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; calledHelp = true;
  65                 vector<string> tempOutNames;
  66                 outputTypes["phylip"] = tempOutNames;
  67                 outputTypes["column"] = tempOutNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
  76         try {
  77                 abort = false; calledHelp = false;
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81
  82                 else {
  83
  84                         //valid paramters for this command
  85                         string AlignArray[] =  {"fasta","align","match","mismatch","gapopen","gapextend", "processors","cutoff","compress","calc","countends","output","outputdir","inputdir"};
  86                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  87
  88                         OptionParser parser(option);
  89                         map<string, string> parameters = parser.getParameters();
  90
  91                         ValidParameters validParameter("pairwise.seqs");
  92                         map<string, string>::iterator it;
  93
  94                         //check to make sure all parameters are valid for command
  95                         for (it = parameters.begin(); it != parameters.end(); it++) {
  96                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["phylip"] = tempOutNames;
 102                         outputTypes["column"] = tempOutNames;
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 106
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110
 111                         if (inputDir == "not found"){   inputDir = "";          }
 112
 113                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 114                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the pairwise.seqs command."); m->mothurOutEndLine(); abort = true;  }
 115                         else {
 116                                 m->splitAtDash(fastaFileName, fastaFileNames);
 117
 118                                 //go through files and make sure they are good, if not, then disregard them
 119                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 120
 121                                         if (inputDir != "") {
 122                                                 string path = m->hasPath(fastaFileNames[i]);
 123                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 124                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 125                                         }
 126
 127                                         int ableToOpen;
 128                                         ifstream in;
 129
 130                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 131
 132                                         //if you can't open it, try default location
 133                                         if (ableToOpen == 1) {
 134                                                 if (m->getDefaultPath() != "") { //default path is set
 135                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 136                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 137                                                         ifstream in2;
 138                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 139                                                         in2.close();
 140                                                         fastaFileNames[i] = tryPath;
 141                                                 }
 142                                         }
 143
 144                                         //if you can't open it, try output location
 145                                         if (ableToOpen == 1) {
 146                                                 if (m->getOutputDir() != "") { //default path is set
 147                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 148                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 149                                                         ifstream in2;
 150                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 151                                                         in2.close();
 152                                                         fastaFileNames[i] = tryPath;
 153                                                 }
 154                                         }
 155
 156                                         in.close();
 157
 158                                         if (ableToOpen == 1) {
 159                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 160                                                 //erase from file list
 161                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 162                                                 i--;
 163                                         }
 164                                 }
 165
 166                                 //make sure there is at least one valid file left
 167                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 168                         }
 169
 170                         //check for optional parameter and set defaults
 171                         // ...at some point should added some additional type checking...
 172                         string temp;
 173                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 174                         convert(temp, match);
 175
 176                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 177                         convert(temp, misMatch);
 178
 179                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 180                         convert(temp, gapOpen);
 181
 182                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 183                         convert(temp, gapExtend);
 184
 185                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 186                         convert(temp, processors);
 187
 188                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 189                         convert(temp, cutoff);
 190
 191                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 192                         countends = m->isTrue(temp);
 193
 194                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 195                         compress = m->isTrue(temp);
 196
 197                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 198
 199                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 200                         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"; }
 201
 202                         calc = validParameter.validFile(parameters, "calc", false);
 203                         if (calc == "not found") { calc = "onegap";  }
 204                         else {
 205                                  if (calc == "default")  {  calc = "onegap";  }
 206                         }
 207                         m->splitAtDash(calc, Estimators);
 208
 209                         ValidCalculators validCalculator;
 210                         if (countends) {
 211                                 for (int i=0; i<Estimators.size(); i++) {
 212                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 213                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 214                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 215                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 216                                         }
 217                                 }
 218                         }else {
 219                                 for (int i=0; i<Estimators.size(); i++) {
 220                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 221                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 222                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 223                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 224                                         }
 225                                 }
 226                         }
 227                 }
 228
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
 232                 exit(1);
 233         }
 234 }
 235 //**********************************************************************************************************************
 236 PairwiseSeqsCommand::~PairwiseSeqsCommand(){}
 237 //**********************************************************************************************************************
 238
 239 void PairwiseSeqsCommand::help(){
 240         try {
 241                 m->mothurOut("The pairwise.seqs command reads a fasta file and creates distance matrix.\n");
 242                 m->mothurOut("The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n");
 243                 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");
 244                 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");
 245                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 246                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 247                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 248                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 249                 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");
 250                 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");
 251                 m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
 252                 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");
 253                 m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n");
 254                 m->mothurOut("The pairwise.seqs command should be in the following format: \n");
 255                 m->mothurOut("pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n");
 256                 m->mothurOut("Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n");
 257                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 258         }
 259         catch(exception& e) {
 260                 m->errorOut(e, "PairwiseSeqsCommand", "help");
 261                 exit(1);
 262         }
 263 }
 264
 265
 266 //**********************************************************************************************************************
 267
 268 int PairwiseSeqsCommand::execute(){
 269         try {
 270                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 271
 272                 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.
