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
  14 /***********************************************************************/
  15
  16 SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, string t, bool l){
  17         m = MothurOut::getInstance();
  18         distFile = distfile;
  19         cutoff = c;
  20         namefile = name;
  21         method = t;
  22         taxFile = tax;
  23         large = l;
  24 }
  25 /***********************************************************************/
  26
  27 SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p, string output){
  28         m = MothurOut::getInstance();
  29         fastafile = ffile;
  30         namefile = name;
  31         taxFile = tax;
  32         cutoff = c;
  33         method = t;
  34         processors = p;
  35         outputDir = output;
  36 }
  37
  38 /***********************************************************************/
  39
  40 int SplitMatrix::split(){
  41         try {
  42
  43                 if (method == "distance") {
  44                         splitDistance();
  45                 }else if ((method == "classify") || (method == "fasta")) {
  46                         splitClassify();
  47                 }else {
  48                         m->mothurOut("Unknown splitting method, aborting split."); m->mothurOutEndLine();
  49                         map<string, string> temp;
  50                         temp[distFile] = namefile;
  51                         dists.push_back(temp);
  52                 }
  53
  54                 return 0;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "SplitMatrix", "split");
  58                 exit(1);
  59         }
  60 }
  61 /***********************************************************************/
  62 int SplitMatrix::splitDistance(){
  63         try {
  64
  65                 if (large)      { splitDistanceLarge(); }
  66                 else            { splitDistanceRAM();   }
  67
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "SplitMatrix", "splitDistance");
  71                 exit(1);
  72         }
  73 }
  74
  75 /***********************************************************************/
  76 int SplitMatrix::splitClassify(){
  77         try {
  78                 cutoff = int(cutoff);
  79
  80                 map<string, int> seqGroup;
  81                 map<string, int>::iterator it;
  82                 map<string, int>::iterator it2;
  83
  84                 int numGroups = 0;
  85
  86                 //build tree from users taxonomy file
  87                 PhyloTree* phylo = new PhyloTree();
  88
  89                 ifstream in;
  90                 openInputFile(taxFile, in);
  91
  92                 //read in users taxonomy file and add sequences to tree
  93                 string seqname, tax;
  94                 while(!in.eof()){
  95                         in >> seqname >> tax; gobble(in);
  96                         phylo->addSeqToTree(seqname, tax);
  97                 }
  98                 in.close();
  99
 100                 phylo->assignHeirarchyIDs(0);
 101
 102                 //make sure the cutoff is not greater than maxlevel
 103                 if (cutoff > phylo->getMaxLevel()) { m->mothurOut("splitcutoff is greater than the longest taxonomy, using " + toString(phylo->getMaxLevel())); m->mothurOutEndLine(); cutoff = phylo->getMaxLevel(); }
 104
 105                 //for each node in tree
 106                 for (int i = 0; i < phylo->getNumNodes(); i++) {
 107
 108                         //is this node within the cutoff
 109                         TaxNode taxon = phylo->get(i);
 110
 111                         if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
 112                                 if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
 113                                         for (int j = 0; j < taxon.accessions.size(); j++) {
 114                                                 seqGroup[taxon.accessions[j]] = numGroups;
 115                                         }
 116                                         numGroups++;
 117                                 }
 118                         }
 119                 }
 120
 121                 delete phylo;
 122
 123                 if (method == "classify") {
 124                         splitDistanceFileByTax(seqGroup, numGroups);
 125                 }else {
 126                         createDistanceFilesFromTax(seqGroup, numGroups);
 127                 }
 128
 129                 return 0;
 130
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "SplitMatrix", "splitClassify");
 134                 exit(1);
 135         }
 136 }
 137 /***********************************************************************/
 138 int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numGroups){
 139         try {
 140                 map<string, int> copyGroups = seqGroup;
 141                 map<string, int>::iterator it;
 142                 set<string> names;
 143
 144                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 145                         remove((fastafile + "." + toString(i) + ".temp").c_str());
 146                 }
 147
 148                 ifstream in;
 149                 openInputFile(fastafile, in);
 150
 151                 //parse fastafile
 152                 ofstream outFile;
 153                 while (!in.eof()) {
 154                         Sequence query(in); gobble(in);
 155                         if (query.getName() != "") {
 156
 157                                 it = seqGroup.find(query.getName());
 158
 159                                 //save names in case no namefile is given
 160                                 if (namefile == "") {  names.insert(query.getName()); }
 161
