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
  18 #include "ignoregaps.h"
  19 #include "eachgapdist.h"
  20 #include "eachgapignore.h"
  21 #include "onegapdist.h"
  22 #include "onegapignore.h"
  23
  24
  25 //**********************************************************************************************************************
  26 vector<string> PairwiseSeqsCommand::setParameters(){
  27         try {
  28                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  29                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  30                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  31                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  32                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  33                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  34                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  35                 CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
  36                 CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
  37                 CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
  38                 CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
  39                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
  40                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  41                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  42
  43                 vector<string> myArray;
  44                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string PairwiseSeqsCommand::getHelpString(){
  54         try {
  55                 string helpString = "";
  56                 helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
  57                 helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
  58                 helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
  59                 helpString += "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";
  60                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  61                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  62                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  63                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  64                 helpString += "The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
  65                 helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n";
  66                 helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
  67                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
  68                 helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
  69                 helpString += "The pairwise.seqs command should be in the following format: \n";
  70                 helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
  71                 helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
  72                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  73                 return helpString;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
  77                 exit(1);
  78         }
  79 }
  80
  81 //**********************************************************************************************************************
  82 PairwiseSeqsCommand::PairwiseSeqsCommand(){
  83         try {
  84                 abort = true; calledHelp = true;
  85                 setParameters();
  86                 vector<string> tempOutNames;
  87                 outputTypes["phylip"] = tempOutNames;
  88                 outputTypes["column"] = tempOutNames;
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
  92                 exit(1);
  93         }
  94 }
  95 //**********************************************************************************************************************
  96 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
  97         try {
  98                 abort = false; calledHelp = false;
  99
 100                 //allow user to run help
 101                 if(option == "help") { help(); abort = true; calledHelp = true; }
 102
 103                 else {
 104                         vector<string> myArray = setParameters();
 105
 106                         OptionParser parser(option);
 107                         map<string, string> parameters = parser.getParameters();
 108
 109                         ValidParameters validParameter("pairwise.seqs");
 110                         map<string, string>::iterator it;
 111
 112                         //check to make sure all parameters are valid for command
 113                         for (it = parameters.begin(); it != parameters.end(); it++) {
 114                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 115                         }
 116
 117                         //initialize outputTypes
 118                         vector<string> tempOutNames;
 119                         outputTypes["phylip"] = tempOutNames;
 120                         outputTypes["column"] = tempOutNames;
 121
 122                         //if the user changes the output directory command factory will send this info to us in the output parameter
 123                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 124
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128
 129                         if (inputDir == "not found"){   inputDir = "";          }
 130
 131                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 132                         if (fastaFileName == "not found") {
 133                                 //if there is a current fasta file, use it
 134                                 string filename = m->getFastaFile();
 135                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 136                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 137                         }
 138                         else {
 139                                 m->splitAtDash(fastaFileName, fastaFileNames);
 140
 141                                 //go through files and make sure they are good, if not, then disregard them
 142                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 143
 144                                         if (inputDir != "") {
 145                                                 string path = m->hasPath(fastaFileNames[i]);
 146                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 147                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 148                                         }
 149
 150                                         int ableToOpen;
 151                                         ifstream in;
 152
 153                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 154
 155                                         //if you can't open it, try default location
 156                                         if (ableToOpen == 1) {
 157                                                 if (m->getDefaultPath() != "") { //default path is set
 158                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 159                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 160                                                         ifstream in2;
 161                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 162                                                         in2.close();
 163                                                         fastaFileNames[i] = tryPath;
 164                                                 }
 165                                         }
 166
 167                                         //if you can't open it, try output location
 168                                         if (ableToOpen == 1) {
 169                                                 if (m->getOutputDir() != "") { //default path is set
 170                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 171                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 172                                                         ifstream in2;
 173                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 174                                                         in2.close();
 175                                                         fastaFileNames[i] = tryPath;
 176                                                 }
 177                                         }
 178
 179                                         in.close();
 180
 181                                         if (ableToOpen == 1) {
 182                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 183                                                 //erase from file list
 184                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 185                                                 i--;
 186                                         }
 187                                 }
 188
 189                                 //make sure there is at least one valid file left
 190                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 191                         }
 192
 193                         //check for optional parameter and set defaults
 194                         // ...at some point should added some additional type checking...
