100                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //initialize outputTypes
 104                         vector<string> tempOutNames;
 105                         outputTypes["phylip"] = tempOutNames;
 106                         outputTypes["column"] = tempOutNames;
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it2 = parameters.find("fasta");
 114                                 //user has given a template file
 115                                 if(it2 != parameters.end()){
 116                                         path = m->hasPath(it2->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
 119                                 }
 120
 121                                 it2 = parameters.find("oldfasta");
 122                                 //user has given a template file
 123                                 if(it2 != parameters.end()){
 124                                         path = m->hasPath(it2->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
 127                                 }
 128
 129                                 it2 = parameters.find("column");
 130                                 //user has given a template file
 131                                 if(it2 != parameters.end()){
 132                                         path = m->hasPath(it2->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
 135                                 }
 136                         }
 137
 138                         //check for required parameters
 139                         fastafile = validParameter.validFile(parameters, "fasta", true);
 140                         if (fastafile == "not found") {
 141                                 fastafile = m->getFastaFile();
 142                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
 143                                         ifstream inFASTA;
 144                                         m->openInputFile(fastafile, inFASTA);
 145                                         alignDB = SequenceDB(inFASTA);
 146                                         inFASTA.close();
 147                                 }else {         m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 148                         }else if (fastafile == "not open") { abort = true; }
 149                         else{
 150                                 ifstream inFASTA;
 151                                 m->openInputFile(fastafile, inFASTA);
 152                                 alignDB = SequenceDB(inFASTA);
 153                                 inFASTA.close();
 154                         }
 155
 156                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
 157                         if (oldfastafile == "not found") { oldfastafile = ""; }
 158                         else if (oldfastafile == "not open") { abort = true; }
 159
 160                         column = validParameter.validFile(parameters, "column", true);
 161                         if (column == "not found") { column = ""; }
 162                         else if (column == "not open") { abort = true; }
 163
 164                         //if the user changes the output directory command factory will send this info to us in the output parameter
 165                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 166                                 outputDir = "";
 167                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 168                         }
 169
 170                         //check for optional parameter and set defaults
 171                         // ...at some point should added some additional type checking...
 172                         calc = validParameter.validFile(parameters, "calc", false);
 173                         if (calc == "not found") { calc = "onegap";  }
 174                         else {
 175                                  if (calc == "default")  {  calc = "onegap";  }
 176                         }
 177                         m->splitAtDash(calc, Estimators);
 178
 179                         string temp;
 180                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 181                         convert(temp, countends);
 182
 183                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 184                         convert(temp, cutoff);
 185
 186                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 187                         m->setProcessors(temp);
 188                         convert(temp, processors);
 189
 190                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 191                         convert(temp, compress);
 192
 193                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 194
 195                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 196
 197                         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; }
 198
 199                         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"; }
 200
 201                         ValidCalculators validCalculator;
 202
 203                         if (m->isTrue(countends) == true) {
 204                                 for (int i=0; i<Estimators.size(); i++) {
 205                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 206                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 207                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 208                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 209                                         }
 210                                 }
 211                         }else {
 212                                 for (int i=0; i<Estimators.size(); i++) {
 213                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 214                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 215                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 216                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 217                                         }
 218                                 }
 219                         }
 220
 221                 }
 222
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 226                 exit(1);
 227         }
 228 }
 229 //**********************************************************************************************************************
 230
 231 int DistanceCommand::execute(){
 232         try {
 233
 234                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 235
 236                 int startTime = time(NULL);
 237
 238                 //save number of new sequence
 239                 numNewFasta = alignDB.getNumSeqs();
 240
 241                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 242                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 243
 244                 if (m->control_pressed) { return 0; }
 245
 246                 int numSeqs = alignDB.getNumSeqs();
 247                 cutoff += 0.005;
 248
 249                 string outputFile;
 250