 273
 274                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 275                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 276                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 277                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 278                 else {
 279                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 280                         m->mothurOutEndLine();
 281                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 282                 }
 283
 284                 cutoff += 0.005;
 285
 286                 for (int s = 0; s < fastaFileNames.size(); s++) {
 287                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 288
 289                         m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 290
 291                         if (outputDir == "") {  outputDir += m->hasPath(fastaFileNames[s]); }
 292
 293                         ifstream inFASTA;
 294                         m->openInputFile(fastaFileNames[s], inFASTA);
 295                         alignDB = SequenceDB(inFASTA);
 296                         inFASTA.close();
 297
 298                         int numSeqs = alignDB.getNumSeqs();
 299                         int startTime = time(NULL);
 300                         string outputFile = "";
 301
 302                         if (output == "lt") { //does the user want lower triangle phylip formatted file
 303                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
 304                                 remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
 305                         }else if (output == "column") { //user wants column format
 306                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
 307                                 outputTypes["column"].push_back(outputFile);
 308                                 remove(outputFile.c_str());
 309                         }else { //assume square
 310                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
 311                                 remove(outputFile.c_str());
 312                                 outputTypes["phylip"].push_back(outputFile);
 313                         }
 314
 315                         #ifdef USE_MPI
 316
 317                         int pid, start, end;
 318                         int tag = 2001;
 319
 320                         MPI_Status status;
 321                         MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 322                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 323
 324                         //each process gets where it should start and stop in the file
 325                         if (output != "square") {
 326                                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 327                                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 328                         }else{
 329                                 start = int ((float(pid)/float(processors)) * numSeqs);
 330                                 end = int ((float(pid+1)/float(processors)) * numSeqs);
 331                         }
 332
 333                         if (output == "column") {
 334                                 MPI_File outMPI;
 335                                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 336
 337                         char filename[1024];
 338                                 strcpy(filename, outputFile.c_str());
 339
 340                                 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 341
 342                                 if (pid == 0) { //you are the root process
 343
 344                                         //do your part
 345                                         string outputMyPart;
 346
 347                                         driverMPI(start, end, outMPI, cutoff);
 348
 349                                         if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 350
 351                                         //wait on chidren
 352                                         for(int i = 1; i < processors; i++) {
 353                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 354
 355                                                 char buf[5];
 356                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 357                                         }
 358                                 }else { //you are a child process
 359                                         //do your part
 360                                         driverMPI(start, end, outMPI, cutoff);
 361
 362                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 363
 364                                         char buf[5];
 365                                         strcpy(buf, "done");
 366                                         //tell parent you are done.
