pairwiseseqscommand.cpp

   1 /*
   2  *  pairwiseseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/20/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "pairwiseseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 #include "gotohoverlap.hpp"
  14 #include "needlemanoverlap.hpp"
  15 #include "blastalign.hpp"
  16 #include "noalign.hpp"
  17 #include "nast.hpp"
  18
  19 #include "ignoregaps.h"
  20 #include "eachgapdist.h"
  21 #include "eachgapignore.h"
  22 #include "onegapdist.h"
  23 #include "onegapignore.h"
  24
  25
  26 //**********************************************************************************************************************
  27 vector<string> PairwiseSeqsCommand::getValidParameters(){
  28         try {
  29                 string AlignArray[] =  {"fasta","align","match","mismatch","gapopen","gapextend", "processors","calc","compress","cutoff","countends","output","outputdir","inputdir"};
  30                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "PairwiseSeqsCommand", "getValidParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> PairwiseSeqsCommand::getRequiredParameters(){
  40         try {
  41                 string AlignArray[] =  {"fasta"};
  42                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "PairwiseSeqsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> PairwiseSeqsCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "PairwiseSeqsCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 PairwiseSeqsCommand::PairwiseSeqsCommand(){
  63         try {
  64                 abort = true;
  65                 //initialize outputTypes
  66                 vector<string> tempOutNames;
  67                 outputTypes["phylip"] = tempOutNames;
  68                 outputTypes["column"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
  77         try {
  78                 abort = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; }
  82
  83                 else {
  84
  85                         //valid paramters for this command
  86                         string AlignArray[] =  {"fasta","align","match","mismatch","gapopen","gapextend", "processors","cutoff","compress","calc","countends","output","outputdir","inputdir"};
  87                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  88
  89                         OptionParser parser(option);
  90                         map<string, string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter("pairwise.seqs");
  93                         map<string, string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["phylip"] = tempOutNames;
 103                         outputTypes["column"] = tempOutNames;
 104
 105                         //if the user changes the output directory command factory will send this info to us in the output parameter
 106                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 107
 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
 112                         if (inputDir == "not found"){   inputDir = "";          }
 113
 114                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 115                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the pairwise.seqs command."); m->mothurOutEndLine(); abort = true;  }
 116                         else {
 117                                 m->splitAtDash(fastaFileName, fastaFileNames);
 118
 119                                 //go through files and make sure they are good, if not, then disregard them
 120                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 121
 122                                         if (inputDir != "") {
 123                                                 string path = m->hasPath(fastaFileNames[i]);
 124                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 125                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 126                                         }
 127
 128                                         int ableToOpen;
 129                                         ifstream in;
 130
 131                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 132
 133                                         //if you can't open it, try default location
 134                                         if (ableToOpen == 1) {
 135                                                 if (m->getDefaultPath() != "") { //default path is set
 136                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 137                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 138                                                         ifstream in2;
 139                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 140                                                         in2.close();
 141                                                         fastaFileNames[i] = tryPath;
 142                                                 }
 143                                         }
 144
 145                                         //if you can't open it, try output location
 146                                         if (ableToOpen == 1) {
 147                                                 if (m->getOutputDir() != "") { //default path is set
 148                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 149                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 150                                                         ifstream in2;
 151                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 152                                                         in2.close();
 153                                                         fastaFileNames[i] = tryPath;
 154                                                 }
 155                                         }
 156
 157                                         in.close();
 158
 159                                         if (ableToOpen == 1) {
 160                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 161                                                 //erase from file list
 162                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 163                                                 i--;
 164                                         }
 165                                 }
 166
 167                                 //make sure there is at least one valid file left
 168                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 169                         }
 170
 171                         //check for optional parameter and set defaults
 172                         // ...at some point should added some additional type checking...