 251                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 252                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
 253                         remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
 254
 255                         //output numSeqs to phylip formatted dist file
 256                 }else if (output == "column") { //user wants column format
 257                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
 258                         outputTypes["column"].push_back(outputFile);
 259
 260                         //so we don't accidentally overwrite
 261                         if (outputFile == column) {
 262                                 string tempcolumn = column + ".old";
 263                                 rename(column.c_str(), tempcolumn.c_str());
 264                         }
 265
 266                         remove(outputFile.c_str());
 267                 }else { //assume square
 268                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
 269                         remove(outputFile.c_str());
 270                         outputTypes["phylip"].push_back(outputFile);
 271                 }
 272
 273
 274 #ifdef USE_MPI
 275
 276                 int pid, start, end;
 277                 int tag = 2001;
 278
 279                 MPI_Status status;
 280                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 281                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 282
 283                 //each process gets where it should start and stop in the file
 284                 if (output != "square") {
 285                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 286                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 287                 }else{
 288                         start = int ((float(pid)/float(processors)) * numSeqs);
 289                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 290                 }
 291
 292                 if (output == "column") {
 293                         MPI_File outMPI;
 294                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 295
 296                         //char* filename = new char[outputFile.length()];
 297                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 298
 299                         char filename[1024];
 300                         strcpy(filename, outputFile.c_str());
 301
 302                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 303                         //delete filename;
 304
 305                         if (pid == 0) { //you are the root process
 306
 307                                 //do your part
 308                                 string outputMyPart;
 309
 310                                 driverMPI(start, end, outMPI, cutoff);
 311
 312                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator;  return 0; }
 313
 314                                 //wait on chidren
 315                                 for(int i = 1; i < processors; i++) {
 316                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 317
 318                                         char buf[5];
 319                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 320                                 }
 321                         }else { //you are a child process
 322                                 //do your part
 323                                 driverMPI(start, end, outMPI, cutoff);
 324
 325                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 326
 327                                 char buf[5];
 328                                 strcpy(buf, "done");
 329                                 //tell parent you are done.
 330                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 331                         }
 332
 333                         MPI_File_close(&outMPI);
 334
 335                 }else { //lower triangle format
 336                         if (pid == 0) { //you are the root process
 337
 338                                 //do your part
 339                                 string outputMyPart;
 340                                 unsigned long int mySize;
 341
 342                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 343                                 else { driverMPI(start, end, outputFile, mySize, output); }
 344
 345                                 if (m->control_pressed) {  outputTypes.clear();  delete distCalculator;  return 0; }
 346
 347                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 348                                 MPI_File outMPI;
 349                                 MPI_File inMPI;
 350
 351                                 //char* filename = new char[outputFile.length()];
 352                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 353
 354                                 char filename[1024];
 355                                 strcpy(filename, outputFile.c_str());
 356
 357                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 358                                 //delete filename;
 359
 360                                 //wait on chidren
 361                                 for(int b = 1; b < processors; b++) {
 362                                         unsigned long int fileSize;
 363
 364                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 365
 366                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 367
 368                                         string outTemp = outputFile + toString(b) + ".temp";
 369
 370                                         char* buf = new char[outTemp.length()];
 371                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 372
 373                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 374                                         delete buf;
 375
 376                                         int count = 0;
 377                                         while (count < fileSize) {
 378                                                 char buf2[1];
 379                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 380                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 381                                                 count += 1;
 382                                         }
 383
 384                                         MPI_File_close(&inMPI); //deleted on close
 385                                 }
 386
 387                                 MPI_File_close(&outMPI);
 388                         }else { //you are a child process
 389                                 //do your part
 390                                 unsigned long int size;
 391                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 392                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 393
 394                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 395
 396                                 //tell parent you are done.
