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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 103
 104                 else {
 105                         vector<string> myArray = setParameters();
 106
 107                         OptionParser parser(option);
 108                         map<string, string> parameters = parser.getParameters();
 109
 110                         ValidParameters validParameter("pairwise.seqs");
 111                         map<string, string>::iterator it;
 112
 113                         //check to make sure all parameters are valid for command
 114                         for (it = parameters.begin(); it != parameters.end(); it++) {
 115                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 116                         }
 117
 118                         //initialize outputTypes
 119                         vector<string> tempOutNames;
 120                         outputTypes["phylip"] = tempOutNames;
 121                         outputTypes["column"] = tempOutNames;
 122
 123                         //if the user changes the output directory command factory will send this info to us in the output parameter
 124                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 125
 126
 127                         //if the user changes the input directory command factory will send this info to us in the output parameter
 128                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 129
 130                         if (inputDir == "not found"){   inputDir = "";          }
 131
 132                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
 133                         if (fastaFileName == "not found") {
 134                                 //if there is a current fasta file, use it
 135                                 string filename = m->getFastaFile();
 136                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 137                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 138                         }
 139                         else {
 140                                 m->splitAtDash(fastaFileName, fastaFileNames);
 141
 142                                 //go through files and make sure they are good, if not, then disregard them
 143                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 144
 145                                         bool ignore = false;
 146                                         if (fastaFileNames[i] == "current") {
 147                                                 fastaFileNames[i] = m->getFastaFile();
 148                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 149                                                 else {
 150                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 151                                                         //erase from file list
 152                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 153                                                         i--;
 154                                                 }
 155                                         }
 156
 157                                         if (!ignore) {
 158
 159                                                 if (inputDir != "") {
 160                                                         string path = m->hasPath(fastaFileNames[i]);
 161                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 163                                                 }
 164
 165                                                 int ableToOpen;
 166                                                 ifstream in;
 167
 168                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 169
 170                                                 //if you can't open it, try default location
 171                                                 if (ableToOpen == 1) {
 172                                                         if (m->getDefaultPath() != "") { //default path is set
 173                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 174                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 175                                                                 ifstream in2;
 176                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 177                                                                 in2.close();
 178                                                                 fastaFileNames[i] = tryPath;
 179                                                         }
 180                                                 }
 181
 182                                                 //if you can't open it, try output location
 183                                                 if (ableToOpen == 1) {
 184                                                         if (m->getOutputDir() != "") { //default path is set
 185                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 186                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 187                                                                 ifstream in2;
 188                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 189                                                                 in2.close();
 190                                                                 fastaFileNames[i] = tryPath;
 191                                                         }
 192                                                 }
 193
 194                                                 in.close();
 195
 196                                                 if (ableToOpen == 1) {
 197                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 198                                                         //erase from file list
 199                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 200                                                         i--;
 201                                                 }else {
 202                                                         m->setFastaFile(fastaFileNames[i]);
 203                                                 }
 204                                         }
 205                                 }
 206
 207                                 //make sure there is at least one valid file left
 208                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 209                         }
 210
 211                         //check for optional parameter and set defaults
 212                         // ...at some point should added some additional type checking...
 213                         string temp;
 214                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 215                         convert(temp, match);
 216
 217                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 218                         convert(temp, misMatch);
 219
 220                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 221                         convert(temp, gapOpen);
 222
 223                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 224                         convert(temp, gapExtend);
 225
 226                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 227                         m->setProcessors(temp);
 228                         convert(temp, processors);
 229
 230                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 231                         convert(temp, cutoff);
 232
 233                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 234                         countends = m->isTrue(temp);
 235
 236                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 237                         compress = m->isTrue(temp);
 238
 239                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 240
 241                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 242                         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"; }
 243
 244                         calc = validParameter.validFile(parameters, "calc", false);
 245                         if (calc == "not found") { calc = "onegap";  }
 246                         else {
 247                                  if (calc == "default")  {  calc = "onegap";  }
 248                         }
 249                         m->splitAtDash(calc, Estimators);
 250
 251                         ValidCalculators validCalculator;
 252                         if (countends) {
 253                                 for (int i=0; i<Estimators.size(); i++) {
 254                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 255                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 256                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 257                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 258                                         }
 259                                 }
 260                         }else {
 261                                 for (int i=0; i<Estimators.size(); i++) {
 262                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 263                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 264                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 265                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 266                                         }
 267                                 }
 268                         }
 269                 }
 270
 271         }
 272         catch(exception& e) {
 273                 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
 274                 exit(1);
 275         }
 276 }
 277 //**********************************************************************************************************************
 278
 279 int PairwiseSeqsCommand::execute(){
 280         try {
 281                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 282
 283                 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.
