splitmatrix.cpp

   1 /*
   2  *  splitmatrix.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/19/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "splitmatrix.h"
  11 #include "phylotree.h"
  12 #include "distancecommand.h"
  13 #include "seqsummarycommand.h"
  14
  15 /***********************************************************************/
  16
  17 SplitMatrix::SplitMatrix(string distfile, string name, string count, string tax, float c, string t, bool l){
  18         m = MothurOut::getInstance();
  19         distFile = distfile;
  20         cutoff = c;
  21         namefile = name;
  22         method = t;
  23         taxFile = tax;
  24     countfile = count;
  25         large = l;
  26 }
  27 /***********************************************************************/
  28
  29 SplitMatrix::SplitMatrix(string ffile, string name, string count, string tax, float c, float cu, string t, int p, bool cl, string output){
  30         m = MothurOut::getInstance();
  31         fastafile = ffile;
  32         namefile = name;
  33     countfile = count;
  34         taxFile = tax;
  35         cutoff = c;  //tax level cutoff
  36         distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
  37         method = t;
  38         processors = p;
  39     classic = cl;
  40         outputDir = output;
  41 }
  42
  43 /***********************************************************************/
  44
  45 int SplitMatrix::split(){
  46         try {
  47
  48                 if (method == "distance") {
  49                         splitDistance();
  50                 }else if ((method == "classify") || (method == "fasta")) {
  51                         splitClassify();
  52                 }else {
  53                         m->mothurOut("Unknown splitting method, aborting split."); m->mothurOutEndLine();
  54                         map<string, string> temp;
  55                         if (namefile != "") {  temp[distFile] = namefile; }
  56             else { temp[distFile] = countfile; }
  57                         dists.push_back(temp);
  58                 }
  59
  60                 return 0;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "SplitMatrix", "split");
  64                 exit(1);
  65         }
  66 }
  67 /***********************************************************************/
  68 int SplitMatrix::splitDistance(){
  69         try {
  70
  71                 if (large)      { splitDistanceLarge(); }
  72                 else            { splitDistanceRAM();   }
  73
  74                 return 0;
  75
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "SplitMatrix", "splitDistance");
  79                 exit(1);
  80         }
  81 }
  82
  83 /***********************************************************************/
  84 int SplitMatrix::splitClassify(){
  85         try {
  86                 cutoff = int(cutoff);
  87
  88                 map<string, int> seqGroup;
  89                 map<string, int>::iterator it;
  90                 map<string, int>::iterator it2;
  91
  92                 int numGroups = 0;
  93
  94                 //build tree from users taxonomy file
  95                 PhyloTree* phylo = new PhyloTree();
  96
  97         map<string, string> temp;
  98         m->readTax(taxFile, temp);
  99
 100         for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
 101             phylo->addSeqToTree(itTemp->first, itTemp->second);
 102             temp.erase(itTemp++);
 103         }
 104
 105                 phylo->assignHeirarchyIDs(0);
 106
 107                 //make sure the cutoff is not greater than maxlevel
 108                 if (cutoff > phylo->getMaxLevel()) { m->mothurOut("splitcutoff is greater than the longest taxonomy, using " + toString(phylo->getMaxLevel())); m->mothurOutEndLine(); cutoff = phylo->getMaxLevel(); }
 109
 110                 //for each node in tree
 111                 for (int i = 0; i < phylo->getNumNodes(); i++) {
 112
 113                         //is this node within the cutoff
 114                         TaxNode taxon = phylo->get(i);
 115
 116                         if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
 117                                 if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
 118                                         for (int j = 0; j < taxon.accessions.size(); j++) {
 119                                                 seqGroup[taxon.accessions[j]] = numGroups;
 120                                         }
 121                                         numGroups++;
 122                                 }
 123                         }
 124                 }
 125
 126                 delete phylo;
 127
 128                 if (method == "classify") {
 129                         splitDistanceFileByTax(seqGroup, numGroups);
 130                 }else {
 131                         createDistanceFilesFromTax(seqGroup, numGroups);
 132                 }
 133
 134                 return 0;