 397                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 398                         }
 399                 }
 400                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 401 #else
 402
 403         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 404                 //if you don't need to fork anything
 405                 if(processors == 1){
 406                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 407                         else { driver(0, numSeqs, outputFile, "square");  }
 408                 }else{ //you have multiple processors
 409
 410                         unsigned long int numDists = 0;
 411
 412                         if (output == "square") {
 413                                  numDists = numSeqs * numSeqs;
 414                         }else {
 415                                 for(int i=0;i<numSeqs;i++){
 416                                         for(int j=0;j<i;j++){
 417                                                 numDists++;
 418                                                 if (numDists > processors) { break; }
 419                                         }
 420                                 }
 421                         }
 422
 423                         if (numDists < processors) { processors = numDists; }
 424
 425                         for (int i = 0; i < processors; i++) {
 426                                 distlinePair tempLine;
 427                                 lines.push_back(tempLine);
 428                                 if (output != "square") {
 429                                         lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 430                                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 431                                 }else{
 432                                         lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 433                                         lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 434                                 }
 435
 436                         }
 437
 438                         createProcesses(outputFile);
 439                 }
 440         #else
 441                 //ifstream inFASTA;
 442                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 443                 else { driver(0, numSeqs, outputFile, "square");  }
 444         #endif
 445
 446 #endif
 447                 if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 448
 449                 #ifdef USE_MPI
 450                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 451
 452                         if (pid == 0) { //only one process should output to screen
 453                 #endif
 454
 455                 //if (output == "square") {  convertMatrix(outputFile); }
 456
 457                 ifstream fileHandle;
 458                 fileHandle.open(outputFile.c_str());
 459                 if(fileHandle) {
 460                         m->gobble(fileHandle);
 461                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 462                 }
 463
 464                 //append the old column file to the new one
 465                 if ((oldfastafile != "") && (column != ""))  {
 466                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 467                         if (outputFile == column) {
 468                                 string tempcolumn = column + ".old";
 469                                 m->appendFiles(tempcolumn, outputFile);
 470                                 remove(tempcolumn.c_str());
 471                         }else{
 472                                 m->appendFiles(outputFile, column);
 473                                 remove(outputFile.c_str());
 474                                 outputFile = column;
 475                         }
 476
 477                         if (outputDir != "") {
 478                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 479                                 rename(outputFile.c_str(), newOutputName.c_str());
 480                                 remove(outputFile.c_str());
 481                                 outputFile = newOutputName;
 482                         }
 483                 }
 484
 485
 486                 #ifdef USE_MPI
 487                         }
 488                 #endif
 489
 490                 if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 491
 492                 delete distCalculator;
 493
 494                 //set phylip file as new current phylipfile
 495                 string current = "";
 496                 itTypes = outputTypes.find("phylip");
 497                 if (itTypes != outputTypes.end()) {
 498                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 499                 }
 500
 501                 //set column file as new current columnfile
 502                 itTypes = outputTypes.find("column");
 503                 if (itTypes != outputTypes.end()) {
 504                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 505                 }
 506
 507                 m->mothurOutEndLine();
 508                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 509                 m->mothurOut(outputFile); m->mothurOutEndLine();
 510                 m->mothurOutEndLine();
 511                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 512
 513
 514                 if (m->isTrue(compress)) {
 515                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 516                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 517                         system(("gzip -v " + outputFile).c_str());
 518                         outputNames.push_back(outputFile + ".gz");
 519                 }else { outputNames.push_back(outputFile); }
 520
 521                 return 0;
 522
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "DistanceCommand", "execute");
 526                 exit(1);
 527         }
 528 }
 529 /**************************************************************************************************/
 530 void DistanceCommand::createProcesses(string filename) {
 531         try {
 532 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 533                 int process = 1;
 534                 processIDS.clear();
 535
 536                 //loop through and create all the processes you want
 537                 while (process != processors) {
 538                         int pid = fork();
 539
 540                         if (pid > 0) {
 541                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 542                                 process++;
 543                         }else if (pid == 0){
 544                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 545                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 546                                 exit(0);
 547                         }else {
 548                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
 549                                 perror(" : ");
 550                                 for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 551                                 exit(0);
