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";
  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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  89
  90                 else {
  91                         vector<string> myArray = setParameters();
  92
  93                         OptionParser parser(option);
  94                         map<string, string> parameters = parser.getParameters();
  95
  96                         ValidParameters validParameter("dist.seqs");
  97                         map<string, string>::iterator it2;
  98
  99                         //check to make sure all parameters are valid for command
 100                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 101                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 102                         }
 103
 104                         //initialize outputTypes
 105                         vector<string> tempOutNames;
 106                         outputTypes["phylip"] = tempOutNames;
 107                         outputTypes["column"] = tempOutNames;
 108
 109                         //if the user changes the input directory command factory will send this info to us in the output parameter
 110                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 111                         if (inputDir == "not found"){   inputDir = "";          }
 112                         else {
 113                                 string path;
 114                                 it2 = parameters.find("fasta");
 115                                 //user has given a template file
 116                                 if(it2 != parameters.end()){
 117                                         path = m->hasPath(it2->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
 120                                 }
 121
 122                                 it2 = parameters.find("oldfasta");
 123                                 //user has given a template file
 124                                 if(it2 != parameters.end()){
 125                                         path = m->hasPath(it2->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
 128                                 }
 129
 130                                 it2 = parameters.find("column");
 131                                 //user has given a template file
 132                                 if(it2 != parameters.end()){
 133                                         path = m->hasPath(it2->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
 136                                 }
 137                         }
 138
 139                         //check for required parameters
 140                         fastafile = validParameter.validFile(parameters, "fasta", true);
 141                         if (fastafile == "not found") {
 142                                 fastafile = m->getFastaFile();
 143                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
 144                                         ifstream inFASTA;
 145                                         m->openInputFile(fastafile, inFASTA);
 146                                         alignDB = SequenceDB(inFASTA);
 147                                         inFASTA.close();
 148                                 }else {         m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 149                         }else if (fastafile == "not open") { abort = true; }
 150                         else{
 151                                 ifstream inFASTA;
 152                                 m->openInputFile(fastafile, inFASTA);
 153                                 alignDB = SequenceDB(inFASTA);
 154                                 inFASTA.close();
 155                                 m->setFastaFile(fastafile);
 156                         }
 157
 158                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
 159                         if (oldfastafile == "not found") { oldfastafile = ""; }
 160                         else if (oldfastafile == "not open") { abort = true; }
 161
 162                         column = validParameter.validFile(parameters, "column", true);
 163                         if (column == "not found") { column = ""; }
 164                         else if (column == "not open") { abort = true; }
 165                         else { m->setColumnFile(column); }
 166
 167                         //if the user changes the output directory command factory will send this info to us in the output parameter
 168                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 169                                 outputDir = "";
 170                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 171                         }
 172
 173                         //check for optional parameter and set defaults
 174                         // ...at some point should added some additional type checking...
 175                         calc = validParameter.validFile(parameters, "calc", false);
 176                         if (calc == "not found") { calc = "onegap";  }
 177                         else {
 178                                  if (calc == "default")  {  calc = "onegap";  }
 179                         }
 180                         m->splitAtDash(calc, Estimators);
 181
 182                         string temp;
 183                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 184                         convert(temp, countends);
 185
 186                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 187                         convert(temp, cutoff);
 188
 189                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 190                         m->setProcessors(temp);
 191                         convert(temp, processors);
 192
 193                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 194                         convert(temp, compress);
 195
 196                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 197
 198                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 199
 200                         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; }
 201
 202                         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"; }
 203
 204                         ValidCalculators validCalculator;
 205
 206                         if (m->isTrue(countends) == true) {
 207                                 for (int i=0; i<Estimators.size(); i++) {
 208                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 209                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 210                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 211                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 212                                         }
 213                                 }
 214                         }else {
 215                                 for (int i=0; i<Estimators.size(); i++) {
 216                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 217                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 218                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 219                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 220                                         }
 221                                 }
 222                         }
 223
 224                 }
 225
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 229                 exit(1);
 230         }
 231 }
 232 //**********************************************************************************************************************
 233
 234 int DistanceCommand::execute(){
 235         try {
 236