 173                         string temp;
 174                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 175                         convert(temp, match);
 176
 177                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 178                         convert(temp, misMatch);
 179
 180                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 181                         convert(temp, gapOpen);
 182
 183                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 184                         convert(temp, gapExtend);
 185
 186                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 187                         convert(temp, processors);
 188
 189                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 190                         convert(temp, cutoff);
 191
 192                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 193                         countends = m->isTrue(temp);
 194
 195                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 196                         compress = m->isTrue(temp);
 197
 198                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 199
 200                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 201                         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"; }
 202
 203                         calc = validParameter.validFile(parameters, "calc", false);
 204                         if (calc == "not found") { calc = "onegap";  }
 205                         else {
 206                                  if (calc == "default")  {  calc = "onegap";  }
 207                         }
 208                         m->splitAtDash(calc, Estimators);
 209
 210                         ValidCalculators validCalculator;
 211                         if (countends) {
 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 eachGapDist();     }
 216                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 217                                         }
 218                                 }
 219                         }else {
 220                                 for (int i=0; i<Estimators.size(); i++) {
 221                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 222                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 223                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 224                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 225                                         }
 226                                 }
 227                         }
 228                 }
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
 233                 exit(1);
 234         }
 235 }
 236 //**********************************************************************************************************************
 237 PairwiseSeqsCommand::~PairwiseSeqsCommand(){}
 238 //**********************************************************************************************************************
 239
 240 void PairwiseSeqsCommand::help(){
 241         try {
 242                 m->mothurOut("The pairwise.seqs command reads a fasta file and creates distance matrix.\n");
 243                 m->mothurOut("The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n");
 244                 m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 245                 m->mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
 246                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 247                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 248                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 249                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 250                 m->mothurOut("The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
 251                 m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n");
 252                 m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
 253                 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
 254                 m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n");
 255                 m->mothurOut("The pairwise.seqs command should be in the following format: \n");
 256                 m->mothurOut("pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n");
 257                 m->mothurOut("Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n");
 258                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "PairwiseSeqsCommand", "help");
 262                 exit(1);
 263         }
 264 }
 265
 266
 267 //**********************************************************************************************************************
 268
 269 int PairwiseSeqsCommand::execute(){
 270         try {
 271                 if (abort == true) {    return 0;       }
 272
 273                 int longestBase = 2000; //will need to update this in driver if we find sequences with more bases.  hardcoded so we don't have the pre-read user fasta file.
 274
 275                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 276                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 277                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 278                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 279                 else {
 280                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 281                         m->mothurOutEndLine();
 282                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 283                 }
 284
 285                 cutoff += 0.005;
 286
 287                 for (int s = 0; s < fastaFileNames.size(); s++) {
 288                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 289
 290                         m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 291
 292                         if (outputDir == "") {  outputDir += m->hasPath(fastaFileNames[s]); }
 293
 294                         ifstream inFASTA;
 295                         m->openInputFile(fastaFileNames[s], inFASTA);
 296                         alignDB = SequenceDB(inFASTA);
 297                         inFASTA.close();
 298
 299                         int numSeqs = alignDB.getNumSeqs();
 300                         int startTime = time(NULL);
 301                         string outputFile = "";
 302
 303                         if (output == "lt") { //does the user want lower triangle phylip formatted file
 304                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
 305                                 remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
 306                         }else if (output == "column") { //user wants column format
 307                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
 308                                 outputTypes["column"].push_back(outputFile);
 309                                 remove(outputFile.c_str());
 310                         }else { //assume square
 311                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
 312                                 remove(outputFile.c_str());
 313                                 outputTypes["phylip"].push_back(outputFile);
 314                         }
 315
 316                         #ifdef USE_MPI
 317
 318                         int pid, start, end;
 319                         int tag = 2001;
 320
 321                         MPI_Status status;
 322                         MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 323                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 324
 325                         //each process gets where it should start and stop in the file
 326                         if (output != "square") {
 327                                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 328                                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 329                         }else{
 330                                 start = int ((float(pid)/float(processors)) * numSeqs);
 331                                 end = int ((float(pid+1)/float(processors)) * numSeqs);
 332                         }
 333
 334                         if (output == "column") {
 335                                 MPI_File outMPI;
 336                                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 337
 338                         char filename[1024];
 339                                 strcpy(filename, outputFile.c_str());
 340
 341                                 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 342
 343                                 if (pid == 0) { //you are the root process
 344
 345                                         //do your part
 346                                         string outputMyPart;
 347
 348                                         driverMPI(start, end, outMPI, cutoff);
 349
 350                                         if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 351
 352                                         //wait on chidren
 353                                         for(int i = 1; i < processors; i++) {
 354                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 355
 356                                                 char buf[5];
 357                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 358                                         }
 359                                 }else { //you are a child process
 360                                         //do your part
 361                                         driverMPI(start, end, outMPI, cutoff);
 362
 363                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 364
 365                                         char buf[5];
 366                                         strcpy(buf, "done");
 367                                         //tell parent you are done.