 135
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "SplitMatrix", "splitClassify");
 139                 exit(1);
 140         }
 141 }
 142 /***********************************************************************/
 143 int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numGroups){
 144         try {
 145                 map<string, int> copyGroups = seqGroup;
 146                 map<string, int>::iterator it;
 147                 set<string> names;
 148
 149                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 150                         m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
 151                 }
 152
 153                 ifstream in;
 154                 m->openInputFile(fastafile, in);
 155
 156                 //parse fastafile
 157                 ofstream outFile;
 158                 while (!in.eof()) {
 159                         Sequence query(in); m->gobble(in);
 160                         if (query.getName() != "") {
 161
 162                                 it = seqGroup.find(query.getName());
 163
 164                                 //save names in case no namefile is given
 165                                 if ((namefile == "") && (countfile == "")) {  names.insert(query.getName()); }
 166
 167                                 if (it != seqGroup.end()) { //not singleton
 168                                         m->openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
 169                                         query.printSequence(outFile);
 170                                         outFile.close();
 171
 172                                         copyGroups.erase(query.getName());
 173                                 }
 174                         }
 175                 }
 176                 in.close();
 177
 178                 //warn about sequence in groups that are not in fasta file
 179                 for(it = copyGroups.begin(); it != copyGroups.end(); it++) {
 180                         m->mothurOut("ERROR: " + it->first + " is missing from your fastafile. This could happen if your taxonomy file is not unique and your fastafile is, or it could indicate and error."); m->mothurOutEndLine();
 181                         exit(1);
 182                 }
 183
 184                 copyGroups.clear();
 185
 186                 //process each distance file
 187                 for (int i = 0; i < numGroups; i++) {
 188
 189                         string options = "";
 190             if (classic) { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", output=lt"; }
 191             else { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff); }
 192                         if (outputDir != "") { options += ", outputdir=" + outputDir; }
 193
 194                         Command* command = new DistanceCommand(options);
 195
 196                         command->execute();
 197                         delete command;
 198
 199                         m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
 200
 201                         //remove old names files just in case
 202                         if (namefile != "") { m->mothurRemove((namefile + "." + toString(i) + ".temp")); }
 203             else { m->mothurRemove((countfile + "." + toString(i) + ".temp")); }
 204                 }
 205
 206         vector<string> tempDistFiles;
 207         for(int i=0;i<numGroups;i++){
 208             if (outputDir == "") { outputDir = m->hasPath(fastafile); }
 209             string tempDistFile = "";
 210             if (classic) { tempDistFile =  outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "phylip.dist";}
 211             else { tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist"; }
 212             tempDistFiles.push_back(tempDistFile);
 213         }
 214
 215         splitNames(seqGroup, numGroups, tempDistFiles);
 216
 217                 if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { m->mothurRemove((dists[i].begin()->first)); m->mothurRemove((dists[i].begin()->second)); } dists.clear(); }
 218
 219                 return 0;
 220         }
 221         catch(exception& e) {
 222                 m->errorOut(e, "SplitMatrix", "createDistanceFilesFromTax");
 223                 exit(1);
 224         }
 225 }
 226 /***********************************************************************/
 227 int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroups){
 228         try {
 229                 map<string, int>::iterator it;
 230                 map<string, int>::iterator it2;
 231
 232         ofstream outFile;
 233                 ifstream dFile;
 234                 m->openInputFile(distFile, dFile);
 235
 236
 237                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 238                         m->mothurRemove((distFile + "." + toString(i) + ".temp"));
 239                 }
 240
 241                 //for buffering the io to improve speed
 242                  //allow for 10 dists to be stored, then output.