 237                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 238
 239                 int startTime = time(NULL);
 240
 241                 //save number of new sequence
 242                 numNewFasta = alignDB.getNumSeqs();
 243
 244                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 245                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 246
 247                 if (m->control_pressed) { return 0; }
 248
 249                 int numSeqs = alignDB.getNumSeqs();
 250                 cutoff += 0.005;
 251
 252                 if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
 253
 254                 string outputFile;
 255
 256                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 257                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
 258                         m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 259
 260                         //output numSeqs to phylip formatted dist file
 261                 }else if (output == "column") { //user wants column format
 262                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
 263                         outputTypes["column"].push_back(outputFile);
 264
 265                         //so we don't accidentally overwrite
 266                         if (outputFile == column) {
 267                                 string tempcolumn = column + ".old";
 268                                 rename(column.c_str(), tempcolumn.c_str());
 269                         }
 270
 271                         m->mothurRemove(outputFile);
 272                 }else { //assume square
 273                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
 274                         m->mothurRemove(outputFile);
 275                         outputTypes["phylip"].push_back(outputFile);
 276                 }
 277
 278
 279 #ifdef USE_MPI
 280
 281                 int pid, start, end;
 282                 int tag = 2001;
 283
 284                 MPI_Status status;
 285                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 286                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 287
 288                 //each process gets where it should start and stop in the file
 289                 if (output != "square") {
 290                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 291                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 292                 }else{
 293                         start = int ((float(pid)/float(processors)) * numSeqs);
 294                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 295                 }
 296
 297                 if (output == "column") {
 298                         MPI_File outMPI;
 299                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 300
 301                         //char* filename = new char[outputFile.length()];
 302                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 303
 304                         char filename[1024];
 305                         strcpy(filename, outputFile.c_str());
 306
 307                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 308                         //delete filename;
 309
 310                         if (pid == 0) { //you are the root process
 311
 312                                 //do your part
 313                                 string outputMyPart;
 314
 315                                 driverMPI(start, end, outMPI, cutoff);
 316
 317                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator;  return 0; }
 318
 319                                 //wait on chidren
 320                                 for(int i = 1; i < processors; i++) {
 321                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 322
 323                                         char buf[5];
 324                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 325                                 }
 326                         }else { //you are a child process
 327                                 //do your part
 328                                 driverMPI(start, end, outMPI, cutoff);
 329
 330                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 331
 332                                 char buf[5];
 333                                 strcpy(buf, "done");
 334                                 //tell parent you are done.
 335                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 336                         }
 337
 338                         MPI_File_close(&outMPI);
 339
 340                 }else { //lower triangle format
 341                         if (pid == 0) { //you are the root process
 342
 343                                 //do your part
 344                                 string outputMyPart;
 345                                 unsigned long int mySize;
 346
 347                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 348                                 else { driverMPI(start, end, outputFile, mySize, output); }
 349
 350                                 if (m->control_pressed) {  outputTypes.clear();  delete distCalculator;  return 0; }
 351
 352                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 353                                 MPI_File outMPI;
 354                                 MPI_File inMPI;
 355
 356                                 //char* filename = new char[outputFile.length()];
 357                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 358
 359                                 char filename[1024];
 360                                 strcpy(filename, outputFile.c_str());
 361
 362                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 363                                 //delete filename;
 364
 365                                 //wait on chidren
 366                                 for(int b = 1; b < processors; b++) {
 367                                         unsigned long int fileSize;
 368
 369                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 370
 371                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 372
 373                                         string outTemp = outputFile + toString(b) + ".temp";
 374
 375                                         char* buf = new char[outTemp.length()];
 376                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 377
 378                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 379                                         delete buf;
 380
 381                                         int count = 0;
 382                                         while (count < fileSize) {
 383                                                 char buf2[1];
 384                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 385                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 386                                                 count += 1;
 387                                         }
 388
 389                                         MPI_File_close(&inMPI); //deleted on close
 390                                 }
 391
 392                                 MPI_File_close(&outMPI);
 393                         }else { //you are a child process
 394                                 //do your part
 395                                 unsigned long int size;
 396                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 397                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 398
 399                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 400
 401                                 //tell parent you are done.
