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