 367                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 368                                 }
 369
 370                                 MPI_File_close(&outMPI);
 371
 372                         }else { //lower triangle format
 373                                 if (pid == 0) { //you are the root process
 374
 375                                         //do your part
 376                                         string outputMyPart;
 377                                         unsigned long int mySize;
 378
 379                                         if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 380                                         else { driverMPI(start, end, outputFile, mySize, output); }
 381
 382                                         if (m->control_pressed) {  outputTypes.clear();   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 383
 384                                         int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 385                                         MPI_File outMPI;
 386                                         MPI_File inMPI;
 387
 388                                         char filename[1024];
 389                                         strcpy(filename, outputFile.c_str());
 390
 391                                         MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 392
 393                                         //wait on chidren
 394                                         for(int b = 1; b < processors; b++) {
 395                                                 unsigned long int fileSize;
 396
 397                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str());  delete distCalculator;  return 0; }
 398
 399                                                 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 400
 401                                                 string outTemp = outputFile + toString(b) + ".temp";
 402
 403                                                 char* buf = new char[outTemp.length()];
 404                                                 memcpy(buf, outTemp.c_str(), outTemp.length());
 405
 406                                                 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 407                                                 delete buf;
 408
 409                                                 int count = 0;
 410                                                 while (count < fileSize) {
 411                                                         char buf2[1];
 412                                                         MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 413                                                         MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 414                                                         count += 1;
 415                                                 }
 416
 417                                                 MPI_File_close(&inMPI); //deleted on close
 418                                         }
 419
 420                                         MPI_File_close(&outMPI);
 421                                 }else { //you are a child process
 422                                         //do your part
 423                                         unsigned long int size;
 424                                         if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 425                                         else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 426
 427                                         if (m->control_pressed) { delete distCalculator;  return 0; }
 428
 429                                         //tell parent you are done.
 430                                         MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 431                                 }
 432                         }
 433                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 434         #else
 435
 436                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 437                         //if you don't need to fork anything
 438                         if(processors == 1){
 439                                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 440                                 else { driver(0, numSeqs, outputFile, "square");  }
 441                         }else{ //you have multiple processors
 442
 443                                 for (int i = 0; i < processors; i++) {
 444                                         distlinePair tempLine;
 445                                         lines.push_back(tempLine);
 446                                         if (output != "square") {
 447                                                 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 448                                                 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 449                                         }else{
 450                                                 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 451                                                 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 452                                         }
 453                                 }
 454
 455                                 createProcesses(outputFile);
 456                         }
 457                 #else
 458                         //ifstream inFASTA;
 459                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 460                         else { driver(0, numSeqs, outputFile, "square");  }
 461                 #endif
 462
 463         #endif
 464                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 465
 466                         #ifdef USE_MPI
 467                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 468
 469                                 if (pid == 0) { //only one process should output to screen
 470                         #endif
 471
 472                         ifstream fileHandle;
 473                         fileHandle.open(outputFile.c_str());
 474                         if(fileHandle) {
 475                                 m->gobble(fileHandle);
 476                                 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 477                         }
 478
 479                         if (compress) {
 480                                 m->mothurOut("Compressing..."); m->mothurOutEndLine();
 481                                 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 482                                 system(("gzip -v " + outputFile).c_str());
 483                                 outputNames.push_back(outputFile + ".gz");
 484                         }else { outputNames.push_back(outputFile); }
 485
 486                         #ifdef USE_MPI
 487                                 }
 488                         #endif
 489
 490                         m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 491
 492                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 493                 }
 494
 495                 delete distCalculator;
 496
 497                 m->mothurOutEndLine();
 498                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 499                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 500                 m->mothurOutEndLine();
 501
 502
 503                 return 0;
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "PairwiseSeqsCommand", "execute");
 507                 exit(1);
 508         }
 509 }
 510
 511 /**************************************************************************************************/
 512 void PairwiseSeqsCommand::createProcesses(string filename) {
 513         try {
 514 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 515                 int process = 1;
 516                 processIDS.clear();
 517
 518                 //loop through and create all the processes you want
 519                 while (process != processors) {