 402                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 403                         }
 404                 }
 405                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 406 #else
 407
 408         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 409                 //if you don't need to fork anything
 410                 if(processors == 1){
 411                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 412                         else { driver(0, numSeqs, outputFile, "square");  }
 413                 }else{ //you have multiple processors
 414
 415                         unsigned long int numDists = 0;
 416
 417                         if (output == "square") {
 418                                  numDists = numSeqs * numSeqs;
 419                         }else {
 420                                 for(int i=0;i<numSeqs;i++){
 421                                         for(int j=0;j<i;j++){
 422                                                 numDists++;
 423                                                 if (numDists > processors) { break; }
 424                                         }
 425                                 }
 426                         }
 427
 428                         if (numDists < processors) { processors = numDists; }
 429
 430                         for (int i = 0; i < processors; i++) {
 431                                 distlinePair tempLine;
 432                                 lines.push_back(tempLine);
 433                                 if (output != "square") {
 434                                         lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 435                                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 436                                 }else{
 437                                         lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 438                                         lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 439                                 }
 440
 441                         }
 442
 443                         createProcesses(outputFile);
 444                 }
 445         #else
 446                 //ifstream inFASTA;
 447                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 448                 else { driver(0, numSeqs, outputFile, "square");  }
 449         #endif
 450
 451 #endif
 452                 if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
 453
 454                 #ifdef USE_MPI
 455                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 456
 457                         if (pid == 0) { //only one process should output to screen
 458                 #endif
 459
 460                 //if (output == "square") {  convertMatrix(outputFile); }
 461
 462                 ifstream fileHandle;
 463                 fileHandle.open(outputFile.c_str());
 464                 if(fileHandle) {
 465                         m->gobble(fileHandle);
 466                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 467                 }
 468
 469                 //append the old column file to the new one
 470                 if ((oldfastafile != "") && (column != ""))  {
 471                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 472                         if (outputFile == column) {
 473                                 string tempcolumn = column + ".old";
 474                                 m->appendFiles(tempcolumn, outputFile);
 475                                 m->mothurRemove(tempcolumn);
 476                         }else{
 477                                 m->appendFiles(outputFile, column);
 478                                 m->mothurRemove(outputFile);
 479                                 outputFile = column;
 480                         }
 481
 482                         if (outputDir != "") {
 483                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 484                                 rename(outputFile.c_str(), newOutputName.c_str());
 485                                 m->mothurRemove(outputFile);
 486                                 outputFile = newOutputName;
 487                         }
 488                 }
 489
 490
 491                 #ifdef USE_MPI
 492                         }
 493                 #endif
 494
 495                 if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
 496
 497                 delete distCalculator;
 498
 499                 //set phylip file as new current phylipfile
 500                 string current = "";
 501                 itTypes = outputTypes.find("phylip");
 502                 if (itTypes != outputTypes.end()) {
 503                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 504                 }
 505
 506                 //set column file as new current columnfile
 507                 itTypes = outputTypes.find("column");
 508                 if (itTypes != outputTypes.end()) {
 509                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 510                 }
 511
 512                 m->mothurOutEndLine();
 513                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 514                 m->mothurOut(outputFile); m->mothurOutEndLine();
 515                 m->mothurOutEndLine();
 516                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 517
 518
 519                 if (m->isTrue(compress)) {
 520                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 521                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 522                         system(("gzip -v " + outputFile).c_str());
 523                         outputNames.push_back(outputFile + ".gz");
 524                 }else { outputNames.push_back(outputFile); }
 525
 526                 return 0;
 527
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "DistanceCommand", "execute");
 531                 exit(1);
 532         }
 533 }
 534 /**************************************************************************************************/
 535 void DistanceCommand::createProcesses(string filename) {
 536         try {
 537 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 538                 int process = 1;
 539                 processIDS.clear();
 540
 541                 //loop through and create all the processes you want
 542                 while (process != processors) {