 162                                 if (it != seqGroup.end()) { //not singleton
 163                                         openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
 164                                         query.printSequence(outFile);
 165                                         outFile.close();
 166
 167                                         copyGroups.erase(query.getName());
 168                                 }
 169                         }
 170                 }
 171                 in.close();
 172
 173                 //warn about sequence in groups that are not in fasta file
 174                 for(it = copyGroups.begin(); it != copyGroups.end(); it++) {
 175                         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();
 176                         exit(1);
 177                 }
 178
 179                 copyGroups.clear();
 180
 181                 //process each distance file
 182                 for (int i = 0; i < numGroups; i++) {
 183
 184                         string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(cutoff);
 185
 186                         Command* command = new DistanceCommand(options);
 187                         command->execute();
 188                         delete command;
 189
 190                         remove((fastafile + "." + toString(i) + ".temp").c_str());
 191
 192                         //remove old names files just in case
 193                         remove((namefile + "." + toString(i) + ".temp").c_str());
 194                 }
 195
 196                 singleton = namefile + ".extra.temp";
 197                 ofstream remainingNames;
 198                 openOutputFile(singleton, remainingNames);
 199
 200                 bool wroteExtra = false;
 201
 202                 ifstream bigNameFile;
 203                 openInputFile(namefile, bigNameFile);
 204
 205                 string name, nameList;
 206                 while(!bigNameFile.eof()){
 207                         bigNameFile >> name >> nameList;  gobble(bigNameFile);
 208
 209                         //did this sequence get assigned a group
 210                         it = seqGroup.find(name);
 211
 212                         if (it != seqGroup.end()) {
 213                                 openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
 214                                 outFile << name << '\t' << nameList << endl;
 215                                 outFile.close();
 216                         }else{
 217                                 wroteExtra = true;
 218                                 remainingNames << name << '\t' << nameList << endl;
 219                         }
 220                 }
 221                 bigNameFile.close();
 222
 223                 for(int i=0;i<numGroups;i++){
 224                         string tempNameFile = namefile + "." + toString(i) + ".temp";
 225                         string tempDistFile = outputDir + getRootName(getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
 226
 227                         //if there are valid distances
 228                         ifstream fileHandle;
 229                         fileHandle.open(tempDistFile.c_str());
 230                         if(fileHandle)  {
 231                                 gobble(fileHandle);
 232                                 if (!fileHandle.eof()) {  //check for blank file - this could occur if all dists in group are above cutoff
 233                                         map<string, string> temp;
 234                                         temp[tempDistFile] = tempNameFile;
 235                                         dists.push_back(temp);
 236                                 }else {
 237                                         ifstream in;
 238                                         openInputFile(tempNameFile, in);
 239
 240                                         while(!in.eof()) {
 241                                                 in >> name >> nameList;  gobble(in);
 242                                                 wroteExtra = true;
 243                                                 remainingNames << name << '\t' << nameList << endl;
 244                                         }
 245                                         in.close();
 246                                         remove(tempNameFile.c_str());
 247                                 }
 248                         }
 249                         fileHandle.close();
 250                 }
 251
 252                 remainingNames.close();
 253                 if (!wroteExtra) {
 254                         remove(singleton.c_str());
 255                         singleton = "none";
 256                 }
 257
 258                 if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { remove((dists[i].begin()->first).c_str()); remove((dists[i].begin()->second).c_str()); } dists.clear(); }
 259
 260                 return 0;
 261         }
 262         catch(exception& e) {
 263                 m->errorOut(e, "SplitMatrix", "createDistanceFilesFromTax");
 264                 exit(1);
 265         }
 266 }
 267 /***********************************************************************/
 268 int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroups){
 269         try {
 270                 map<string, int>::iterator it;
 271                 map<string, int>::iterator it2;
 272
 273                 ifstream dFile;
 274                 openInputFile(distFile, dFile);
 275                 ofstream outFile;
 276
 277                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 278                         remove((distFile + "." + toString(i) + ".temp").c_str());
 279                 }
 280
 281                 //for buffering the io to improve speed
 282                  //allow for 10 dists to be stored, then output.