 284
 285                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 286                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 287                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 288                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 289                 else {
 290                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 291                         m->mothurOutEndLine();
 292                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 293                 }
 294
 295                 cutoff += 0.005;
 296
 297                 for (int s = 0; s < fastaFileNames.size(); s++) {
 298                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 299
 300                         m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 301
 302                         if (outputDir == "") {  outputDir += m->hasPath(fastaFileNames[s]); }
 303
 304                         ifstream inFASTA;
 305                         m->openInputFile(fastaFileNames[s], inFASTA);
 306                         alignDB = SequenceDB(inFASTA);
 307                         inFASTA.close();
 308
 309                         int numSeqs = alignDB.getNumSeqs();
 310                         int startTime = time(NULL);
 311                         string outputFile = "";
 312
 313                         if (output == "lt") { //does the user want lower triangle phylip formatted file
 314                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
 315                                 m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 316                         }else if (output == "column") { //user wants column format
 317                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
 318                                 outputTypes["column"].push_back(outputFile);
 319                                 m->mothurRemove(outputFile);
 320                         }else { //assume square
 321                                 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
 322                                 m->mothurRemove(outputFile);
 323                                 outputTypes["phylip"].push_back(outputFile);
 324                         }
 325
 326                         #ifdef USE_MPI
 327
 328                         int pid, start, end;
 329                         int tag = 2001;
 330
 331                         MPI_Status status;
 332                         MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 333                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 334
 335                         //each process gets where it should start and stop in the file
 336                         if (output != "square") {
 337                                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 338                                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 339                         }else{
 340                                 start = int ((float(pid)/float(processors)) * numSeqs);
 341                                 end = int ((float(pid+1)/float(processors)) * numSeqs);
 342                         }
 343
 344                         if (output == "column") {
 345                                 MPI_File outMPI;
 346                                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 347
 348                         char filename[1024];
 349                                 strcpy(filename, outputFile.c_str());
 350
 351                                 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 352
 353                                 if (pid == 0) { //you are the root process
 354
 355                                         //do your part
 356                                         string outputMyPart;
 357
 358                                         driverMPI(start, end, outMPI, cutoff);
 359
 360                                         if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  m->mothurRemove(outputFile); delete distCalculator;  return 0; }
 361
 362                                         //wait on chidren
 363                                         for(int i = 1; i < processors; i++) {
 364                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   m->mothurRemove(outputFile); delete distCalculator;  return 0; }
 365
 366                                                 char buf[5];
 367                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 368                                         }
 369                                 }else { //you are a child process
 370                                         //do your part
 371                                         driverMPI(start, end, outMPI, cutoff);
 372
 373                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile); delete distCalculator;  return 0; }
 374
 375                                         char buf[5];
 376                                         strcpy(buf, "done");
 377                                         //tell parent you are done.
 378                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 379                                 }
 380
 381                                 MPI_File_close(&outMPI);
 382
 383                         }else { //lower triangle format
 384                                 if (pid == 0) { //you are the root process
 385
 386                                         //do your part
 387                                         string outputMyPart;
 388                                         unsigned long int mySize;
 389
 390                                         if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 391                                         else { driverMPI(start, end, outputFile, mySize, output); }
 392
 393                                         if (m->control_pressed) {  outputTypes.clear();   m->mothurRemove(outputFile); delete distCalculator;  return 0; }
 394
 395                                         int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 396                                         MPI_File outMPI;
 397                                         MPI_File inMPI;
 398
 399                                         char filename[1024];
 400                                         strcpy(filename, outputFile.c_str());
 401
 402                                         MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 403
 404                                         //wait on chidren
 405                                         for(int b = 1; b < processors; b++) {
 406                                                 unsigned long int fileSize;
 407
 408                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);  delete distCalculator;  return 0; }
 409
 410                                                 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 411
 412                                                 string outTemp = outputFile + toString(b) + ".temp";
 413
 414                                                 char* buf = new char[outTemp.length()];
 415                                                 memcpy(buf, outTemp.c_str(), outTemp.length());
 416
 417                                                 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 418                                                 delete buf;
 419
 420                                                 int count = 0;
 421                                                 while (count < fileSize) {
 422                                                         char buf2[1];
 423                                                         MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 424                                                         MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 425                                                         count += 1;
 426                                                 }
 427
 428                                                 MPI_File_close(&inMPI); //deleted on close
 429                                         }
 430
 431                                         MPI_File_close(&outMPI);
 432                                 }else { //you are a child process
 433                                         //do your part
 434                                         unsigned long int size;
 435                                         if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 436                                         else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 437
 438                                         if (m->control_pressed) { delete distCalculator;  return 0; }
 439
 440                                         //tell parent you are done.
