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