 520                         int pid = fork();
 521
 522                         if (pid > 0) {
 523                                 processIDS.push_back(pid);
 524                                 process++;
 525                         }else if (pid == 0){
 526                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 527                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 528                                 exit(0);
 529                         }else {
 530                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 531                                 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
 532                                 exit(0);
 533                         }
 534                 }
 535
 536                 //parent do my part
 537                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 538                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 539
 540
 541                 //force parent to wait until all the processes are done
 542                 for (int i=0;i<processIDS.size();i++) {
 543                         int temp = processIDS[i];
 544                         wait(&temp);
 545                 }
 546
 547                 //append and remove temp files
 548                 for (int i=0;i<processIDS.size();i++) {
 549                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 550                         remove((filename + toString(processIDS[i]) + ".temp").c_str());
 551                 }
 552 #endif
 553         }
 554         catch(exception& e) {
 555                 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
 556                 exit(1);
 557         }
 558 }
 559
 560 /**************************************************************************************************/
 561 /////// need to fix to work with calcs and sequencedb
 562 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 563         try {
 564
 565                 int startTime = time(NULL);
 566
 567                 //column file
 568                 ofstream outFile(dFileName.c_str(), ios::trunc);
 569                 outFile.setf(ios::fixed, ios::showpoint);
 570                 outFile << setprecision(4);
 571
 572                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 573
 574                 for(int i=startLine;i<endLine;i++){
 575                         if(output == "lt")      {
 576                                 string name = alignDB.get(i).getName();
 577                                 if (name.length() < 10) { //pad with spaces to make compatible
 578                                         while (name.length() < 10) {  name += " ";  }
 579                                 }
 580                                 outFile << name << '\t';
 581                         }
 582
 583                         for(int j=0;j<i;j++){
 584
 585                                 if (m->control_pressed) { outFile.close(); return 0;  }
 586
 587                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 588                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 589                                 }
 590
 591                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 592                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 593                                 }
 594
 595                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 596                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 597
 598                                 Nast(alignment, seqI, seqJ);
 599
 600                                 distCalculator->calcDist(*seqI, *seqJ);
 601                                 double dist = distCalculator->getDist();
 602
 603                                 delete seqI; delete seqJ;
 604
 605                                 if(dist <= cutoff){
 606                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 607                                 }
 608                                 if (output == "lt") {  outFile << dist << '\t'; }
 609                         }
 610
 611                         if (output == "lt") { outFile << endl; }
 612
 613                         if(i % 100 == 0){
 614                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 615                         }
 616
 617                 }
 618                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 619
 620                 outFile.close();
 621
 622                 return 1;
 623         }
 624         catch(exception& e) {
 625                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 626                 exit(1);
 627         }
 628 }
 629 /**************************************************************************************************/
 630 /////// need to fix to work with calcs and sequencedb
 631 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
 632         try {
 633
 634                 int startTime = time(NULL);
 635
 636                 //column file
 637                 ofstream outFile(dFileName.c_str(), ios::trunc);
 638                 outFile.setf(ios::fixed, ios::showpoint);
 639                 outFile << setprecision(4);
 640
 641                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 642
 643                 for(int i=startLine;i<endLine;i++){
 644
 645                         string name = alignDB.get(i).getName();
 646                         //pad with spaces to make compatible
 647                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 648
 649                         outFile << name << '\t';
 650
 651                         for(int j=0;j<alignDB.getNumSeqs();j++){
 652
 653                                 if (m->control_pressed) { outFile.close(); return 0;  }
 654
 655                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 656                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 657                                 }
 658
 659                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 660                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 661                                 }
 662
 663                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 664                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 665
 666                                 Nast(alignment, seqI, seqJ);
 667
 668                                 distCalculator->calcDist(*seqI, *seqJ);
 669                                 double dist = distCalculator->getDist();
 670
 671                                 delete seqI; delete seqJ;
 672
 673                                 outFile << dist << '\t';
 674                         }
 675
 676                         outFile << endl;
 677
 678                         if(i % 100 == 0){
 679                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 680                         }
 681
 682                 }
 683                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 684
 685                 outFile.close();
 686
 687                 return 1;
 688         }
 689         catch(exception& e) {
 690                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 691                 exit(1);
 692         }
 693 }
 694 #ifdef USE_MPI
 695 /**************************************************************************************************/
 696 /////// need to fix to work with calcs and sequencedb
 697 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 698         try {
 699                 MPI_Status status;
 700                 int startTime = time(NULL);
 701
 702                 string outputString = "";
 703
 704                 for(int i=startLine;i<endLine;i++){
 705
 706                         for(int j=0;j<i;j++){
 707
 708                                 if (m->control_pressed) {  return 0;  }
 709
 710                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 711                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 712                                 }
 713