 283                 vector<string> outputs;  outputs.resize(numGroups, "");
 284                 vector<int> numOutputs;  numOutputs.resize(numGroups, 0);
 285
 286                 //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
 287                 //this can occur if we have converted the phylip to column, since we reduce the size at that step by using the cutoff value
 288                 vector<bool> validDistances;   validDistances.resize(numGroups, false);
 289
 290                 //for each distance
 291                 while(dFile){
 292                         string seqA, seqB;
 293                         float dist;
 294
 295                         if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str());        } }
 296
 297                         dFile >> seqA >> seqB >> dist;  gobble(dFile);
 298
 299                         //if both sequences are in the same group then they are within the cutoff
 300                         it = seqGroup.find(seqA);
 301                         it2 = seqGroup.find(seqB);
 302
 303                         if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons
 304                                 if (it->second == it2->second) { //they are from the same group so add the distance
 305                                         if (numOutputs[it->second] > 30) {
 306                                                 openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
 307                                                 outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
 308                                                 outFile.close();
 309                                                 outputs[it->second] = "";
 310                                                 numOutputs[it->second] = 0;
 311                                                 validDistances[it->second] = true;
 312                                         }else{
 313                                                 outputs[it->second] += seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 314                                                 numOutputs[it->second]++;
 315                                         }
 316                                 }
 317                         }
 318                 }
 319                 dFile.close();
 320
 321                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 322                         remove((namefile + "." + toString(i) + ".temp").c_str());
 323
 324                         //write out any remaining buffers
 325                         if (numOutputs[i] > 0) {
 326                                 openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
 327                                 outFile << outputs[i];
 328                                 outFile.close();
 329                                 outputs[i] = "";
 330                                 numOutputs[i] = 0;
 331                                 validDistances[i] = true;
 332                         }
 333                 }
 334
 335                 ifstream bigNameFile;
 336                 openInputFile(namefile, bigNameFile);
 337
 338                 singleton = namefile + ".extra.temp";
 339                 ofstream remainingNames;
 340                 openOutputFile(singleton, remainingNames);
 341
 342                 bool wroteExtra = false;
 343
 344                 string name, nameList;
 345                 while(!bigNameFile.eof()){
 346                         bigNameFile >> name >> nameList;  gobble(bigNameFile);
 347
 348                         //did this sequence get assigned a group
 349                         it = seqGroup.find(name);
 350
 351                         if (it != seqGroup.end()) {
 352                                 openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
 353                                 outFile << name << '\t' << nameList << endl;
 354                                 outFile.close();
 355                         }else{
 356                                 wroteExtra = true;
 357                                 remainingNames << name << '\t' << nameList << endl;
 358                         }
 359                 }
 360                 bigNameFile.close();
 361
 362                 for(int i=0;i<numGroups;i++){
 363                         string tempNameFile = namefile + "." + toString(i) + ".temp";
 364                         string tempDistFile = distFile + "." + toString(i) + ".temp";
 365
 366                         //if there are valid distances
 367                         if (validDistances[i]) {
 368                                 map<string, string> temp;
 369                                 temp[tempDistFile] = tempNameFile;
 370                                 dists.push_back(temp);
 371                         }else{
 372                                 ifstream in;
 373                                 openInputFile(tempNameFile, in);
 374
 375                                 while(!in.eof()) {
 376                                         in >> name >> nameList;  gobble(in);
 377                                         wroteExtra = true;
 378                                         remainingNames << name << '\t' << nameList << endl;
 379                                 }
 380                                 in.close();
 381                                 remove(tempNameFile.c_str());
 382                         }
 383                 }
 384
 385                 remainingNames.close();
 386
 387                 if (!wroteExtra) {
 388                         remove(singleton.c_str());
 389                         singleton = "none";
 390                 }
 391
 392                 if (m->control_pressed)  {
 393                         for (int i = 0; i < dists.size(); i++) {
 394                                 remove((dists[i].begin()->first).c_str());
 395                                 remove((dists[i].begin()->second).c_str());
 396                         }
 397                         dists.clear();
 398                 }
 399
 400                 return 0;
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "SplitMatrix", "splitDistanceFileByTax");
 404                 exit(1);
 405         }
 406 }
 407 /***********************************************************************/
 408 int SplitMatrix::splitDistanceLarge(){
 409         try {
 410                 vector<set<string> > groups;
 411
 412                 //for buffering the io to improve speed
 413                  //allow for 30 dists to be stored, then output.