 543                         int pid = fork();
 544
 545                         if (pid > 0) {
 546                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 547                                 process++;
 548                         }else if (pid == 0){
 549                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 550                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 551                                 exit(0);
 552                         }else {
 553                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
 554                                 perror(" : ");
 555                                 for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 556                                 exit(0);
 557                         }
 558                 }
 559
 560                 //parent does its part
 561                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 562                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 563
 564
 565                 //force parent to wait until all the processes are done
 566                 for (int i=0;i<processIDS.size();i++) {
 567                         int temp = processIDS[i];
 568                         wait(&temp);
 569                 }
 570
 571                 //append and remove temp files
 572                 for (int i=0;i<processIDS.size();i++) {
 573                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 574                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 575                 }
 576 #endif
 577         }
 578         catch(exception& e) {
 579                 m->errorOut(e, "DistanceCommand", "createProcesses");
 580                 exit(1);
 581         }
 582 }
 583
 584 /**************************************************************************************************/
 585 /////// need to fix to work with calcs and sequencedb
 586 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 587         try {
 588
 589                 int startTime = time(NULL);
 590
 591                 //column file
 592                 ofstream outFile(dFileName.c_str(), ios::trunc);
 593                 outFile.setf(ios::fixed, ios::showpoint);
 594                 outFile << setprecision(4);
 595
 596                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 597
 598                 for(int i=startLine;i<endLine;i++){
 599                         if(output == "lt")      {
 600                                 string name = alignDB.get(i).getName();
 601                                 if (name.length() < 10) { //pad with spaces to make compatible
 602                                         while (name.length() < 10) {  name += " ";  }
 603                                 }
 604                                 outFile << name << '\t';
 605                         }
 606                         for(int j=0;j<i;j++){
 607
 608                                 if (m->control_pressed) { outFile.close(); return 0;  }
 609
 610                                 //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
 611                                 //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
 612                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 613
 614                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 615                                 double dist = distCalculator->getDist();
 616
 617                                 if(dist <= cutoff){
 618                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 619                                 }
 620                                 if (output == "lt") {  outFile << dist << '\t'; }
 621                         }
 622
 623                         if (output == "lt") { outFile << endl; }
 624
 625                         if(i % 100 == 0){
 626                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 627                         }
 628
 629                 }
 630                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 631
 632                 outFile.close();
 633
 634                 return 1;
 635         }
 636         catch(exception& e) {
 637                 m->errorOut(e, "DistanceCommand", "driver");
 638                 exit(1);
 639         }
 640 }
 641 /**************************************************************************************************/
 642 /////// need to fix to work with calcs and sequencedb
 643 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 644         try {
 645
 646                 int startTime = time(NULL);
 647
 648                 //column file
 649                 ofstream outFile(dFileName.c_str(), ios::trunc);
 650                 outFile.setf(ios::fixed, ios::showpoint);
 651                 outFile << setprecision(4);
 652
 653                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 654
 655                 for(int i=startLine;i<endLine;i++){
 656
 657                         string name = alignDB.get(i).getName();
 658                         //pad with spaces to make compatible
 659                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 660
 661                         outFile << name << '\t';
 662
 663                         for(int j=0;j<alignDB.getNumSeqs();j++){
 664
 665                                 if (m->control_pressed) { outFile.close(); return 0;  }
 666
 667                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 668                                 double dist = distCalculator->getDist();
 669
 670                                 outFile << dist << '\t';
 671                         }
 672
 673                         outFile << endl;
 674
 675                         if(i % 100 == 0){
 676                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 677                         }
 678
 679                 }
 680                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 681
 682                 outFile.close();
 683
 684                 return 1;
 685         }
 686         catch(exception& e) {
 687                 m->errorOut(e, "DistanceCommand", "driver");
 688                 exit(1);
 689         }
 690 }
 691 #ifdef USE_MPI
 692 /**************************************************************************************************/
 693 /////// need to fix to work with calcs and sequencedb
 694 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 695         try {