 714                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 715                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 716                                 }
 717
 718                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 719                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 720
 721                                 Nast(alignment, seqI, seqJ);
 722
 723                                 distCalculator->calcDist(*seqI, *seqJ);
 724                                 double dist = distCalculator->getDist();
 725
 726                                 delete seqI; delete seqJ;
 727
 728                                 if(dist <= cutoff){
 729                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 730                                 }
 731                         }
 732
 733                         if(i % 100 == 0){
 734                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 735                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 736                         }
 737
 738
 739                         //send results to parent
 740                         int length = outputString.length();
 741
 742                         char* buf = new char[length];
 743                         memcpy(buf, outputString.c_str(), length);
 744
 745                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 746                         outputString = "";
 747                         delete buf;
 748
 749                 }
 750
 751                 return 1;
 752         }
 753         catch(exception& e) {
 754                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 755                 exit(1);
 756         }
 757 }
 758 /**************************************************************************************************/
 759 /////// need to fix to work with calcs and sequencedb
 760 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 761         try {
 762                 MPI_Status status;
 763
 764                 MPI_File outMPI;
 765                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 766
 767                 char filename[1024];
 768                 strcpy(filename, file.c_str());
 769
 770                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 771
 772
 773
 774                 string outputString = "";
 775                 size = 0;
 776
 777                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 778
 779                 for(int i=startLine;i<endLine;i++){
 780
 781                         string name = alignDB.get(i).getName();
 782                         if (name.length() < 10) { //pad with spaces to make compatible
 783                                 while (name.length() < 10) {  name += " ";  }
 784                         }
 785                         outputString += name + "\t";
 786
 787                         for(int j=0;j<i;j++){
 788
 789                                 if (m->control_pressed) {  return 0;  }
 790
 791                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 792                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 793                                 }
 794
 795                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 796                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 797                                 }
 798
 799                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 800                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 801
 802                                 Nast(alignment, seqI, seqJ);
 803
 804                                 distCalculator->calcDist(*seqI, *seqJ);
 805                                 double dist = distCalculator->getDist();
 806
 807                                 delete seqI; delete seqJ;
 808
 809                                 outputString += toString(dist) + "\t";
 810                         }
 811
 812                         outputString += "\n";
 813
 814                         //send results to parent
 815                         int length = outputString.length();
 816                         char* buf = new char[length];
 817                         memcpy(buf, outputString.c_str(), length);
 818
 819                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 820                         size += outputString.length();
 821                         outputString = "";
 822                         delete buf;
 823                 }
 824
 825                 MPI_File_close(&outMPI);
 826
 827                 return 1;
 828         }
 829         catch(exception& e) {
 830                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 831                 exit(1);
 832         }
 833 }
 834 /**************************************************************************************************/
 835 /////// need to fix to work with calcs and sequencedb
 836 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 837         try {
 838                 MPI_Status status;
 839
 840                 MPI_File outMPI;
 841                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 842
 843                 char filename[1024];
 844                 strcpy(filename, file.c_str());
 845
 846                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 847
 848
 849
 850                 string outputString = "";
 851                 size = 0;
 852
 853                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 854
 855                 for(int i=startLine;i<endLine;i++){
 856
 857                         string name = alignDB.get(i).getName();
 858                         if (name.length() < 10) { //pad with spaces to make compatible
 859                                 while (name.length() < 10) {  name += " ";  }
 860                         }
 861                         outputString += name + "\t";
 862
 863                         for(int j=0;j<alignDB.getNumSeqs();j++){
 864
 865                                 if (m->control_pressed) {  return 0;  }
 866
 867                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 868                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 869                                 }
 870
 871                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 872                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 873                                 }
 874
 875                                 Sequence* seqI = new Sequence(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 876                                 Sequence* seqJ = new Sequence(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 877
 878                                 Nast(alignment, seqI, seqJ);
 879
 880                                 distCalculator->calcDist(*seqI, *seqJ);
 881                                 double dist = distCalculator->getDist();
 882
 883                                 delete seqI; delete seqJ;
 884
 885                                 outputString += toString(dist) + "\t";
 886                         }
 887
 888                         outputString += "\n";
 889
 890                         //send results to parent
 891                         int length = outputString.length();
 892                         char* buf = new char[length];
 893                         memcpy(buf, outputString.c_str(), length);
 894
 895                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 896                         size += outputString.length();
 897                         outputString = "";
 898                         delete buf;
 899                 }
 900
 901                 MPI_File_close(&outMPI);
 902
 903                 return 1;
 904         }
 905         catch(exception& e) {
 906                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 907                 exit(1);
 908         }
 909 }
 910 #endif
 911 /**************************************************************************************************/
 912