sharedcommand.cpp

   1 /*
   2  *  sharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedcommand.h"
  11 //********************************************************************************************************************
  12 //sorts lowest to highest
  13 inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
  14         return (left->getGroup() < right->getGroup());
  15 }
  16 //**********************************************************************************************************************
  17 vector<string> SharedCommand::getValidParameters(){
  18         try {
  19                 vector<string> myArray;
  20                 return myArray;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "SharedCommand", "getValidParameters");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 SharedCommand::SharedCommand(){
  29         try {
  30
  31                 //initialize outputTypes
  32                 vector<string> tempOutNames;
  33                 outputTypes["rabund"] = tempOutNames;
  34                 outputTypes["shared"] = tempOutNames;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "SharedCommand", "SharedCommand");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> SharedCommand::getRequiredParameters(){
  43         try {
  44                 vector<string> myArray;
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SharedCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 vector<string> SharedCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "SharedCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64
  65 SharedCommand::SharedCommand(string o) : outputDir(o) {
  66         try {
  67                 globaldata = GlobalData::getInstance();
  68
  69                 //initialize outputTypes
  70                 vector<string> tempOutNames;
  71                 outputTypes["rabund"] = tempOutNames;
  72                 outputTypes["shared"] = tempOutNames;
  73
  74                 //getting output filename
  75                 filename = globaldata->inputFileName;
  76                 if (outputDir == "") { outputDir += m->hasPath(filename); }
  77
  78                 filename = outputDir + m->getRootName(m->getSimpleName(filename));
  79                 filename = filename + "shared";
  80                 outputTypes["shared"].push_back(filename);
  81
  82                 m->openOutputFile(filename, out);
  83                 pickedGroups = false;
  84
  85                 groupMap = globaldata->gGroupmap;
  86
  87                 //if hte user has not specified any groups then use them all
  88                 if (globaldata->Groups.size() == 0) {
  89                         groups = groupMap->namesOfGroups;
  90                 }else{ //they have specified groups
  91                         groups = globaldata->Groups;
  92                         pickedGroups = true;
  93                 }
  94
  95                 //fill filehandles with neccessary ofstreams
  96                 int i;
  97                 ofstream* temp;
  98                 for (i=0; i<groups.size(); i++) {
  99                         temp = new ofstream;
 100                         filehandles[groups[i]] = temp;
 101                 }
 102
 103                 //set fileroot
 104                 fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
 105
 106                 //clears file before we start to write to it below
 107                 for (int i=0; i<groups.size(); i++) {
 108                         remove((fileroot + groups[i] + ".rabund").c_str());
 109                         outputNames.push_back((fileroot + groups[i] + ".rabund"));
 110                         outputTypes["rabund"].push_back((fileroot + groups[i] + ".rabund"));
 111                 }
 112
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "SharedCommand", "SharedCommand");
 116                 exit(1);
 117         }
 118 }
 119 //**********************************************************************************************************************
 120
 121 int SharedCommand::execute(){
 122         try {
 123
 124                 //lookup.clear();
 125                 string errorOff = "no error";
 126                 //errorOff = "";
 127
 128                 //if user provided an order file containing the order the shared file should be in read it
 129                 if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
 130
 131                 //read in listfile
 132                 read = new ReadOTUFile(globaldata->inputFileName);
 133                 read->read(&*globaldata);
 134                 delete read;
 135
 136                 input = globaldata->ginput;
 137                 SharedList = globaldata->gSharedList;
 138                 string lastLabel = SharedList->getLabel();
 139                 vector<SharedRAbundVector*> lookup;
 140
 141                 if (m->control_pressed) {
 142                         delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
 143                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 144                         out.close(); remove(filename.c_str());
 145                         for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 146                         return 1;
 147                 }
 148
 149                 if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
 150                         m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
 151
 152                         out.close();
 153                         remove(filename.c_str()); //remove blank shared file you made
 154
 155                         createMisMatchFile();
 156
 157                         //delete memory
 158                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 159                                 delete it3->second;
 160                         }
 161                         delete input;
 162                         globaldata->ginput = NULL;
 163                         delete SharedList;
 164                         globaldata->gSharedList = NULL;
 165
 166                         return 1;
 167                 }
 168
 169                 //if user has specified groups make new groupfile for them
 170                 if (globaldata->Groups.size() != 0) { //make new group file
 171                         string groups = "";
 172                         for (int i = 0; i < globaldata->Groups.size(); i++) {
 173                                 groups += globaldata->Groups[i] + ".";
 174                         }
 175
 176                         string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
 177                         ofstream outGroups;