 414                 vector<string> outputs;
 415                 vector<int> numOutputs;
 416                 vector<bool> wroteOutPut;
 417
 418                 int numGroups = 0;
 419
 420                 ofstream outFile;
 421                 ifstream dFile;
 422                 openInputFile(distFile, dFile);
 423
 424                 while(dFile){
 425                         string seqA, seqB;
 426                         float dist;
 427
 428                         dFile >> seqA >> seqB >> dist;
 429
 430                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
 431
 432                         if(dist < cutoff){
 433                                 //cout << "in cutoff: " << dist << endl;
 434                                 int groupIDA = -1;
 435                                 int groupIDB = -1;
 436                                 int groupID = -1;
 437
 438                                 for(int i=0;i<numGroups;i++){
 439                                         set<string>::iterator aIt = groups[i].find(seqA);
 440                                         set<string>::iterator bIt = groups[i].find(seqB);
 441
 442                                         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]
 443                                                 groups[i].insert(seqB);
 444                                                 groupIDA = i;
 445                                                 groupID = groupIDA;
 446
 447                                                 //cout << "in aIt: " << groupID << endl;
 448         //                                      break;
 449                                         }
 450                                         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]
 451                                                 groups[i].insert(seqA);
 452                                                 groupIDB = i;
 453                                                 groupID = groupIDB;
 454
 455                                         //      cout << "in bIt: " << groupID << endl;
 456         //                                      break;
 457                                         }
 458
 459                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 460                                                 if(groupIDA < groupIDB){
 461                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 462                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 463                                                         groups[groupIDB].clear();
 464                                                         groupID = groupIDA;
 465                                                 }
 466                                                 else{
 467                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 468                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 469                                                         groups[groupIDA].clear();
 470                                                         groupID = groupIDB;
 471                                                 }
 472                                                 break;
 473                                         }
 474                                 }
 475
 476         //windows is gonna gag on the reuse of outFile, will need to make it local...
 477
 478                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 479                                         set<string> newGroup;
 480                                         newGroup.insert(seqA);
 481                                         newGroup.insert(seqB);
 482                                         groups.push_back(newGroup);
 483
 484                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 485                                         outputs.push_back(tempOut);
 486                                         numOutputs.push_back(1);
 487                                         wroteOutPut.push_back(false);
 488
 489                                         numGroups++;
 490                                 }
 491                                 else{
 492                                         string fileName = distFile + "." + toString(groupID) + ".temp";
 493
 494                                         //have we reached the max buffer size
 495                                         if (numOutputs[groupID] > 60) { //write out sequence
 496                                                 outFile.open(fileName.c_str(), ios::app);
 497                                                 outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
 498                                                 outFile.close();
 499
 500                                                 outputs[groupID] = "";
 501                                                 numOutputs[groupID] = 0;
 502                                                 wroteOutPut[groupID] = true;
 503                                         }else {
 504                                                 outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 505                                                 numOutputs[groupID]++;
 506                                         }
 507
 508                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 509                                                 string row, column, distance;
 510                                                 if(groupIDA<groupIDB){
 511
 512                                                         //merge memory
 513                                                         numOutputs[groupID] += numOutputs[groupIDB];
 514                                                         outputs[groupID] += outputs[groupIDB];
 515
 516                                                         outputs[groupIDB] = "";
 517                                                         numOutputs[groupIDB] = 0;
 518
 519                                                         //if groupB is written to file it is above buffer size so read and write to new merged file
 520                                                         if (wroteOutPut[groupIDB]) {
 521                                                                 string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
 522                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 523
 524                                                                 outFile.open(fileName.c_str(), ios::app);
 525
 526                                                                 long size;
 527                                                                 char* memblock;
 528
 529                                                                 size = fileB.tellg();
 530
 531                                                                 fileB.seekg (0, ios::beg);
 532
 533                                                                 int numRead = size / 1024;
 534                                                                 int lastRead = size % 1024;
 535
 536                                                                 for (int i = 0; i < numRead; i++) {
 537
 538                                                                         memblock = new char [1024];
 539
 540                                                                         fileB.read (memblock, 1024);
 541
 542                                                                         string temp = memblock;
 543                                                                         outFile << temp.substr(0, 1024);
 544
 545                                                                         delete memblock;
 546                                                                 }
 547
 548                                                                 memblock = new char [lastRead];
 549
 550                                                                 fileB.read (memblock, lastRead);
 551
 552                                                                 //not sure why but it will read more than lastRead char...??