 243                 vector<string> outputs;  outputs.resize(numGroups, "");
 244                 vector<int> numOutputs;  numOutputs.resize(numGroups, 0);
 245
 246                 //you can have a group made, but their may be no distances in the file for this group if the taxonomy file and distance file don't match
 247                 //this can occur if we have converted the phylip to column, since we reduce the size at that step by using the cutoff value
 248                 vector<bool> validDistances;   validDistances.resize(numGroups, false);
 249
 250                 //for each distance
 251                 while(dFile){
 252                         string seqA, seqB;
 253                         float dist;
 254
 255                         if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { m->mothurRemove((distFile + "." + toString(i) + ".temp"));       } }
 256
 257                         dFile >> seqA >> seqB >> dist;  m->gobble(dFile);
 258
 259                         //if both sequences are in the same group then they are within the cutoff
 260                         it = seqGroup.find(seqA);
 261                         it2 = seqGroup.find(seqB);
 262
 263                         if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons
 264                                 if (it->second == it2->second) { //they are from the same group so add the distance
 265                                         if (numOutputs[it->second] > 30) {
 266                                                 m->openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
 267                                                 outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
 268                                                 outFile.close();
 269                                                 outputs[it->second] = "";
 270                                                 numOutputs[it->second] = 0;
 271                                                 validDistances[it->second] = true;
 272                                         }else{
 273                                                 outputs[it->second] += seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 274                                                 numOutputs[it->second]++;
 275                                         }
 276                                 }
 277                         }
 278                 }
 279                 dFile.close();
 280
 281         string inputFile = namefile;
 282         if (countfile != "") { inputFile = countfile; }
 283
 284         vector<string> tempDistFiles;
 285                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 286             string tempDistFile = distFile + "." + toString(i) + ".temp";
 287             tempDistFiles.push_back(tempDistFile);
 288                         m->mothurRemove((inputFile + "." + toString(i) + ".temp"));
 289
 290                         //write out any remaining buffers
 291                         if (numOutputs[i] > 0) {
 292                                 m->openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
 293                                 outFile << outputs[i];
 294                                 outFile.close();
 295                                 outputs[i] = "";
 296                                 numOutputs[i] = 0;
 297                                 validDistances[i] = true;
 298                         }
 299                 }
 300
 301         splitNames(seqGroup, numGroups, tempDistFiles);
 302
 303                 if (m->control_pressed)  {
 304                         for (int i = 0; i < dists.size(); i++) {
 305                                 m->mothurRemove((dists[i].begin()->first));
 306                                 m->mothurRemove((dists[i].begin()->second));
 307                         }
 308                         dists.clear();
 309                 }
 310
 311                 return 0;
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "SplitMatrix", "splitDistanceFileByTax");
 315                 exit(1);
 316         }
 317 }
 318 /***********************************************************************/
 319 int SplitMatrix::splitDistanceLarge(){
 320         try {
 321                 vector<set<string> > groups;
 322
 323                 //for buffering the io to improve speed
 324                  //allow for 30 dists to be stored, then output.
 325                 vector<string> outputs;
 326                 vector<int> numOutputs;
 327                 vector<bool> wroteOutPut;
 328
 329                 int numGroups = 0;
 330
 331                 ofstream outFile;
 332                 ifstream dFile;
 333                 m->openInputFile(distFile, dFile);
 334
 335                 while(dFile){
 336                         string seqA, seqB;
 337                         float dist;
 338
 339                         dFile >> seqA >> seqB >> dist;
 340
 341                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
 342
 343                         if(dist < cutoff){
 344                                 //cout << "in cutoff: " << dist << endl;
 345                                 int groupIDA = -1;
 346                                 int groupIDB = -1;
 347                                 int groupID = -1;
 348
 349                                 for(int i=0;i<numGroups;i++){
 350                                         set<string>::iterator aIt = groups[i].find(seqA);
 351                                         set<string>::iterator bIt = groups[i].find(seqB);
 352
 353                                         if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
 354                                                 groups[i].insert(seqB);
 355                                                 groupIDA = i;
 356                                                 groupID = groupIDA;
 357
 358                                                 //cout << "in aIt: " << groupID << endl;
 359         //                                      break;
 360                                         }
 361                                         else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
 362                                                 groups[i].insert(seqA);
 363                                                 groupIDB = i;
 364                                                 groupID = groupIDB;
 365
 366                                         //      cout << "in bIt: " << groupID << endl;
 367         //                                      break;
 368                                         }
 369
 370                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 371                                                 if(groupIDA < groupIDB){
 372                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 373                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 374                                                         groups[groupIDB].clear();
 375                                                         groupID = groupIDA;
 376                                                 }
 377                                                 else{
 378                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 379                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 380                                                         groups[groupIDA].clear();
 381                                                         groupID = groupIDB;
 382                                                 }
 383                                                 break;
 384                                         }
 385                                 }
 386
 387         //windows is gonna gag on the reuse of outFile, will need to make it local...