 195                         string temp;
 196                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 197                         convert(temp, match);
 198
 199                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 200                         convert(temp, misMatch);
 201
 202                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 203                         convert(temp, gapOpen);
 204
 205                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 206                         convert(temp, gapExtend);
 207
 208                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 209                         m->setProcessors(temp);
 210                         convert(temp, processors);
 211
 212                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 213                         convert(temp, cutoff);
 214
 215                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 216                         countends = m->isTrue(temp);
 217
 218                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 219                         compress = m->isTrue(temp);
 220
 221                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 222
 223                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 224                         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"; }
 225
 226                         calc = validParameter.validFile(parameters, "calc", false);
 227                         if (calc == "not found") { calc = "onegap";  }
 228                         else {
 229                                  if (calc == "default")  {  calc = "onegap";  }
 230                         }
 231                         m->splitAtDash(calc, Estimators);
 232
 233                         ValidCalculators validCalculator;
 234                         if (countends) {
 235                                 for (int i=0; i<Estimators.size(); i++) {
 236                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 237                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 238                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 239                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 240                                         }
 241                                 }
 242                         }else {
 243                                 for (int i=0; i<Estimators.size(); i++) {
 244                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 245                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 246                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 247                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 248                                         }
 249                                 }
 250                         }
 251                 }
 252
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
 256                 exit(1);
 257         }
 258 }
 259 //**********************************************************************************************************************
 260
 261 int PairwiseSeqsCommand::execute(){
 262         try {
 263                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 264
 265                 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.
 266
 267                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 268                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 269                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 270                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 271                 else {
 272                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 273                         m->mothurOutEndLine();
 274                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 275                 }
 276
 277                 cutoff += 0.005;
 278
 279                 for (int s = 0; s < fastaFileNames.size(); s++) {
 280                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 281
 282                         m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 283
 284                         if (outputDir == "") {  outputDir += m->hasPath(fastaFileNames[s]); }
 285
 286                         ifstream inFASTA;
 287                         m->openInputFile(fastaFileNames[s], inFASTA);
 288                         alignDB = SequenceDB(inFASTA);
 289                         inFASTA.close();
 290
 291                         int numSeqs = alignDB.getNumSeqs();
 292                         int startTime = time(NULL);
 293                         string outputFile = "";
 294
 295                         if (output == "lt") { //does the user want lower triangle phylip formatted file
 296                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
 297                                 remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
 298                         }else if (output == "column") { //user wants column format
 299                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
 300                                 outputTypes["column"].push_back(outputFile);
 301                                 remove(outputFile.c_str());
 302                         }else { //assume square
 303                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
 304                                 remove(outputFile.c_str());
 305                                 outputTypes["phylip"].push_back(outputFile);
 306                         }
 307
 308                         #ifdef USE_MPI
 309
 310                         int pid, start, end;
 311                         int tag = 2001;
 312
 313                         MPI_Status status;
 314                         MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 315                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 316
 317                         //each process gets where it should start and stop in the file
 318                         if (output != "square") {
 319                                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 320                                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 321                         }else{
 322                                 start = int ((float(pid)/float(processors)) * numSeqs);
 323                                 end = int ((float(pid+1)/float(processors)) * numSeqs);
 324                         }
 325
 326                         if (output == "column") {
 327                                 MPI_File outMPI;
 328                                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 329
 330                         char filename[1024];
 331                                 strcpy(filename, outputFile.c_str());
 332
 333                                 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 334
 335                                 if (pid == 0) { //you are the root process
 336
 337                                         //do your part
 338                                         string outputMyPart;
 339
 340                                         driverMPI(start, end, outMPI, cutoff);
 341
 342                                         if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 343
 344                                         //wait on chidren
 345                                         for(int i = 1; i < processors; i++) {
 346                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 347
 348                                                 char buf[5];
 349                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 350                                         }
 351                                 }else { //you are a child process
 352                                         //do your part
 353                                         driverMPI(start, end, outMPI, cutoff);
 354
 355                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str()); delete distCalculator;  return 0; }
 356
 357                                         char buf[5];
 358                                         strcpy(buf, "done");
 359                                         //tell parent you are done.