 553                                                                 string temp = memblock;
 554                                                                 outFile << temp.substr(0, lastRead);
 555                                                                 delete memblock;
 556
 557                                                                 fileB.close();
 558                                                                 remove(fileName2.c_str());
 559
 560                                                                 //write out the merged memory
 561                                                                 if (numOutputs[groupID] > 60) {
 562                                                                         outFile << outputs[groupID];
 563                                                                         outputs[groupID] = "";
 564                                                                         numOutputs[groupID] = 0;
 565                                                                 }
 566
 567                                                                 outFile.close();
 568
 569                                                                 wroteOutPut[groupID] = true;
 570                                                                 wroteOutPut[groupIDB] = false;
 571                                                         }else{ } //just merge b's memory with a's memory
 572                                                 }
 573                                                 else{
 574                                                         numOutputs[groupID] += numOutputs[groupIDA];
 575                                                         outputs[groupID] += outputs[groupIDA];
 576
 577                                                         outputs[groupIDA] = "";
 578                                                         numOutputs[groupIDA] = 0;
 579
 580                                                         if (wroteOutPut[groupIDA]) {
 581                                                                 string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
 582                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 583
 584                                                                 outFile.open(fileName.c_str(), ios::app);
 585
 586                                                                 long size;
 587                                                                 char* memblock;
 588
 589                                                                 size = fileB.tellg();
 590
 591                                                                 fileB.seekg (0, ios::beg);
 592
 593                                                                 int numRead = size / 1024;
 594                                                                 int lastRead = size % 1024;
 595
 596                                                                 for (int i = 0; i < numRead; i++) {
 597
 598                                                                         memblock = new char [1024];
 599
 600                                                                         fileB.read (memblock, 1024);
 601                                                                         string temp = memblock;
 602                                                                         outFile << temp.substr(0, 1024);
 603
 604                                                                         delete memblock;
 605                                                                 }
 606
 607                                                                 memblock = new char [lastRead];
 608
 609                                                                 fileB.read (memblock, lastRead);
 610
 611                                                                 //not sure why but it will read more than lastRead char...??
 612                                                                 string temp = memblock;
 613                                                                 outFile << temp.substr(0, lastRead);
 614
 615                                                                 delete memblock;
 616
 617                                                                 fileB.close();
 618                                                                 remove(fileName2.c_str());
 619
 620                                                                 //write out the merged memory
 621                                                                 if (numOutputs[groupID] > 60) {
 622                                                                         outFile << outputs[groupID];
 623                                                                         outputs[groupID] = "";
 624                                                                         numOutputs[groupID] = 0;
 625                                                                 }
 626
 627                                                                 outFile.close();
 628
 629                                                                 wroteOutPut[groupID] = true;
 630                                                                 wroteOutPut[groupIDA] = false;
 631                                                         }else { } //just merge memory
 632                                                 }
 633                                         }
 634                                 }
 635                         }
 636                         gobble(dFile);
 637                 }
 638                 dFile.close();
 639
 640                 for (int i = 0; i < numGroups; i++) {
 641                         if (numOutputs[i] > 0) {
 642                                 string fileName = distFile + "." + toString(i) + ".temp";
 643                                 outFile.open(fileName.c_str(), ios::app);
 644                                 outFile << outputs[i];
 645                                 outFile.close();
 646                         }
 647                 }
 648
 649                 splitNames(groups);
 650
 651                 return 0;
 652         }
 653         catch(exception& e) {
 654                 m->errorOut(e, "SplitMatrix", "splitDistanceLarge");
 655                 exit(1);
 656         }
 657 }
 658 //********************************************************************************************************************
 659 int SplitMatrix::splitNames(vector<set<string> >& groups){
 660         try {
 661                 int numGroups = groups.size();
 662
 663                 ifstream bigNameFile(namefile.c_str());
 664                 if(!bigNameFile){
 665                         cerr << "Error: We can't open the name file\n";
 666                         exit(1);
 667                 }