 388
 389                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 390                                         set<string> newGroup;
 391                                         newGroup.insert(seqA);
 392                                         newGroup.insert(seqB);
 393                                         groups.push_back(newGroup);
 394
 395                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 396                                         outputs.push_back(tempOut);
 397                                         numOutputs.push_back(1);
 398                                         wroteOutPut.push_back(false);
 399
 400                                         numGroups++;
 401                                 }
 402                                 else{
 403                                         string fileName = distFile + "." + toString(groupID) + ".temp";
 404
 405                                         //have we reached the max buffer size
 406                                         if (numOutputs[groupID] > 60) { //write out sequence
 407                                                 outFile.open(fileName.c_str(), ios::app);
 408                                                 outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
 409                                                 outFile.close();
 410
 411                                                 outputs[groupID] = "";
 412                                                 numOutputs[groupID] = 0;
 413                                                 wroteOutPut[groupID] = true;
 414                                         }else {
 415                                                 outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 416                                                 numOutputs[groupID]++;
 417                                         }
 418
 419                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 420                                                 string row, column, distance;
 421                                                 if(groupIDA<groupIDB){
 422
 423                                                         //merge memory
 424                                                         numOutputs[groupID] += numOutputs[groupIDB];
 425                                                         outputs[groupID] += outputs[groupIDB];
 426
 427                                                         outputs[groupIDB] = "";
 428                                                         numOutputs[groupIDB] = 0;
 429
 430                                                         //if groupB is written to file it is above buffer size so read and write to new merged file
 431                                                         if (wroteOutPut[groupIDB]) {
 432                                                                 string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
 433                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 434
 435                                                                 outFile.open(fileName.c_str(), ios::app);
 436
 437                                                                 long size;
 438                                                                 char* memblock;
 439
 440                                                                 size = fileB.tellg();
 441
 442                                                                 fileB.seekg (0, ios::beg);
 443
 444                                                                 int numRead = size / 1024;
 445                                                                 int lastRead = size % 1024;
 446
 447                                                                 for (int i = 0; i < numRead; i++) {
 448
 449                                                                         memblock = new char [1024];
 450
 451                                                                         fileB.read (memblock, 1024);
 452
 453                                                                         string temp = memblock;
 454                                                                         outFile << temp.substr(0, 1024);
 455
 456                                                                         delete memblock;
 457                                                                 }
 458
 459                                                                 memblock = new char [lastRead];
 460
 461                                                                 fileB.read (memblock, lastRead);
 462
 463                                                                 //not sure why but it will read more than lastRead char...??
 464                                                                 string temp = memblock;
 465                                                                 outFile << temp.substr(0, lastRead);
 466                                                                 delete memblock;
 467
 468                                                                 fileB.close();
 469                                                                 m->mothurRemove(fileName2);
 470
 471                                                                 //write out the merged memory
 472                                                                 if (numOutputs[groupID] > 60) {
 473                                                                         outFile << outputs[groupID];
 474                                                                         outputs[groupID] = "";
 475                                                                         numOutputs[groupID] = 0;
 476                                                                 }
 477
 478                                                                 outFile.close();
 479
 480                                                                 wroteOutPut[groupID] = true;
 481                                                                 wroteOutPut[groupIDB] = false;
 482                                                         }else{ } //just merge b's memory with a's memory
 483                                                 }
 484                                                 else{
 485                                                         numOutputs[groupID] += numOutputs[groupIDA];
 486                                                         outputs[groupID] += outputs[groupIDA];
 487
 488                                                         outputs[groupIDA] = "";
 489                                                         numOutputs[groupIDA] = 0;
 490
 491                                                         if (wroteOutPut[groupIDA]) {
 492                                                                 string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
 493                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 494
 495                                                                 outFile.open(fileName.c_str(), ios::app);
 496
 497                                                                 long size;
 498                                                                 char* memblock;
 499
 500                                                                 size = fileB.tellg();
 501
 502                                                                 fileB.seekg (0, ios::beg);
 503
 504                                                                 int numRead = size / 1024;
 505                                                                 int lastRead = size % 1024;
 506
 507                                                                 for (int i = 0; i < numRead; i++) {
 508
 509                                                                         memblock = new char [1024];
 510
 511                                                                         fileB.read (memblock, 1024);
 512                                                                         string temp = memblock;
 513                                                                         outFile << temp.substr(0, 1024);
 514
 515                                                                         delete memblock;
 516                                                                 }
 517
 518                                                                 memblock = new char [lastRead];
 519
 520                                                                 fileB.read (memblock, lastRead);
 521
 522                                                                 //not sure why but it will read more than lastRead char...??