 360                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 361                                 }
 362
 363                                 MPI_File_close(&outMPI);
 364
 365                         }else { //lower triangle format
 366                                 if (pid == 0) { //you are the root process
 367
 368                                         //do your part
 369                                         string outputMyPart;
 370                                         unsigned long int mySize;
 371
 372                                         if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 373                                         else { driverMPI(start, end, outputFile, mySize, output); }
 374
 375                                         if (m->control_pressed) {  outputTypes.clear();   remove(outputFile.c_str()); delete distCalculator;  return 0; }
 376
 377                                         int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 378                                         MPI_File outMPI;
 379                                         MPI_File inMPI;
 380
 381                                         char filename[1024];
 382                                         strcpy(filename, outputFile.c_str());
 383
 384                                         MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 385
 386                                         //wait on chidren
 387                                         for(int b = 1; b < processors; b++) {
 388                                                 unsigned long int fileSize;
 389
 390                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  remove(outputFile.c_str());  delete distCalculator;  return 0; }
 391
 392                                                 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 393
 394                                                 string outTemp = outputFile + toString(b) + ".temp";
 395
 396                                                 char* buf = new char[outTemp.length()];
 397                                                 memcpy(buf, outTemp.c_str(), outTemp.length());
 398
 399                                                 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 400                                                 delete buf;
 401
 402                                                 int count = 0;
 403                                                 while (count < fileSize) {
 404                                                         char buf2[1];
 405                                                         MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 406                                                         MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 407                                                         count += 1;
 408                                                 }
 409
 410                                                 MPI_File_close(&inMPI); //deleted on close
 411                                         }
 412
 413                                         MPI_File_close(&outMPI);
 414                                 }else { //you are a child process
 415                                         //do your part
 416                                         unsigned long int size;
 417                                         if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 418                                         else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 419
 420                                         if (m->control_pressed) { delete distCalculator;  return 0; }
 421
 422                                         //tell parent you are done.
 423                                         MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 424                                 }
 425                         }
 426                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 427         #else
 428
 429                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 430                         //if you don't need to fork anything
 431                         if(processors == 1){
 432                                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 433                                 else { driver(0, numSeqs, outputFile, "square");  }
 434                         }else{ //you have multiple processors
 435
 436                                 for (int i = 0; i < processors; i++) {
 437                                         distlinePair tempLine;
 438                                         lines.push_back(tempLine);
 439                                         if (output != "square") {
 440                                                 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 441                                                 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 442                                         }else{
 443                                                 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 444                                                 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 445                                         }
 446                                 }
 447
 448                                 createProcesses(outputFile);
 449                         }
 450                 #else
 451                         //ifstream inFASTA;
 452                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 453                         else { driver(0, numSeqs, outputFile, "square");  }
 454                 #endif
 455
 456         #endif
 457                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 458
 459                         #ifdef USE_MPI
 460                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 461
 462                                 if (pid == 0) { //only one process should output to screen
 463                         #endif
 464
 465                         ifstream fileHandle;
 466                         fileHandle.open(outputFile.c_str());
 467                         if(fileHandle) {
 468                                 m->gobble(fileHandle);
 469                                 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 470                         }
 471
 472                         if (compress) {
 473                                 m->mothurOut("Compressing..."); m->mothurOutEndLine();
 474                                 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 475                                 system(("gzip -v " + outputFile).c_str());
 476                                 outputNames.push_back(outputFile + ".gz");
 477                         }else { outputNames.push_back(outputFile); }
 478
 479                         #ifdef USE_MPI
 480                                 }
 481                         #endif
 482
 483                         m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 484
 485                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
 486                 }
 487
 488                 delete distCalculator;
 489
 490                 //set phylip file as new current phylipfile
 491                 string current = "";
 492                 itTypes = outputTypes.find("phylip");
 493                 if (itTypes != outputTypes.end()) {
 494                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 495                 }
 496
 497                 //set column file as new current columnfile
 498                 itTypes = outputTypes.find("column");
 499                 if (itTypes != outputTypes.end()) {
 500                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 501                 }
 502
 503                 m->mothurOutEndLine();
 504                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 505                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 506                 m->mothurOutEndLine();
 507
 508
 509                 return 0;
 510         }
 511         catch(exception& e) {
 512                 m->errorOut(e, "PairwiseSeqsCommand", "execute");
 513                 exit(1);
 514         }
 515 }
 516
 517 /**************************************************************************************************/