 552                         }
 553                 }
 554
 555                 //parent does its part
 556                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 557                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 558
 559
 560                 //force parent to wait until all the processes are done
 561                 for (int i=0;i<processIDS.size();i++) {
 562                         int temp = processIDS[i];
 563                         wait(&temp);
 564                 }
 565
 566                 //append and remove temp files
 567                 for (int i=0;i<processIDS.size();i++) {
 568                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 569                         remove((filename + toString(processIDS[i]) + ".temp").c_str());
 570                 }
 571 #endif
 572         }
 573         catch(exception& e) {
 574                 m->errorOut(e, "DistanceCommand", "createProcesses");
 575                 exit(1);
 576         }
 577 }
 578
 579 /**************************************************************************************************/
 580 /////// need to fix to work with calcs and sequencedb
 581 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 582         try {
 583
 584                 int startTime = time(NULL);
 585
 586                 //column file
 587                 ofstream outFile(dFileName.c_str(), ios::trunc);
 588                 outFile.setf(ios::fixed, ios::showpoint);
 589                 outFile << setprecision(4);
 590
 591                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 592
 593                 for(int i=startLine;i<endLine;i++){
 594                         if(output == "lt")      {
 595                                 string name = alignDB.get(i).getName();
 596                                 if (name.length() < 10) { //pad with spaces to make compatible
 597                                         while (name.length() < 10) {  name += " ";  }
 598                                 }
 599                                 outFile << name << '\t';
 600                         }
 601                         for(int j=0;j<i;j++){
 602
 603                                 if (m->control_pressed) { outFile.close(); return 0;  }
 604
 605                                 //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
 606                                 //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
 607                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 608
 609                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 610                                 double dist = distCalculator->getDist();
 611
 612                                 if(dist <= cutoff){
 613                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 614                                 }
 615                                 if (output == "lt") {  outFile << dist << '\t'; }
 616                         }
 617
 618                         if (output == "lt") { outFile << endl; }
 619
 620                         if(i % 100 == 0){
 621                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 622                         }
 623
 624                 }
 625                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 626
 627                 outFile.close();
 628
 629                 return 1;
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "DistanceCommand", "driver");
 633                 exit(1);
 634         }
 635 }
 636 /**************************************************************************************************/
 637 /////// need to fix to work with calcs and sequencedb
 638 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 639         try {
 640
 641                 int startTime = time(NULL);
 642
 643                 //column file
 644                 ofstream outFile(dFileName.c_str(), ios::trunc);
 645                 outFile.setf(ios::fixed, ios::showpoint);
 646                 outFile << setprecision(4);
 647
 648                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 649
 650                 for(int i=startLine;i<endLine;i++){
 651
 652                         string name = alignDB.get(i).getName();
 653                         //pad with spaces to make compatible
 654                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 655
 656                         outFile << name << '\t';
 657
 658                         for(int j=0;j<alignDB.getNumSeqs();j++){
 659
 660                                 if (m->control_pressed) { outFile.close(); return 0;  }
 661
 662                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 663                                 double dist = distCalculator->getDist();
 664
 665                                 outFile << dist << '\t';
 666                         }
 667
 668                         outFile << endl;
 669
 670                         if(i % 100 == 0){
 671                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 672                         }
 673
 674                 }
 675                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 676
 677                 outFile.close();
 678
 679                 return 1;
 680         }
 681         catch(exception& e) {
 682                 m->errorOut(e, "DistanceCommand", "driver");
 683                 exit(1);
 684         }
 685 }
 686 #ifdef USE_MPI
 687 /**************************************************************************************************/
 688 /////// need to fix to work with calcs and sequencedb
 689 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 690         try {
 691                 MPI_Status status;
 692                 int startTime = time(NULL);
 693
 694                 string outputString = "";
 695
 696                 for(int i=startLine;i<endLine;i++){
 697
 698                         for(int j=0;j<i;j++){
 699
 700                                 if (m->control_pressed) {  return 0;  }
 701
 702                                 //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
 703                                 //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
 704                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 705
 706                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 707                                 double dist = distCalculator->getDist();
 708
 709                                 if(dist <= cutoff){
 710                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 711                                 }
 712                         }
 713
 714                         if(i % 100 == 0){
 715                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 716                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 717                         }
 718
 719
 720                         //send results to parent
 721                         int length = outputString.length();
 722
 723                         char* buf = new char[length];