 696                 MPI_Status status;
 697                 int startTime = time(NULL);
 698
 699                 string outputString = "";
 700
 701                 for(int i=startLine;i<endLine;i++){
 702
 703                         for(int j=0;j<i;j++){
 704
 705                                 if (m->control_pressed) {  return 0;  }
 706
 707                                 //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
 708                                 //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
 709                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 710
 711                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 712                                 double dist = distCalculator->getDist();
 713
 714                                 if(dist <= cutoff){
 715                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 716                                 }
 717                         }
 718
 719                         if(i % 100 == 0){
 720                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 721                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 722                         }
 723
 724
 725                         //send results to parent
 726                         int length = outputString.length();
 727
 728                         char* buf = new char[length];
 729                         memcpy(buf, outputString.c_str(), length);
 730
 731                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 732                         outputString = "";
 733                         delete buf;
 734
 735                 }
 736
 737                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 738                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 739                 return 1;
 740         }
 741         catch(exception& e) {
 742                 m->errorOut(e, "DistanceCommand", "driverMPI");
 743                 exit(1);
 744         }
 745 }
 746 /**************************************************************************************************/
 747 /////// need to fix to work with calcs and sequencedb
 748 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 749         try {
 750                 MPI_Status status;
 751
 752                 MPI_File outMPI;
 753                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 754
 755                 //char* filename = new char[file.length()];
 756                 //memcpy(filename, file.c_str(), file.length());
 757
 758                 char filename[1024];
 759                 strcpy(filename, file.c_str());
 760
 761                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 762                 //delete filename;
 763
 764                 int startTime = time(NULL);
 765
 766                 string outputString = "";
 767                 size = 0;
 768
 769                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 770
 771                 for(int i=startLine;i<endLine;i++){
 772
 773                         string name = alignDB.get(i).getName();
 774                         if (name.length() < 10) { //pad with spaces to make compatible
 775                                 while (name.length() < 10) {  name += " ";  }
 776                         }
 777                         outputString += name + "\t";
 778
 779                         for(int j=0;j<i;j++){
 780
 781                                 if (m->control_pressed) {  return 0;  }
 782
 783                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 784                                 double dist = distCalculator->getDist();
 785
 786                                 outputString += toString(dist) + "\t";
 787                         }
 788
 789                         outputString += "\n";
 790
 791
 792                         if(i % 100 == 0){
 793                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 794                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 795                         }
 796
 797
 798                         //send results to parent
 799                         int length = outputString.length();
 800                         char* buf = new char[length];
 801                         memcpy(buf, outputString.c_str(), length);
 802
 803                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 804                         size += outputString.length();
 805                         outputString = "";
 806                         delete buf;
 807                 }
 808
 809                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 810                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 811                 MPI_File_close(&outMPI);
 812
 813                 return 1;
 814         }
 815         catch(exception& e) {
 816                 m->errorOut(e, "DistanceCommand", "driverMPI");
 817                 exit(1);
 818         }
 819 }
 820 /**************************************************************************************************/
 821 /////// need to fix to work with calcs and sequencedb
 822 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 823         try {
 824                 MPI_Status status;
 825
 826                 MPI_File outMPI;
 827                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 828
 829                 //char* filename = new char[file.length()];
 830                 //memcpy(filename, file.c_str(), file.length());
 831
 832                 char filename[1024];
 833                 strcpy(filename, file.c_str());
 834
 835                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 836                 //delete filename;
 837
 838                 int startTime = time(NULL);
 839
 840                 string outputString = "";
 841                 size = 0;
 842
 843                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 844
 845                 for(int i=startLine;i<endLine;i++){
 846
 847                         string name = alignDB.get(i).getName();
 848                         if (name.length() < 10) { //pad with spaces to make compatible
 849                                 while (name.length() < 10) {  name += " ";  }
 850                         }
 851                         outputString += name + "\t";
 852
 853                         for(int j=0;j<alignDB.getNumSeqs();j++){
 854