 523                                                                 string temp = memblock;
 524                                                                 outFile << temp.substr(0, lastRead);
 525
 526                                                                 delete memblock;
 527
 528                                                                 fileB.close();
 529                                                                 m->mothurRemove(fileName2);
 530
 531                                                                 //write out the merged memory
 532                                                                 if (numOutputs[groupID] > 60) {
 533                                                                         outFile << outputs[groupID];
 534                                                                         outputs[groupID] = "";
 535                                                                         numOutputs[groupID] = 0;
 536                                                                 }
 537
 538                                                                 outFile.close();
 539
 540                                                                 wroteOutPut[groupID] = true;
 541                                                                 wroteOutPut[groupIDA] = false;
 542                                                         }else { } //just merge memory
 543                                                 }
 544                                         }
 545                                 }
 546                         }
 547                         m->gobble(dFile);
 548                 }
 549                 dFile.close();
 550
 551                 vector<string> tempDistFiles;
 552                 for (int i = 0; i < numGroups; i++) {
 553             string fileName = distFile + "." + toString(i) + ".temp";
 554             tempDistFiles.push_back(fileName);
 555             //remove old names files just in case
 556
 557                         if (numOutputs[i] > 0) {
 558                                 outFile.open(fileName.c_str(), ios::app);
 559                                 outFile << outputs[i];
 560                                 outFile.close();
 561                         }
 562                 }
 563
 564         map<string, int> seqGroup;
 565         for (int i = 0; i < groups.size(); i++) {
 566             for (set<string>::iterator itNames = groups[i].begin(); itNames != groups[i].end();) {
 567                 seqGroup[*itNames] = i;
 568                 groups[i].erase(itNames++);
 569             }
 570         }
 571
 572                 splitNames(seqGroup, numGroups, tempDistFiles);
 573
 574                 return 0;
 575         }
 576         catch(exception& e) {
 577                 m->errorOut(e, "SplitMatrix", "splitDistanceLarge");
 578                 exit(1);
 579         }
 580 }
 581 //********************************************************************************************************************
 582 int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<string>& tempDistFiles){
 583         try {
 584         ofstream outFile;
 585         map<string, int>::iterator it;
 586
 587         string inputFile = namefile;
 588         if (countfile != "") { inputFile = countfile; }
 589
 590         for(int i=0;i<numGroups;i++){  m->mothurRemove((inputFile + "." + toString(i) + ".temp")); }
 591
 592         singleton = inputFile + ".extra.temp";
 593         ofstream remainingNames;
 594         m->openOutputFile(singleton, remainingNames);
 595
 596         bool wroteExtra = false;
 597
 598         ifstream bigNameFile;
 599         m->openInputFile(inputFile, bigNameFile);
 600
 601         //grab header line
 602         string headers = "";
 603         if (countfile != "") { headers = m->getline(bigNameFile); m->gobble(bigNameFile); }
 604
 605         string name, nameList;
 606         while(!bigNameFile.eof()){
 607             bigNameFile >> name >> nameList;
 608             m->getline(bigNameFile); m->gobble(bigNameFile); //extra getline is for rest of countfile line if groups are given.