 724                         memcpy(buf, outputString.c_str(), length);
 725
 726                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 727                         outputString = "";
 728                         delete buf;
 729
 730                 }
 731
 732                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 733                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 734                 return 1;
 735         }
 736         catch(exception& e) {
 737                 m->errorOut(e, "DistanceCommand", "driverMPI");
 738                 exit(1);
 739         }
 740 }
 741 /**************************************************************************************************/
 742 /////// need to fix to work with calcs and sequencedb
 743 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 744         try {
 745                 MPI_Status status;
 746
 747                 MPI_File outMPI;
 748                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 749
 750                 //char* filename = new char[file.length()];
 751                 //memcpy(filename, file.c_str(), file.length());
 752
 753                 char filename[1024];
 754                 strcpy(filename, file.c_str());
 755
 756                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 757                 //delete filename;
 758
 759                 int startTime = time(NULL);
 760
 761                 string outputString = "";
 762                 size = 0;
 763
 764                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 765
 766                 for(int i=startLine;i<endLine;i++){
 767
 768                         string name = alignDB.get(i).getName();
 769                         if (name.length() < 10) { //pad with spaces to make compatible
 770                                 while (name.length() < 10) {  name += " ";  }
 771                         }
 772                         outputString += name + "\t";
 773
 774                         for(int j=0;j<i;j++){
 775
 776                                 if (m->control_pressed) {  return 0;  }
 777
 778                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 779                                 double dist = distCalculator->getDist();
 780
 781                                 outputString += toString(dist) + "\t";
 782                         }
 783
 784                         outputString += "\n";
 785
 786
 787                         if(i % 100 == 0){
 788                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 789                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 790                         }
 791
 792
 793                         //send results to parent
 794                         int length = outputString.length();
 795                         char* buf = new char[length];
 796                         memcpy(buf, outputString.c_str(), length);
 797
 798                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 799                         size += outputString.length();
 800                         outputString = "";
 801                         delete buf;
 802                 }
 803
 804                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 805                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 806                 MPI_File_close(&outMPI);
 807
 808                 return 1;
 809         }
 810         catch(exception& e) {
 811                 m->errorOut(e, "DistanceCommand", "driverMPI");
 812                 exit(1);
 813         }
 814 }
 815 /**************************************************************************************************/
 816 /////// need to fix to work with calcs and sequencedb
 817 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 818         try {
 819                 MPI_Status status;
 820
 821                 MPI_File outMPI;
 822                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 823
 824                 //char* filename = new char[file.length()];
 825                 //memcpy(filename, file.c_str(), file.length());
 826
 827                 char filename[1024];
 828                 strcpy(filename, file.c_str());
 829
 830                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 831                 //delete filename;
 832
 833                 int startTime = time(NULL);
 834
 835                 string outputString = "";
 836                 size = 0;
 837
 838                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 839
 840                 for(int i=startLine;i<endLine;i++){
 841
 842                         string name = alignDB.get(i).getName();
 843                         if (name.length() < 10) { //pad with spaces to make compatible
 844                                 while (name.length() < 10) {  name += " ";  }
 845                         }
 846                         outputString += name + "\t";
 847
 848                         for(int j=0;j<alignDB.getNumSeqs();j++){
 849
 850                                 if (m->control_pressed) {  return 0;  }
 851
 852                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 853                                 double dist = distCalculator->getDist();
 854
 855                                 outputString += toString(dist) + "\t";
 856                         }
 857
 858                         outputString += "\n";
 859
 860
 861                         if(i % 100 == 0){
 862                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 863                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 864                         }
 865
 866
 867                         //send results to parent
 868                         int length = outputString.length();
 869                         char* buf = new char[length];
 870                         memcpy(buf, outputString.c_str(), length);
 871
 872                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 873                         size += outputString.length();
 874                         outputString = "";
 875                         delete buf;
 876                 }
 877
 878                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 879                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 880                 MPI_File_close(&outMPI);
 881
 882                 return 1;
 883         }
 884         catch(exception& e) {
 885                 m->errorOut(e, "DistanceCommand", "driverMPI");
 886                 exit(1);
 887         }
 888 }
 889 #endif
 890 /**************************************************************************************************
 891 int DistanceCommand::convertMatrix(string outputFile) {
 892         try{
 893
 894                 //sort file by first column so the distances for each row are together
 895                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 896
 897                 //use the unix sort
 898                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 899                         string command = "sort -n " + outputFile + " -o " + outfile;