 855                                 if (m->control_pressed) {  return 0;  }
 856
 857                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 858                                 double dist = distCalculator->getDist();
 859
 860                                 outputString += toString(dist) + "\t";
 861                         }
 862
 863                         outputString += "\n";
 864
 865
 866                         if(i % 100 == 0){
 867                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 868                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 869                         }
 870
 871
 872                         //send results to parent
 873                         int length = outputString.length();
 874                         char* buf = new char[length];
 875                         memcpy(buf, outputString.c_str(), length);
 876
 877                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 878                         size += outputString.length();
 879                         outputString = "";
 880                         delete buf;
 881                 }
 882
 883                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 884                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 885                 MPI_File_close(&outMPI);
 886
 887                 return 1;
 888         }
 889         catch(exception& e) {
 890                 m->errorOut(e, "DistanceCommand", "driverMPI");
 891                 exit(1);
 892         }
 893 }
 894 #endif
 895 /**************************************************************************************************
 896 int DistanceCommand::convertMatrix(string outputFile) {
 897         try{
 898
 899                 //sort file by first column so the distances for each row are together
 900                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 901
 902                 //use the unix sort
 903                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 904                         string command = "sort -n " + outputFile + " -o " + outfile;
 905                         system(command.c_str());
 906                 #else //sort using windows sort
 907                         string command = "sort " + outputFile + " /O " + outfile;
 908                         system(command.c_str());
 909                 #endif
 910
 911
 912                 //output to new file distance for each row and save positions in file where new row begins
 913                 ifstream in;
 914                 m->openInputFile(outfile, in);
 915
 916                 ofstream out;
 917                 m->openOutputFile(outputFile, out);
 918
 919                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 920
 921                 out << alignDB.getNumSeqs() << endl;
 922
 923                 //get first currentRow
 924                 string first, currentRow, second;
 925                 float dist;
 926                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 927                 map<string, float>::iterator it;
 928
 929                 in >> first;
 930                 currentRow = first;
 931
 932                 rowDists[first] = 0.00; //distance to yourself is 0.0
 933
 934                 in.seekg(0);
 935                 //m->openInputFile(outfile, in);
 936
 937                 while(!in.eof()) {
 938                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
 939
 940                         in >> first >> second >> dist; m->gobble(in);
 941
 942                         if (first != currentRow) {
 943                                 //print out last row
 944                                 out << currentRow << '\t'; //print name
 945
 946                                 //print dists
 947                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 948                                         out << it->second << '\t';
 949                                 }
 950                                 out << endl;
 951
 952                                 //start new row
 953                                 currentRow = first;
 954                                 rowDists.clear();
 955                                 rowDists[first] = 0.00;
 956                                 rowDists[second] = dist;
 957                         }else{
 958                                 rowDists[second] = dist;
 959                         }
 960                 }
 961                 //print out last row
 962                 out << currentRow << '\t'; //print name
 963
 964                 //print dists
 965                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 966                         out << it->second << '\t';
 967                 }
 968                 out << endl;
 969
 970                 in.close();
 971                 out.close();
 972
 973                 m->mothurRemove(outfile);
 974
 975                 return 1;
 976
 977         }
 978         catch(exception& e) {
 979                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 980                 exit(1);
 981         }
 982 }
 983 /**************************************************************************************************
 984 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 985         try{
 986
 987                 //sort file by first column so the distances for each row are together
 988                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 989
 990                 //use the unix sort
 991                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 992                         string command = "sort -n " + outputFile + " -o " + outfile;
 993                         system(command.c_str());
 994                 #else //sort using windows sort
 995                         string command = "sort " + outputFile + " /O " + outfile;
 996                         system(command.c_str());
 997                 #endif
 998
 999
1000                 //output to new file distance for each row and save positions in file where new row begins
1001                 ifstream in;
1002                 m->openInputFile(outfile, in);
1003
1004                 ofstream out;
1005                 m->openOutputFile(outputFile, out);
1006
1007                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1008
1009                 out << alignDB.getNumSeqs() << endl;
1010
1011                 //get first currentRow