 441                                         MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 442                                 }
 443                         }
 444                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 445         #else
 446
 447                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 448                         //if you don't need to fork anything
 449                         if(processors == 1){
 450                                 if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 451                                 else { driver(0, numSeqs, outputFile, "square");  }
 452                         }else{ //you have multiple processors
 453
 454                                 for (int i = 0; i < processors; i++) {
 455                                         distlinePair tempLine;
 456                                         lines.push_back(tempLine);
 457                                         if (output != "square") {
 458                                                 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 459                                                 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 460                                         }else{
 461                                                 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 462                                                 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 463                                         }
 464                                 }
 465
 466                                 createProcesses(outputFile);
 467                         }
 468                 #else
 469                         //ifstream inFASTA;
 470                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 471                         else { driver(0, numSeqs, outputFile, "square");  }
 472                 #endif
 473
 474         #endif
 475                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
 476
 477                         #ifdef USE_MPI
 478                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 479
 480                                 if (pid == 0) { //only one process should output to screen
 481                         #endif
 482
 483                         ifstream fileHandle;
 484                         fileHandle.open(outputFile.c_str());
 485                         if(fileHandle) {
 486                                 m->gobble(fileHandle);
 487                                 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 488                         }
 489
 490                         if (compress) {
 491                                 m->mothurOut("Compressing..."); m->mothurOutEndLine();
 492                                 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 493                                 system(("gzip -v " + outputFile).c_str());
 494                                 outputNames.push_back(outputFile + ".gz");
 495                         }else { outputNames.push_back(outputFile); }
 496
 497                         #ifdef USE_MPI
 498                                 }
 499                         #endif
 500
 501                         m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 502
 503                         if (m->control_pressed) { outputTypes.clear();  delete distCalculator; m->mothurRemove(outputFile); return 0; }
 504                 }
 505
 506                 delete distCalculator;
 507
 508                 //set phylip file as new current phylipfile
 509                 string current = "";
 510                 itTypes = outputTypes.find("phylip");
 511                 if (itTypes != outputTypes.end()) {
 512                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 513                 }
 514
 515                 //set column file as new current columnfile
 516                 itTypes = outputTypes.find("column");
 517                 if (itTypes != outputTypes.end()) {
 518                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 519                 }
 520
 521                 m->mothurOutEndLine();
 522                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 523                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 524                 m->mothurOutEndLine();
 525
 526
 527                 return 0;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "PairwiseSeqsCommand", "execute");
 531                 exit(1);
 532         }
 533 }
 534
 535 /**************************************************************************************************/
 536 void PairwiseSeqsCommand::createProcesses(string filename) {
 537         try {
 538 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 539                 int process = 1;
 540                 processIDS.clear();
 541
 542                 //loop through and create all the processes you want
 543                 while (process != processors) {
 544                         int pid = fork();
 545
 546                         if (pid > 0) {
 547                                 processIDS.push_back(pid);
 548                                 process++;
 549                         }else if (pid == 0){
 550                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 551                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 552                                 exit(0);
 553                         }else {
 554                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 555                                 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
 556                                 exit(0);
 557                         }
 558                 }
 559
 560                 //parent do my part
 561                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 562                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 563
 564
 565                 //force parent to wait until all the processes are done
 566                 for (int i=0;i<processIDS.size();i++) {
 567                         int temp = processIDS[i];
 568                         wait(&temp);
 569                 }
 570
 571                 //append and remove temp files
 572                 for (int i=0;i<processIDS.size();i++) {
 573                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 574                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 575                 }
 576 #endif
 577         }
 578         catch(exception& e) {
 579                 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
 580                 exit(1);
 581         }
 582 }
 583
 584 /**************************************************************************************************/
 585 /////// need to fix to work with calcs and sequencedb
 586 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 587         try {
 588
 589                 int startTime = time(NULL);
 590
 591                 //column file
 592                 ofstream outFile(dFileName.c_str(), ios::trunc);
 593                 outFile.setf(ios::fixed, ios::showpoint);
 594                 outFile << setprecision(4);
 595