 900                         system(command.c_str());
 901                 #else //sort using windows sort
 902                         string command = "sort " + outputFile + " /O " + outfile;
 903                         system(command.c_str());
 904                 #endif
 905
 906
 907                 //output to new file distance for each row and save positions in file where new row begins
 908                 ifstream in;
 909                 m->openInputFile(outfile, in);
 910
 911                 ofstream out;
 912                 m->openOutputFile(outputFile, out);
 913
 914                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 915
 916                 out << alignDB.getNumSeqs() << endl;
 917
 918                 //get first currentRow
 919                 string first, currentRow, second;
 920                 float dist;
 921                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 922                 map<string, float>::iterator it;
 923
 924                 in >> first;
 925                 currentRow = first;
 926
 927                 rowDists[first] = 0.00; //distance to yourself is 0.0
 928
 929                 in.seekg(0);
 930                 //m->openInputFile(outfile, in);
 931
 932                 while(!in.eof()) {
 933                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 934
 935                         in >> first >> second >> dist; m->gobble(in);
 936
 937                         if (first != currentRow) {
 938                                 //print out last row
 939                                 out << currentRow << '\t'; //print name
 940
 941                                 //print dists
 942                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 943                                         out << it->second << '\t';
 944                                 }
 945                                 out << endl;
 946
 947                                 //start new row
 948                                 currentRow = first;
 949                                 rowDists.clear();
 950                                 rowDists[first] = 0.00;
 951                                 rowDists[second] = dist;
 952                         }else{
 953                                 rowDists[second] = dist;
 954                         }
 955                 }
 956                 //print out last row
 957                 out << currentRow << '\t'; //print name
 958
 959                 //print dists
 960                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 961                         out << it->second << '\t';
 962                 }
 963                 out << endl;
 964
 965                 in.close();
 966                 out.close();
 967
 968                 remove(outfile.c_str());
 969
 970                 return 1;
 971
 972         }
 973         catch(exception& e) {
 974                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 975                 exit(1);
 976         }
 977 }
 978 /**************************************************************************************************
 979 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 980         try{
 981
 982                 //sort file by first column so the distances for each row are together
 983                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 984
 985                 //use the unix sort
 986                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 987                         string command = "sort -n " + outputFile + " -o " + outfile;
 988                         system(command.c_str());
 989                 #else //sort using windows sort
 990                         string command = "sort " + outputFile + " /O " + outfile;
 991                         system(command.c_str());
 992                 #endif
 993
 994
 995                 //output to new file distance for each row and save positions in file where new row begins
 996                 ifstream in;
 997                 m->openInputFile(outfile, in);
 998
 999                 ofstream out;
1000                 m->openOutputFile(outputFile, out);
1001
1002                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1003
1004                 out << alignDB.getNumSeqs() << endl;
1005
1006                 //get first currentRow
1007                 string first, currentRow, second;
1008                 float dist;
1009                 int i, j;
1010                 i = 0; j = 0;
1011                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1012                 map<string, float>::iterator it;
1013
1014                 in >> first;
1015                 currentRow = first;
1016
1017                 rowDists[first] = 0.00; //distance to yourself is 0.0
1018
1019                 in.seekg(0);
1020                 //m->openInputFile(outfile, in);
1021
1022                 while(!in.eof()) {
1023                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
1024
1025                         in >> first >> second >> dist; m->gobble(in);
1026
1027                         if (first != currentRow) {
1028                                 //print out last row
1029                                 out << currentRow << '\t'; //print name
1030
1031                                 //print dists
1032                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1033                                         if (j >= i) { break; }
1034                                         out << it->second << '\t';
1035                                         j++;
1036                                 }
1037                                 out << endl;
1038
1039                                 //start new row
1040                                 currentRow = first;
1041                                 rowDists.clear();
1042                                 rowDists[first] = 0.00;
1043                                 rowDists[second] = dist;
1044                                 j = 0;
1045                                 i++;
1046                         }else{
1047                                 rowDists[second] = dist;
1048                         }
1049                 }
1050                 //print out last row
1051                 out << currentRow << '\t'; //print name
1052
1053                 //print dists
1054                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1055                         out << it->second << '\t';
1056                 }
1057                 out << endl;
1058
1059                 in.close();
1060                 out.close();
1061
1062                 remove(outfile.c_str());
1063
1064                 return 1;
1065
1066         }
1067         catch(exception& e) {
1068                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1069                 exit(1);
1070         }
1071 }
1072 /**************************************************************************************************/
1073 //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,
1074 //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.