1012                 string first, currentRow, second;
1013                 float dist;
1014                 int i, j;
1015                 i = 0; j = 0;
1016                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1017                 map<string, float>::iterator it;
1018
1019                 in >> first;
1020                 currentRow = first;
1021
1022                 rowDists[first] = 0.00; //distance to yourself is 0.0
1023
1024                 in.seekg(0);
1025                 //m->openInputFile(outfile, in);
1026
1027                 while(!in.eof()) {
1028                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1029
1030                         in >> first >> second >> dist; m->gobble(in);
1031
1032                         if (first != currentRow) {
1033                                 //print out last row
1034                                 out << currentRow << '\t'; //print name
1035
1036                                 //print dists
1037                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1038                                         if (j >= i) { break; }
1039                                         out << it->second << '\t';
1040                                         j++;
1041                                 }
1042                                 out << endl;
1043
1044                                 //start new row
1045                                 currentRow = first;
1046                                 rowDists.clear();
1047                                 rowDists[first] = 0.00;
1048                                 rowDists[second] = dist;
1049                                 j = 0;
1050                                 i++;
1051                         }else{
1052                                 rowDists[second] = dist;
1053                         }
1054                 }
1055                 //print out last row
1056                 out << currentRow << '\t'; //print name
1057
1058                 //print dists
1059                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1060                         out << it->second << '\t';
1061                 }
1062                 out << endl;
1063
1064                 in.close();
1065                 out.close();
1066
1067                 m->mothurRemove(outfile);
1068
1069                 return 1;
1070
1071         }
1072         catch(exception& e) {
1073                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1074                 exit(1);
1075         }
1076 }
1077 /**************************************************************************************************/
1078 //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,
1079 //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.
1080 //also check to make sure the 2 files have the same alignment length.
1081 bool DistanceCommand::sanityCheck() {
1082         try{
1083                 bool good = true;
1084
1085                 //make sure the 2 fasta files have the same alignment length
1086                 ifstream in;
1087                 m->openInputFile(fastafile, in);
1088                 int fastaAlignLength = 0;
1089                 if (in) {
1090                         Sequence tempIn(in);
1091                         fastaAlignLength = tempIn.getAligned().length();
1092                 }
1093                 in.close();
1094
1095                 ifstream in2;
1096                 m->openInputFile(oldfastafile, in2);
1097                 int oldfastaAlignLength = 0;
1098                 if (in2) {
1099                         Sequence tempIn2(in2);
1100                         oldfastaAlignLength = tempIn2.getAligned().length();
1101                 }
1102                 in2.close();
1103
1104                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1105
1106                 //read fasta file and save names as well as adding them to the alignDB
1107                 set<string> namesOldFasta;
1108
1109                 ifstream inFasta;
1110                 m->openInputFile(oldfastafile, inFasta);
1111
1112                 while (!inFasta.eof()) {
1113                         if (m->control_pressed) {  inFasta.close(); return good;  }
1114
1115                         Sequence temp(inFasta);
1116
1117                         if (temp.getName() != "") {
1118                                 namesOldFasta.insert(temp.getName());  //save name
1119                                 alignDB.push_back(temp);  //add to DB
1120                         }
1121
1122                         m->gobble(inFasta);
1123                 }
1124
1125                 inFasta.close();
1126
1127                 //read through the column file checking names and removing distances above the cutoff
1128                 ifstream inDist;
1129                 m->openInputFile(column, inDist);
1130
1131                 ofstream outDist;
1132                 string outputFile = column + ".temp";
1133                 m->openOutputFile(outputFile, outDist);
1134
1135                 string name1, name2;
1136                 float dist;
1137                 while (!inDist.eof()) {
1138                         if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
1139
1140                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1141
1142                         //both names are in fasta file and distance is below cutoff
1143                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1144                         else{
1145                                 if (dist <= cutoff) {
1146                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1147                                 }
1148                         }
1149                 }
1150
1151                 inDist.close();
1152                 outDist.close();
1153
1154                 if (good) {
1155                         m->mothurRemove(column);
1156                         rename(outputFile.c_str(), column.c_str());
1157                 }else{
1158                         m->mothurRemove(outputFile); //temp file is bad because file mismatch above
1159                 }
1160
1161                 return good;
1162
1163         }
1164         catch(exception& e) {
1165                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1166                 exit(1);
1167         }
1168 }
1169 /**************************************************************************************************/
1170
1171
1172
1173