 668
 669                 map<string, string> nameMap;
 670                 string name, nameList;
 671                 while(bigNameFile){
 672                         bigNameFile >> name >> nameList;
 673                         nameMap[name] = nameList;
 674                         gobble(bigNameFile);
 675                 }
 676                 bigNameFile.close();
 677
 678                 for(int i=0;i<numGroups;i++){  //parse names file to match distance files
 679                         int numSeqsInGroup = groups[i].size();
 680
 681                         if(numSeqsInGroup > 0){
 682                                 string fileName = namefile + "." + toString(i) + ".temp";
 683                                 ofstream smallNameFile(fileName.c_str(), ios::ate);
 684
 685                                 for(set<string>::iterator gIt=groups[i].begin();gIt!=groups[i].end();gIt++){
 686                                         map<string,string>::iterator nIt = nameMap.find(*gIt);
 687                                         if (nIt != nameMap.end()) {
 688                                                 smallNameFile << nIt->first << '\t' << nIt->second << endl;
 689                                                 nameMap.erase(nIt);
 690                                         }else{
 691                                                 m->mothurOut((*gIt) + " is in your distance file and not in your namefile.  Please correct."); m->mothurOutEndLine(); exit(1);
 692                                         }
 693                                 }
 694                                 smallNameFile.close();
 695                         }
 696                 }
 697
 698                 //names of singletons
 699                 if (nameMap.size() != 0) {
 700                         singleton = namefile + ".extra.temp";
 701                         ofstream remainingNames(singleton.c_str(), ios::ate);
 702                         for(map<string,string>::iterator nIt=nameMap.begin();nIt!=nameMap.end();nIt++){
 703                                 remainingNames << nIt->first << '\t' << nIt->second << endl;
 704                         }
 705                         remainingNames.close();
 706                 }else { singleton = "none"; }
 707
 708                 for(int i=0;i<numGroups;i++){
 709                         if(groups[i].size() > 0){
 710                                 string tempNameFile = namefile + "." + toString(i) + ".temp";
 711                                 string tempDistFile = distFile + "." + toString(i) + ".temp";
 712
 713                                 map<string, string> temp;
 714                                 temp[tempDistFile] = tempNameFile;
 715                                 dists.push_back(temp);
 716                         }
 717                 }
 718
 719                 if (m->control_pressed)  {
 720                         for (int i = 0; i < dists.size(); i++) {
 721                                 remove((dists[i].begin()->first).c_str());
 722                                 remove((dists[i].begin()->second).c_str());
 723                         }
 724                         dists.clear();
 725                 }
 726
 727                 return 0;
 728         }
 729         catch(exception& e) {
 730                 m->errorOut(e, "SplitMatrix", "splitNames");
 731                 exit(1);
 732         }
 733 }
 734 //********************************************************************************************************************
 735 int SplitMatrix::splitDistanceRAM(){
 736         try {
 737                 vector<set<string> > groups;
 738                 vector<string> outputs;
 739
 740                 int numGroups = 0;
 741
 742                 ifstream dFile;
 743                 openInputFile(distFile, dFile);
 744
 745                 while(dFile){
 746                         string seqA, seqB;
 747                         float dist;
 748
 749                         dFile >> seqA >> seqB >> dist;
 750
 751                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
 752
 753                         if(dist < cutoff){
 754                                 //cout << "in cutoff: " << dist << endl;
 755                                 int groupIDA = -1;
 756                                 int groupIDB = -1;
 757                                 int groupID = -1;
 758
 759                                 for(int i=0;i<numGroups;i++){
 760                                         set<string>::iterator aIt = groups[i].find(seqA);
 761                                         set<string>::iterator bIt = groups[i].find(seqB);
 762
 763                                         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]
 764                                                 groups[i].insert(seqB);
 765                                                 groupIDA = i;
 766                                                 groupID = groupIDA;
 767
 768                                                 //cout << "in aIt: " << groupID << endl;
 769         //                                      break;
 770                                         }
 771                                         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]
 772                                                 groups[i].insert(seqA);
 773                                                 groupIDB = i;
 774                                                 groupID = groupIDB;
 775
 776                                         //      cout << "in bIt: " << groupID << endl;
 777         //                                      break;
 778                                         }
 779
 780                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 781                                                 if(groupIDA < groupIDB){
 782                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 783                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 784                                                         groups[groupIDB].clear();
 785                                                         groupID = groupIDA;
 786                                                 }
 787                                                 else{
 788                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 789                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 790                                                         groups[groupIDA].clear();
 791                                                         groupID = groupIDB;
 792                                                 }
 793                                                 break;
 794                                         }
 795                                 }
 796
 797         //windows is gonna gag on the reuse of outFile, will need to make it local...