1075 //also check to make sure the 2 files have the same alignment length.
1076 bool DistanceCommand::sanityCheck() {
1077         try{
1078                 bool good = true;
1079
1080                 //make sure the 2 fasta files have the same alignment length
1081                 ifstream in;
1082                 m->openInputFile(fastafile, in);
1083                 int fastaAlignLength = 0;
1084                 if (in) {
1085                         Sequence tempIn(in);
1086                         fastaAlignLength = tempIn.getAligned().length();
1087                 }
1088                 in.close();
1089
1090                 ifstream in2;
1091                 m->openInputFile(oldfastafile, in2);
1092                 int oldfastaAlignLength = 0;
1093                 if (in2) {
1094                         Sequence tempIn2(in2);
1095                         oldfastaAlignLength = tempIn2.getAligned().length();
1096                 }
1097                 in2.close();
1098
1099                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1100
1101                 //read fasta file and save names as well as adding them to the alignDB
1102                 set<string> namesOldFasta;
1103
1104                 ifstream inFasta;
1105                 m->openInputFile(oldfastafile, inFasta);
1106
1107                 while (!inFasta.eof()) {
1108                         if (m->control_pressed) {  inFasta.close(); return good;  }
1109
1110                         Sequence temp(inFasta);
1111
1112                         if (temp.getName() != "") {
1113                                 namesOldFasta.insert(temp.getName());  //save name
1114                                 alignDB.push_back(temp);  //add to DB
1115                         }
1116
1117                         m->gobble(inFasta);
1118                 }
1119
1120                 inFasta.close();
1121
1122                 //read through the column file checking names and removing distances above the cutoff
1123                 ifstream inDist;
1124                 m->openInputFile(column, inDist);
1125
1126                 ofstream outDist;
1127                 string outputFile = column + ".temp";
1128                 m->openOutputFile(outputFile, outDist);
1129
1130                 string name1, name2;
1131                 float dist;
1132                 while (!inDist.eof()) {
1133                         if (m->control_pressed) {  inDist.close(); outDist.close(); remove(outputFile.c_str()); return good;  }
1134
1135                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1136
1137                         //both names are in fasta file and distance is below cutoff
1138                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1139                         else{
1140                                 if (dist <= cutoff) {
1141                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1142                                 }
1143                         }
1144                 }
1145
1146                 inDist.close();
1147                 outDist.close();
1148
1149                 if (good) {
1150                         remove(column.c_str());
1151                         rename(outputFile.c_str(), column.c_str());
1152                 }else{
1153                         remove(outputFile.c_str()); //temp file is bad because file mismatch above
1154                 }
1155
1156                 return good;
1157
1158         }
1159         catch(exception& e) {
1160                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1161                 exit(1);
1162         }
1163 }
1164 /**************************************************************************************************/
1165
1166
1167
1168