 368                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 369                                 }
 370
 371                                 MPI_File_close(&outMPI);
 372
 373                         }else { //lower triangle format
 374                                 if (pid == 0) { //you are the root process
 375
 376                                         //do your part
 377                                         string outputMyPart;
 378                                         unsigned long int mySize;
 379
 380                                         if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 381                                         else { driverMPI(start, end, outputFile, mySize, output); }
 382
 383                                         if (m->control_pressed) {  outputTypes.clear();   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 384
 385                                         int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 386                                         MPI_File outMPI;
 387                                         MPI_File inMPI;
 388
 389                                         char filename[1024];
 390                                         strcpy(filename, outputFile.c_str());
 391
 392                                         MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 393
 394                                         //wait on chidren
 395                                         for(int b = 1; b < processors; b++) {
 396                                                 unsigned long int fileSize;
 397
 398                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str());  delete distCalculator;  return 0; }
 399
 400                                                 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 401
 402                                                 string outTemp = outputFile + toString(b) + ".temp";
 403
 404                                                 char* buf = new char[outTemp.length()];
 405                                                 memcpy(buf, outTemp.c_str(), outTemp.length());
 406
 407                                                 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 408                                                 delete buf;
 409
 410                                                 int count = 0;
 411                                                 while (count < fileSize) {
 412                                                         char buf2[1];
 413                                                         MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 414                                                         MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 415                                                         count += 1;
 416                                                 }
 417
 418                                                 MPI_File_close(&inMPI); //deleted on close
 419                                         }
 420
 421                                         MPI_File_close(&outMPI);
 422                                 }else { //you are a child process
 423                                         //do your part
 424                                         unsigned long int size;
 425                                         if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 426                                         else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 427
 428                                         if (m->control_pressed) { delete distCalculator;  return 0; }
 429
 430                                         //tell parent you are done.
 431                                         MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 432                                 }
 433                         }
 434                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 435         #else
 436
 437                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 438                         //if you don't need to fork anything
 439                         if(processors == 1){
 440                                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 441                                 else { driver(0, numSeqs, outputFile, "square");  }
 442                         }else{ //you have multiple processors
 443
 444                                 for (int i = 0; i < processors; i++) {
 445                                         distlinePair tempLine;
 446                                         lines.push_back(tempLine);
 447                                         if (output != "square") {
 448                                                 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 449                                                 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 450                                         }else{
 451                                                 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 452                                                 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 453                                         }
 454                                 }
 455
 456                                 createProcesses(outputFile);
 457                         }
 458                 #else
 459                         //ifstream inFASTA;
 460                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 461                         else { driver(0, numSeqs, outputFile, "square");  }
 462                 #endif
 463
 464         #endif
 465                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 466
 467                         #ifdef USE_MPI
 468                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 469
 470                                 if (pid == 0) { //only one process should output to screen
 471                         #endif
 472
 473                         ifstream fileHandle;
 474                         fileHandle.open(outputFile.c_str());
 475                         if(fileHandle) {
 476                                 m->gobble(fileHandle);
 477                                 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 478                         }
 479
 480                         if (compress) {
 481                                 m->mothurOut("Compressing..."); m->mothurOutEndLine();
 482                                 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 483                                 system(("gzip -v " + outputFile).c_str());
 484                                 outputNames.push_back(outputFile + ".gz");
 485                         }else { outputNames.push_back(outputFile); }
 486
 487                         #ifdef USE_MPI
 488                                 }
 489                         #endif
 490
 491                         m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 492
 493                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 494                 }
 495
 496                 delete distCalculator;
 497
 498                 m->mothurOutEndLine();
 499                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 500                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 501                 m->mothurOutEndLine();
 502
 503
 504                 return 0;
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "PairwiseSeqsCommand", "execute");
 508                 exit(1);
 509         }
 510 }
 511
 512 /**************************************************************************************************/
 513 void PairwiseSeqsCommand::createProcesses(string filename) {
 514         try {
 515 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 516                 int process = 1;
 517                 processIDS.clear();
 518
 519                 //loop through and create all the processes you want
 520                 while (process != processors) {