 518 void PairwiseSeqsCommand::createProcesses(string filename) {
 519         try {
 520 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 521                 int process = 1;
 522                 processIDS.clear();
 523
 524                 //loop through and create all the processes you want
 525                 while (process != processors) {
 526                         int pid = fork();
 527
 528                         if (pid > 0) {
 529                                 processIDS.push_back(pid);
 530                                 process++;
 531                         }else if (pid == 0){
 532                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 533                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 534                                 exit(0);
 535                         }else {
 536                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 537                                 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
 538                                 exit(0);
 539                         }
 540                 }
 541
 542                 //parent do my part
 543                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 544                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 545
 546
 547                 //force parent to wait until all the processes are done
 548                 for (int i=0;i<processIDS.size();i++) {
 549                         int temp = processIDS[i];
 550                         wait(&temp);
 551                 }
 552
 553                 //append and remove temp files
 554                 for (int i=0;i<processIDS.size();i++) {
 555                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 556                         remove((filename + toString(processIDS[i]) + ".temp").c_str());
 557                 }
 558 #endif
 559         }
 560         catch(exception& e) {
 561                 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
 562                 exit(1);
 563         }
 564 }
 565
 566 /**************************************************************************************************/
 567 /////// need to fix to work with calcs and sequencedb
 568 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 569         try {
 570
 571                 int startTime = time(NULL);
 572
 573                 //column file
 574                 ofstream outFile(dFileName.c_str(), ios::trunc);
 575                 outFile.setf(ios::fixed, ios::showpoint);
 576                 outFile << setprecision(4);
 577
 578                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 579
 580                 for(int i=startLine;i<endLine;i++){
 581                         if(output == "lt")      {
 582                                 string name = alignDB.get(i).getName();
 583                                 if (name.length() < 10) { //pad with spaces to make compatible
 584                                         while (name.length() < 10) {  name += " ";  }
 585                                 }
 586                                 outFile << name << '\t';
 587                         }
 588
 589                         for(int j=0;j<i;j++){
 590
 591                                 if (m->control_pressed) { outFile.close(); return 0;  }
 592
 593                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 594                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 595                                 }
 596
 597                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 598                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 599                                 }
 600
 601                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 602                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 603
 604                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 605                                 seqI.setAligned(alignment->getSeqAAln());
 606                                 seqJ.setAligned(alignment->getSeqBAln());
 607
 608
 609                                 distCalculator->calcDist(seqI, seqJ);
 610                                 double dist = distCalculator->getDist();
 611
 612                                 if(dist <= cutoff){
 613                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 614                                 }
 615                                 if (output == "lt") {  outFile << dist << '\t'; }
 616                         }
 617
 618                         if (output == "lt") { outFile << endl; }
 619
 620                         if(i % 100 == 0){
 621                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 622                         }
 623
 624                 }
 625                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 626
 627                 outFile.close();
 628
 629                 return 1;
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 633                 exit(1);
 634         }
 635 }
 636 /**************************************************************************************************/
 637 /////// need to fix to work with calcs and sequencedb
 638 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
 639         try {
 640
 641                 int startTime = time(NULL);
 642
 643                 //column file
 644                 ofstream outFile(dFileName.c_str(), ios::trunc);
 645                 outFile.setf(ios::fixed, ios::showpoint);
 646                 outFile << setprecision(4);
 647
 648                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 649
 650                 for(int i=startLine;i<endLine;i++){
 651
 652                         string name = alignDB.get(i).getName();
 653                         //pad with spaces to make compatible
 654                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 655
 656                         outFile << name << '\t';
 657
 658                         for(int j=0;j<alignDB.getNumSeqs();j++){
 659
 660                                 if (m->control_pressed) { outFile.close(); return 0;  }
 661
 662                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 663                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 664                                 }
 665
 666                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 667                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 668                                 }
 669
 670                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 671                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 672
 673                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 674                                 seqI.setAligned(alignment->getSeqAAln());
 675                                 seqJ.setAligned(alignment->getSeqBAln());
 676
 677                                 distCalculator->calcDist(seqI, seqJ);
 678                                 double dist = distCalculator->getDist();
 679
 680                                 outFile << dist << '\t';
 681                         }
 682
 683                         outFile << endl;
 684
 685                         if(i % 100 == 0){
 686                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 687                         }
 688
 689                 }
 690                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 691
 692                 outFile.close();
 693
 694                 return 1;
 695         }
 696         catch(exception& e) {
 697                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 698                 exit(1);
 699         }
 700 }
 701 #ifdef USE_MPI
 702 /**************************************************************************************************/
 703 /////// need to fix to work with calcs and sequencedb
 704 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 705         try {
 706                 MPI_Status status;
 707                 int startTime = time(NULL);
 708
 709                 string outputString = "";
 710
 711                 for(int i=startLine;i<endLine;i++){
 712
 713                         for(int j=0;j<i;j++){
 714
 715                                 if (m->control_pressed) {  return 0;  }
 716