 596                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 597
 598                 for(int i=startLine;i<endLine;i++){
 599                         if(output == "lt")      {
 600                                 string name = alignDB.get(i).getName();
 601                                 if (name.length() < 10) { //pad with spaces to make compatible
 602                                         while (name.length() < 10) {  name += " ";  }
 603                                 }
 604                                 outFile << name << '\t';
 605                         }
 606
 607                         for(int j=0;j<i;j++){
 608
 609                                 if (m->control_pressed) { outFile.close(); return 0;  }
 610
 611                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 612                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 613                                 }
 614
 615                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 616                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 617                                 }
 618
 619                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 620                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 621
 622                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 623                                 seqI.setAligned(alignment->getSeqAAln());
 624                                 seqJ.setAligned(alignment->getSeqBAln());
 625
 626
 627                                 distCalculator->calcDist(seqI, seqJ);
 628                                 double dist = distCalculator->getDist();
 629
 630                                 if(dist <= cutoff){
 631                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 632                                 }
 633                                 if (output == "lt") {  outFile << dist << '\t'; }
 634                         }
 635
 636                         if (output == "lt") { outFile << endl; }
 637
 638                         if(i % 100 == 0){
 639                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 640                         }
 641
 642                 }
 643                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 644
 645                 outFile.close();
 646
 647                 return 1;
 648         }
 649         catch(exception& e) {
 650                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 651                 exit(1);
 652         }
 653 }
 654 /**************************************************************************************************/
 655 /////// need to fix to work with calcs and sequencedb
 656 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
 657         try {
 658
 659                 int startTime = time(NULL);
 660
 661                 //column file
 662                 ofstream outFile(dFileName.c_str(), ios::trunc);
 663                 outFile.setf(ios::fixed, ios::showpoint);
 664                 outFile << setprecision(4);
 665
 666                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 667
 668                 for(int i=startLine;i<endLine;i++){
 669
 670                         string name = alignDB.get(i).getName();
 671                         //pad with spaces to make compatible
 672                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 673
 674                         outFile << name << '\t';
 675
 676                         for(int j=0;j<alignDB.getNumSeqs();j++){
 677
 678                                 if (m->control_pressed) { outFile.close(); return 0;  }
 679
 680                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 681                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 682                                 }
 683
 684                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 685                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 686                                 }
 687
 688                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 689                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 690
 691                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 692                                 seqI.setAligned(alignment->getSeqAAln());
 693                                 seqJ.setAligned(alignment->getSeqBAln());
 694
 695                                 distCalculator->calcDist(seqI, seqJ);
 696                                 double dist = distCalculator->getDist();
 697
 698                                 outFile << dist << '\t';
 699                         }
 700
 701                         outFile << endl;
 702
 703                         if(i % 100 == 0){
 704                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 705                         }
 706
 707                 }
 708                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 709
 710                 outFile.close();
 711
 712                 return 1;
 713         }
 714         catch(exception& e) {
 715                 m->errorOut(e, "PairwiseSeqsCommand", "driver");
 716                 exit(1);
 717         }
 718 }
 719 #ifdef USE_MPI
 720 /**************************************************************************************************/
 721 /////// need to fix to work with calcs and sequencedb
 722 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 723         try {
 724                 MPI_Status status;
 725                 int startTime = time(NULL);
 726
 727                 string outputString = "";
 728
 729                 for(int i=startLine;i<endLine;i++){
 730
 731                         for(int j=0;j<i;j++){
 732
 733                                 if (m->control_pressed) {  return 0;  }
 734
 735                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 736                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 737                                 }
 738
 739                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 740                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 741                                 }
 742
 743                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 744                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 745
 746                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 747                                 seqI.setAligned(alignment->getSeqAAln());
 748                                 seqJ.setAligned(alignment->getSeqBAln());
 749
 750                                 distCalculator->calcDist(seqI, seqJ);
 751                                 double dist = distCalculator->getDist();
 752
 753                                 if(dist <= cutoff){
 754                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 755                                 }
 756                         }
 757
 758                         if(i % 100 == 0){
 759                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 760                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 761                         }
 762
 763