 798
 799                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 800                                         set<string> newGroup;
 801                                         newGroup.insert(seqA);
 802                                         newGroup.insert(seqB);
 803                                         groups.push_back(newGroup);
 804
 805                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 806                                         outputs.push_back(tempOut);
 807                                         numGroups++;
 808                                 }
 809                                 else{
 810
 811                                         outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 812
 813                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 814                                                 string row, column, distance;
 815                                                 if(groupIDA<groupIDB){
 816                                                         //merge memory
 817                                                         outputs[groupID] += outputs[groupIDB];
 818                                                         outputs[groupIDB] = "";
 819                                                 }else{
 820                                                         outputs[groupID] += outputs[groupIDA];
 821                                                         outputs[groupIDA] = "";
 822                                                 }
 823                                         }
 824                                 }
 825                         }
 826                         gobble(dFile);
 827                 }
 828                 dFile.close();
 829
 830                 for (int i = 0; i < numGroups; i++) {
 831                         if (outputs[i] != "") {
 832                                 ofstream outFile;
 833                                 string fileName = distFile + "." + toString(i) + ".temp";
 834                                 outFile.open(fileName.c_str(), ios::ate);
 835                                 outFile << outputs[i];
 836                                 outFile.close();
 837                         }
 838                 }
 839
 840                 splitNames(groups);
 841
 842                 return 0;
 843         }
 844         catch(exception& e) {
 845                 m->errorOut(e, "SplitMatrix", "splitDistanceRAM");
 846                 exit(1);
 847         }
 848 }
 849 //********************************************************************************************************************
 850 //sorts biggest to smallest
 851 inline bool compareFileSizes(map<string, string> left, map<string, string> right){
 852
 853         FILE * pFile;
 854         long leftsize = 0;
 855
 856         //get num bytes in file
 857         string filename = left.begin()->first;
 858         pFile = fopen (filename.c_str(),"rb");
 859         string error = "Error opening " + filename;
 860         if (pFile==NULL) perror (error.c_str());
 861         else{
 862                 fseek (pFile, 0, SEEK_END);
 863                 leftsize=ftell (pFile);
 864                 fclose (pFile);
 865         }
 866
 867         FILE * pFile2;
 868         long rightsize = 0;
 869
 870         //get num bytes in file
 871         filename = right.begin()->first;
 872         pFile2 = fopen (filename.c_str(),"rb");
 873         error = "Error opening " + filename;
 874         if (pFile2==NULL) perror (error.c_str());
 875         else{
 876                 fseek (pFile2, 0, SEEK_END);
 877                 rightsize=ftell (pFile2);
 878                 fclose (pFile2);
 879         }
 880
 881         return (leftsize > rightsize);
 882 }
 883 /***********************************************************************/
 884 //returns map of distance files -> namefile sorted by distance file size
 885 vector< map< string, string> > SplitMatrix::getDistanceFiles(){
 886         try {
 887
 888                 sort(dists.begin(), dists.end(), compareFileSizes);
 889
 890                 return dists;
 891         }
 892         catch(exception& e) {
 893                 m->errorOut(e, "SplitMatrix", "getDistanceFiles");
 894                 exit(1);
 895         }
 896 }
 897 /***********************************************************************/
 898 SplitMatrix::~SplitMatrix(){}
 899 /***********************************************************************/
 900