 521                         int pid = fork();
 522
 523                         if (pid > 0) {
 524                                 processIDS.push_back(pid);
 525                                 process++;
 526                         }else if (pid == 0){
 527                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 528                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 529                                 exit(0);
 530                         }else {
 531                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 532                                 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
 533                                 exit(0);
 534                         }
 535                 }
 536
 537                 //parent do my part
 538                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 539                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 540
 541
 542                 //force parent to wait until all the processes are done
 543                 for (int i=0;i<processIDS.size();i++) {
 544                         int temp = processIDS[i];
 545                         wait(&temp);
 546                 }
 547
 548                 //append and remove temp files
 549                 for (int i=0;i<processIDS.size();i++) {
 550                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 551                         remove((filename + toString(processIDS[i]) + ".temp").c_str());
 552                 }
 553 #endif
 554         }
 555         catch(exception& e) {
 556                 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
 557                 exit(1);
 558         }
 559 }
 560
 561 /**************************************************************************************************/
 562 /////// need to fix to work with calcs and sequencedb
 563 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 564         try {
 565
 566                 int startTime = time(NULL);
 567
 568                 //column file
 569                 ofstream outFile(dFileName.c_str(), ios::trunc);
 570                 outFile.setf(ios::fixed, ios::showpoint);
 571                 outFile << setprecision(4);
 572
 573                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 574
 575                 for(int i=startLine;i<endLine;i++){
 576                         if(output == "lt")      {
 577                                 string name = alignDB.get(i).getName();
 578                                 if (name.length() < 10) { //pad with spaces to make compatible
 579                                         while (name.length() < 10) {  name += " ";  }
 580                                 }
 581                                 outFile << name << '\t';
 582                         }
 583
 584                         for(int j=0;j<i;j++){
 585
 586                                 if (m->control_pressed) { outFile.close(); return 0;  }
 587
 588                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 589                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 590                                 }
 591
 592                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 593                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 594                                 }
 595
 596                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 597                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 598
 599                                 Nast(alignment, seqI, seqJ);
 600
 601                                 distCalculator->calcDist(*seqI, *seqJ);
 602                                 double dist = distCalculator->getDist();
 603
 604                                 delete seqI; delete seqJ;
 605
 606                                 if(dist <= cutoff){
 607                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 608                                 }
 609                                 if (output == "lt") {  outFile << dist << '\t'; }
 610                         }
 611
 612                         if (output == "lt") { outFile << endl; }
 613
 614                         if(i % 100 == 0){
 615                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 616                         }
 617
 618                 }
 619                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 620
 621                 outFile.close();
 622
 623                 return 1;
 624         }
 625         catch(exception& e) {
 626                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 627                 exit(1);
 628         }
 629 }
 630 /**************************************************************************************************/
 631 /////// need to fix to work with calcs and sequencedb
 632 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
 633         try {
 634
 635                 int startTime = time(NULL);
 636
 637                 //column file
 638                 ofstream outFile(dFileName.c_str(), ios::trunc);
 639                 outFile.setf(ios::fixed, ios::showpoint);
 640                 outFile << setprecision(4);
 641
 642                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 643
 644                 for(int i=startLine;i<endLine;i++){
 645
 646                         string name = alignDB.get(i).getName();
 647                         //pad with spaces to make compatible
 648                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 649
 650                         outFile << name << '\t';
 651
 652                         for(int j=0;j<alignDB.getNumSeqs();j++){
 653
 654                                 if (m->control_pressed) { outFile.close(); return 0;  }
 655
 656                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 657                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 658                                 }
 659
 660                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 661                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 662                                 }
 663
 664                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 665                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 666
 667                                 Nast(alignment, seqI, seqJ);
 668
 669                                 distCalculator->calcDist(*seqI, *seqJ);
 670                                 double dist = distCalculator->getDist();
 671
 672                                 delete seqI; delete seqJ;
 673
 674                                 outFile << dist << '\t';
 675                         }
 676
 677                         outFile << endl;
 678
 679                         if(i % 100 == 0){
 680                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 681                         }
 682
 683                 }
 684                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 685
 686                 outFile.close();
 687
 688                 return 1;
 689         }
 690         catch(exception& e) {
 691                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 692                 exit(1);
 693         }
 694 }
 695 #ifdef USE_MPI
 696 /**************************************************************************************************/
 697 /////// need to fix to work with calcs and sequencedb
 698 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 699         try {
 700                 MPI_Status status;
 701                 int startTime = time(NULL);
 702
 703                 string outputString = "";
 704
 705                 for(int i=startLine;i<endLine;i++){
 706
 707                         for(int j=0;j<i;j++){
 708
 709                                 if (m->control_pressed) {  return 0;  }
 710
 711                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 712                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 713                                 }
 714