 764                         //send results to parent
 765                         int length = outputString.length();
 766
 767                         char* buf = new char[length];
 768                         memcpy(buf, outputString.c_str(), length);
 769
 770                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 771                         outputString = "";
 772                         delete buf;
 773
 774                 }
 775
 776                 return 1;
 777         }
 778         catch(exception& e) {
 779                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 780                 exit(1);
 781         }
 782 }
 783 /**************************************************************************************************/
 784 /////// need to fix to work with calcs and sequencedb
 785 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
 786         try {
 787                 MPI_Status status;
 788
 789                 MPI_File outMPI;
 790                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 791
 792                 char filename[1024];
 793                 strcpy(filename, file.c_str());
 794
 795                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 796
 797
 798
 799                 string outputString = "";
 800                 size = 0;
 801
 802                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 803
 804                 for(int i=startLine;i<endLine;i++){
 805
 806                         string name = alignDB.get(i).getName();
 807                         if (name.length() < 10) { //pad with spaces to make compatible
 808                                 while (name.length() < 10) {  name += " ";  }
 809                         }
 810                         outputString += name + "\t";
 811
 812                         for(int j=0;j<i;j++){
 813
 814                                 if (m->control_pressed) {  return 0;  }
 815
 816                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 817                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 818                                 }
 819
 820                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 821                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 822                                 }
 823
 824                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 825                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 826
 827                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 828                                 seqI.setAligned(alignment->getSeqAAln());
 829                                 seqJ.setAligned(alignment->getSeqBAln());
 830
 831                                 distCalculator->calcDist(seqI, seqJ);
 832                                 double dist = distCalculator->getDist();
 833
 834                                 outputString += toString(dist) + "\t";
 835                         }
 836
 837                         outputString += "\n";
 838
 839                         //send results to parent
 840                         int length = outputString.length();
 841                         char* buf = new char[length];
 842                         memcpy(buf, outputString.c_str(), length);
 843
 844                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 845                         size += outputString.length();
 846                         outputString = "";
 847                         delete buf;
 848                 }
 849
 850                 MPI_File_close(&outMPI);
 851
 852                 return 1;
 853         }
 854         catch(exception& e) {
 855                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 856                 exit(1);
 857         }
 858 }
 859 /**************************************************************************************************/
 860 /////// need to fix to work with calcs and sequencedb
 861 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
 862         try {
 863                 MPI_Status status;
 864
 865                 MPI_File outMPI;
 866                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 867
 868                 char filename[1024];
 869                 strcpy(filename, file.c_str());
 870
 871                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 872
 873
 874
 875                 string outputString = "";
 876                 size = 0;
 877
 878                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 879
 880                 for(int i=startLine;i<endLine;i++){
 881
 882                         string name = alignDB.get(i).getName();
 883                         if (name.length() < 10) { //pad with spaces to make compatible
 884                                 while (name.length() < 10) {  name += " ";  }
 885                         }
 886                         outputString += name + "\t";
 887
 888                         for(int j=0;j<alignDB.getNumSeqs();j++){
 889
 890                                 if (m->control_pressed) {  return 0;  }
 891
 892                                 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 893                                         alignment->resize(alignDB.get(i).getUnaligned().length()+1);
 894                                 }
 895
 896                                 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 897                                         alignment->resize(alignDB.get(j).getUnaligned().length()+1);
 898                                 }
 899
 900                                 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
 901                                 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
 902
 903                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 904                                 seqI.setAligned(alignment->getSeqAAln());
 905                                 seqJ.setAligned(alignment->getSeqBAln());
 906
 907                                 distCalculator->calcDist(seqI, seqJ);
 908                                 double dist = distCalculator->getDist();
 909
 910                                 outputString += toString(dist) + "\t";
 911                         }
 912
 913                         outputString += "\n";
 914
 915                         //send results to parent
 916                         int length = outputString.length();
 917                         char* buf = new char[length];
 918                         memcpy(buf, outputString.c_str(), length);
 919
 920                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 921                         size += outputString.length();
 922                         outputString = "";
 923                         delete buf;
 924                 }
 925
 926                 MPI_File_close(&outMPI);
 927
 928                 return 1;
 929         }
 930         catch(exception& e) {
 931                 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
 932                 exit(1);
 933         }
 934 }
 935 #endif
 936 /**************************************************************************************************/
 937