 609
 610             //did this sequence get assigned a group
 611             it = seqGroup.find(name);
 612
 613             if (it != seqGroup.end()) {
 614                 m->openOutputFileAppend((inputFile + "." + toString(it->second) + ".temp"), outFile);
 615                 outFile << name << '\t' << nameList << endl;
 616                 outFile.close();
 617             }else{
 618                 wroteExtra = true;
 619                 remainingNames << name << '\t' << nameList << endl;
 620             }
 621         }
 622         bigNameFile.close();
 623
 624                 for(int i=0;i<numGroups;i++){
 625                         string tempNameFile = inputFile + "." + toString(i) + ".temp";
 626                         string tempDistFile = tempDistFiles[i];
 627
 628             //if there are valid distances
 629             ifstream fileHandle;
 630             fileHandle.open(tempDistFile.c_str());
 631             if(fileHandle)      {
 632                 m->gobble(fileHandle);
 633                 if (!fileHandle.eof()) {  //check
 634                                 map<string, string> temp;
 635                 if (countfile != "") {
 636                     //add header
 637                     ofstream out;
 638                     string newtempNameFile = tempNameFile + "2";
 639                     m->openOutputFile(newtempNameFile, out);
 640                     out << headers << endl;
 641                     out.close();
 642                     m->appendFiles(tempNameFile, newtempNameFile);
 643                     m->mothurRemove(tempNameFile);
 644                     m->renameFile(newtempNameFile, tempNameFile);
 645                 }
 646                                 temp[tempDistFile] = tempNameFile;
 647                                 dists.push_back(temp);
 648                         }else{
 649                                 ifstream in;
 650                                 m->openInputFile(tempNameFile, in);
 651
 652                                 while(!in.eof()) {
 653                                         in >> name >> nameList;  m->gobble(in);
 654                                         wroteExtra = true;
 655                                         remainingNames << name << '\t' << nameList << endl;
 656                                 }
 657                                 in.close();
 658                                 m->mothurRemove(tempNameFile);
 659                         }
 660             }
 661             fileHandle.close();
 662                 }
 663
 664                 remainingNames.close();
 665
 666                 if (!wroteExtra) {
 667                         m->mothurRemove(singleton);
 668                         singleton = "none";
 669                 }else if (countfile != "") {
 670             //add header
 671             ofstream out;
 672             string newtempNameFile = singleton + "2";
 673             m->openOutputFile(newtempNameFile, out);
 674             out << headers << endl;
 675             out.close();
 676             m->appendFiles(singleton, newtempNameFile);
 677             m->mothurRemove(singleton);
 678             m->renameFile(newtempNameFile, singleton);
 679         }
 680
 681                 return 0;
 682         }
 683         catch(exception& e) {
 684                 m->errorOut(e, "SplitMatrix", "splitNames");
 685                 exit(1);
 686         }
 687 }
 688 //********************************************************************************************************************
 689 int SplitMatrix::splitDistanceRAM(){
 690         try {
 691                 vector<set<string> > groups;
 692                 vector<string> outputs;
 693
 694                 int numGroups = 0;
 695
 696                 ifstream dFile;
 697                 m->openInputFile(distFile, dFile);
 698
 699                 while(dFile){
 700                         string seqA, seqB;
 701                         float dist;
 702
 703                         dFile >> seqA >> seqB >> dist;
 704
 705                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
 706
 707                         if(dist < cutoff){
 708                                 //cout << "in cutoff: " << dist << endl;
 709                                 int groupIDA = -1;
 710                                 int groupIDB = -1;
 711                                 int groupID = -1;
 712
 713                                 for(int i=0;i<numGroups;i++){
 714                                         set<string>::iterator aIt = groups[i].find(seqA);
 715                                         set<string>::iterator bIt = groups[i].find(seqB);
 716
 717                                         if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
 718                                                 groups[i].insert(seqB);
 719                                                 groupIDA = i;
 720                                                 groupID = groupIDA;
 721
 722                                                 //cout << "in aIt: " << groupID << endl;
 723         //                                      break;
 724                                         }
 725                                         else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
 726                                                 groups[i].insert(seqA);
 727                                                 groupIDB = i;
 728                                                 groupID = groupIDB;
 729
 730                                         //      cout << "in bIt: " << groupID << endl;
 731         //                                      break;
 732                                         }
 733
 734                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 735                                                 if(groupIDA < groupIDB){
 736                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 737                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 738                                                         groups[groupIDB].clear();
 739                                                         groupID = groupIDA;
 740                                                 }
 741                                                 else{
 742                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 743                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 744                                                         groups[groupIDA].clear();
 745                                                         groupID = groupIDB;
 746                                                 }
 747                                                 break;
 748                                         }
 749                                 }
 750
 751         //windows is gonna gag on the reuse of outFile, will need to make it local...