 715                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 716                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 717                                 }
 718
 719                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 720                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 721
 722                                 Nast(alignment, seqI, seqJ);
 723
 724                                 distCalculator->calcDist(*seqI, *seqJ);
 725                                 double dist = distCalculator->getDist();
 726
 727                                 delete seqI; delete seqJ;
 728
 729                                 if(dist <= cutoff){
 730                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 731                                 }
 732                         }
 733
 734                         if(i % 100 == 0){
 735                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 736                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 737                         }
 738
 739
 740                         //send results to parent
 741                         int length = outputString.length();
 742
 743                         char* buf = new char[length];
 744                         memcpy(buf, outputString.c_str(), length);
 745
 746                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 747                         outputString = "";
 748                         delete buf;
 749
 750                 }
 751
 752                 return 1;
 753         }
 754         catch(exception& e) {
 755                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 756                 exit(1);
 757         }
 758 }
 759 /**************************************************************************************************/
 760 /////// need to fix to work with calcs and sequencedb
 761 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 762         try {
 763                 MPI_Status status;
 764
 765                 MPI_File outMPI;
 766                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 767
 768                 char filename[1024];
 769                 strcpy(filename, file.c_str());
 770
 771                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 772
 773                 int startTime = time(NULL);
 774
 775                 string outputString = "";
 776                 size = 0;
 777
 778                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 779
 780                 for(int i=startLine;i<endLine;i++){
 781
 782                         string name = alignDB.get(i).getName();
 783                         if (name.length() < 10) { //pad with spaces to make compatible
 784                                 while (name.length() < 10) {  name += " ";  }
 785                         }
 786                         outputString += name + "\t";
 787
 788                         for(int j=0;j<i;j++){
 789
 790                                 if (m->control_pressed) {  return 0;  }
 791
 792                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 793                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 794                                 }
 795
 796                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 797                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 798                                 }
 799
 800                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 801                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 802
 803                                 Nast(alignment, seqI, seqJ);
 804
 805                                 distCalculator->calcDist(*seqI, *seqJ);
 806                                 double dist = distCalculator->getDist();
 807
 808                                 delete seqI; delete seqJ;
 809
 810                                 outputString += toString(dist) + "\t";
 811                         }
 812
 813                         outputString += "\n";
 814
 815                         //send results to parent
 816                         int length = outputString.length();
 817                         char* buf = new char[length];
 818                         memcpy(buf, outputString.c_str(), length);
 819
 820                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 821                         size += outputString.length();
 822                         outputString = "";
 823                         delete buf;
 824                 }
 825
 826                 MPI_File_close(&outMPI);
 827
 828                 return 1;
 829         }
 830         catch(exception& e) {
 831                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 832                 exit(1);
 833         }
 834 }
 835 /**************************************************************************************************/
 836 /////// need to fix to work with calcs and sequencedb
 837 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 838         try {
 839                 MPI_Status status;
 840
 841                 MPI_File outMPI;
 842                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 843
 844                 char filename[1024];
 845                 strcpy(filename, file.c_str());
 846
 847                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 848
 849                 int startTime = time(NULL);
 850
 851                 string outputString = "";
 852                 size = 0;
 853
 854                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 855
 856                 for(int i=startLine;i<endLine;i++){
 857
 858                         string name = alignDB.get(i).getName();
 859                         if (name.length() < 10) { //pad with spaces to make compatible
 860                                 while (name.length() < 10) {  name += " ";  }
 861                         }
 862                         outputString += name + "\t";
 863
 864                         for(int j=0;j<alignDB.getNumSeqs();j++){
 865
 866                                 if (m->control_pressed) {  return 0;  }
 867
 868                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 869                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 870                                 }
 871
 872                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 873                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 874                                 }
 875
 876                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 877                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 878
 879                                 Nast(alignment, seqI, seqJ);
 880
 881                                 distCalculator->calcDist(*seqI, *seqJ);
 882                                 double dist = distCalculator->getDist();
 883
 884                                 delete seqI; delete seqJ;
 885
 886                                 outputString += toString(dist) + "\t";
 887                         }
 888
 889                         outputString += "\n";
 890
 891                         //send results to parent
 892                         int length = outputString.length();
 893                         char* buf = new char[length];
 894                         memcpy(buf, outputString.c_str(), length);
 895
 896                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 897                         size += outputString.length();
 898                         outputString = "";
 899                         delete buf;
 900                 }
 901
 902                 MPI_File_close(&outMPI);
 903
 904                 return 1;
 905         }
 906         catch(exception& e) {
 907                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 908                 exit(1);
 909         }
 910 }
 911 #endif
 912 /**************************************************************************************************/
 913