 717                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 718                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 719                                 }
 720
 721                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 722                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 723                                 }
 724
 725                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 726                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 727
 728                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 729                                 seqI.setAligned(alignment->getSeqAAln());
 730                                 seqJ.setAligned(alignment->getSeqBAln());
 731
 732                                 distCalculator->calcDist(seqI, seqJ);
 733                                 double dist = distCalculator->getDist();
 734
 735                                 if(dist <= cutoff){
 736                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 737                                 }
 738                         }
 739
 740                         if(i % 100 == 0){
 741                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 742                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 743                         }
 744
 745
 746                         //send results to parent
 747                         int length = outputString.length();
 748
 749                         char* buf = new char[length];
 750                         memcpy(buf, outputString.c_str(), length);
 751
 752                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 753                         outputString = "";
 754                         delete buf;
 755
 756                 }
 757
 758                 return 1;
 759         }
 760         catch(exception& e) {
 761                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 762                 exit(1);
 763         }
 764 }
 765 /**************************************************************************************************/
 766 /////// need to fix to work with calcs and sequencedb
 767 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 768         try {
 769                 MPI_Status status;
 770
 771                 MPI_File outMPI;
 772                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 773
 774                 char filename[1024];
 775                 strcpy(filename, file.c_str());
 776
 777                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 778
 779
 780
 781                 string outputString = "";
 782                 size = 0;
 783
 784                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 785
 786                 for(int i=startLine;i<endLine;i++){
 787
 788                         string name = alignDB.get(i).getName();
 789                         if (name.length() < 10) { //pad with spaces to make compatible
 790                                 while (name.length() < 10) {  name += " ";  }
 791                         }
 792                         outputString += name + "\t";
 793
 794                         for(int j=0;j<i;j++){
 795
 796                                 if (m->control_pressed) {  return 0;  }
 797
 798                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 799                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 800                                 }
 801
 802                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 803                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 804                                 }
 805
 806                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 807                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 808
 809                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 810                                 seqI.setAligned(alignment->getSeqAAln());
 811                                 seqJ.setAligned(alignment->getSeqBAln());
 812
 813                                 distCalculator->calcDist(seqI, seqJ);
 814                                 double dist = distCalculator->getDist();
 815
 816                                 outputString += toString(dist) + "\t";
 817                         }
 818
 819                         outputString += "\n";
 820
 821                         //send results to parent
 822                         int length = outputString.length();
 823                         char* buf = new char[length];
 824                         memcpy(buf, outputString.c_str(), length);
 825
 826                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 827                         size += outputString.length();
 828                         outputString = "";
 829                         delete buf;
 830                 }
 831
 832                 MPI_File_close(&outMPI);
 833
 834                 return 1;
 835         }
 836         catch(exception& e) {
 837                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 838                 exit(1);
 839         }
 840 }
 841 /**************************************************************************************************/
 842 /////// need to fix to work with calcs and sequencedb
 843 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 844         try {
 845                 MPI_Status status;
 846
 847                 MPI_File outMPI;
 848                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 849
 850                 char filename[1024];
 851                 strcpy(filename, file.c_str());
 852
 853                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 854
 855
 856
 857                 string outputString = "";
 858                 size = 0;
 859
 860                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 861
 862                 for(int i=startLine;i<endLine;i++){
 863
 864                         string name = alignDB.get(i).getName();
 865                         if (name.length() < 10) { //pad with spaces to make compatible
 866                                 while (name.length() < 10) {  name += " ";  }
 867                         }
 868                         outputString += name + "\t";
 869
 870                         for(int j=0;j<alignDB.getNumSeqs();j++){
 871
 872                                 if (m->control_pressed) {  return 0;  }
 873
 874                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 875                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 876                                 }
 877
 878                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 879                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 880                                 }
 881
 882                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 883                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 884
 885                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 886                                 seqI.setAligned(alignment->getSeqAAln());
 887                                 seqJ.setAligned(alignment->getSeqBAln());
 888
 889                                 distCalculator->calcDist(seqI, seqJ);
 890                                 double dist = distCalculator->getDist();
 891
 892                                 outputString += toString(dist) + "\t";
 893                         }
 894
 895                         outputString += "\n";
 896
 897                         //send results to parent
 898                         int length = outputString.length();
 899                         char* buf = new char[length];
 900                         memcpy(buf, outputString.c_str(), length);
 901
 902                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 903                         size += outputString.length();
 904                         outputString = "";
 905                         delete buf;
 906                 }
 907
 908                 MPI_File_close(&outMPI);
 909
 910                 return 1;
 911         }
 912         catch(exception& e) {
 913                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 914                 exit(1);
 915         }
 916 }
 917 #endif
 918 /**************************************************************************************************/
 919