 752
 753                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 754                                         set<string> newGroup;
 755                                         newGroup.insert(seqA);
 756                                         newGroup.insert(seqB);
 757                                         groups.push_back(newGroup);
 758
 759                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 760                                         outputs.push_back(tempOut);
 761                                         numGroups++;
 762                                 }
 763                                 else{
 764
 765                                         outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 766
 767                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 768                                                 string row, column, distance;
 769                                                 if(groupIDA<groupIDB){
 770                                                         //merge memory
 771                                                         outputs[groupID] += outputs[groupIDB];
 772                                                         outputs[groupIDB] = "";
 773                                                 }else{
 774                                                         outputs[groupID] += outputs[groupIDA];
 775                                                         outputs[groupIDA] = "";
 776                                                 }
 777                                         }
 778                                 }
 779                         }
 780                         m->gobble(dFile);
 781                 }
 782                 dFile.close();
 783
 784         vector<string> tempDistFiles;
 785                 for (int i = 0; i < numGroups; i++) {
 786             string fileName = distFile + "." + toString(i) + ".temp";
 787             tempDistFiles.push_back(fileName);
 788                         if (outputs[i] != "") {
 789                                 ofstream outFile;
 790                                 outFile.open(fileName.c_str(), ios::ate);
 791                                 outFile << outputs[i];
 792                                 outFile.close();
 793                         }
 794                 }
 795
 796         map<string, int> seqGroup;
 797         for (int i = 0; i < groups.size(); i++) {
 798             for (set<string>::iterator itNames = groups[i].begin(); itNames != groups[i].end();) {
 799                 seqGroup[*itNames] = i;
 800                 groups[i].erase(itNames++);
 801             }
 802         }
 803
 804                 splitNames(seqGroup, numGroups, tempDistFiles);
 805
 806                 return 0;
 807         }
 808         catch(exception& e) {
 809                 m->errorOut(e, "SplitMatrix", "splitDistanceRAM");
 810                 exit(1);
 811         }
 812 }
 813 //********************************************************************************************************************
 814 //sorts biggest to smallest
 815 inline bool compareFileSizes(map<string, string> left, map<string, string> right){
 816
 817         FILE * pFile;
 818         long leftsize = 0;
 819
 820         //get num bytes in file
 821         string filename = left.begin()->first;
 822         pFile = fopen (filename.c_str(),"rb");
 823         string error = "Error opening " + filename;
 824         if (pFile==NULL) perror (error.c_str());
 825         else{
 826                 fseek (pFile, 0, SEEK_END);
 827                 leftsize=ftell (pFile);
 828                 fclose (pFile);
 829         }
 830
 831         FILE * pFile2;
 832         long rightsize = 0;
 833
 834         //get num bytes in file
 835         filename = right.begin()->first;
 836         pFile2 = fopen (filename.c_str(),"rb");
 837         error = "Error opening " + filename;
 838         if (pFile2==NULL) perror (error.c_str());
 839         else{
 840                 fseek (pFile2, 0, SEEK_END);
 841                 rightsize=ftell (pFile2);
 842                 fclose (pFile2);
 843         }
 844
 845         return (leftsize > rightsize);
 846 }
 847 /***********************************************************************/
 848 //returns map of distance files -> namefile sorted by distance file size
 849 vector< map< string, string> > SplitMatrix::getDistanceFiles(){
 850         try {
 851
 852                 sort(dists.begin(), dists.end(), compareFileSizes);
 853
 854                 return dists;
 855         }
 856         catch(exception& e) {
 857                 m->errorOut(e, "SplitMatrix", "getDistanceFiles");
 858                 exit(1);
 859         }
 860 }
 861 /***********************************************************************/
 862 SplitMatrix::~SplitMatrix(){}
 863 /***********************************************************************/
 864