 178                         m->openOutputFile(newGroupFile, outGroups);
 179
 180                         vector<string> names = groupMap->getNamesSeqs();
 181                         string groupName;
 182                         for (int i = 0; i < names.size(); i++) {
 183                                 groupName = groupMap->getGroup(names[i]);
 184                                 if (isValidGroup(groupName, globaldata->Groups)) {
 185                                         outGroups << names[i] << '\t' << groupName << endl;
 186                                 }
 187                         }
 188                         outGroups.close();
 189                 }
 190
 191                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 192                 set<string> processedLabels;
 193                 set<string> userLabels = globaldata->labels;
 194
 195                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 196                         if (m->control_pressed) {
 197                                 delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
 198                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 199                                 out.close(); remove(filename.c_str());
 200                                 for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 201                                 return 1;
 202                         }
 203
 204                         if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
 205
 206                                         lookup = SharedList->getSharedRAbundVector();
 207
 208                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 209                                         if (pickedGroups) { //check for otus with no seqs in them
 210                                                 eliminateZeroOTUS(lookup);
 211                                         }
 212
 213                                         if (m->control_pressed) {
 214                                                 delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
 215                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 216                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 217                                                 out.close(); remove(filename.c_str());
 218                                                 for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 219                                                 return 1;
 220                                         }
 221
 222                                         printSharedData(lookup); //prints info to the .shared file
 223                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 224
 225                                         processedLabels.insert(SharedList->getLabel());
 226                                         userLabels.erase(SharedList->getLabel());
 227                         }
 228
 229                         if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 230                                         string saveLabel = SharedList->getLabel();
 231
 232                                         delete SharedList;
 233                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 234
 235                                         lookup = SharedList->getSharedRAbundVector();
 236                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 237                                         if (pickedGroups) { //check for otus with no seqs in them
 238                                                 eliminateZeroOTUS(lookup);
 239                                         }
 240
 241
 242                                         if (m->control_pressed) {
 243                                                 delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
 244                                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 245                                                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
 246                                                 out.close(); remove(filename.c_str());
 247                                                 for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 248                                                 return 1;
 249                                         }
 250
 251                                         printSharedData(lookup); //prints info to the .shared file
 252                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 253
 254                                         processedLabels.insert(SharedList->getLabel());
 255                                         userLabels.erase(SharedList->getLabel());
 256
 257                                         //restore real lastlabel to save below
 258                                         SharedList->setLabel(saveLabel);
 259                         }
 260
 261
 262                         lastLabel = SharedList->getLabel();
 263
 264                         delete SharedList;
 265                         SharedList = input->getSharedListVector(); //get new list vector to process
 266                 }
 267
 268                 //output error messages about any remaining user labels
 269                 set<string>::iterator it;
 270                 bool needToRun = false;
 271                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 272                         if (processedLabels.count(lastLabel) != 1) {
 273                                 needToRun = true;
 274                         }
 275                 }
 276
 277                 //run last label if you need to
 278                 if (needToRun == true)  {
 279                         if (SharedList != NULL) {       delete SharedList;      }
 280                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 281
 282                         lookup = SharedList->getSharedRAbundVector();
 283                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 284                         if (pickedGroups) { //check for otus with no seqs in them
 285                                 eliminateZeroOTUS(lookup);
 286                         }
 287
 288                         if (m->control_pressed) {
 289                                         delete input;  globaldata->ginput = NULL;
 290                                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
 291                                         out.close(); remove(filename.c_str());
 292                                         for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 293                                         return 1;
 294                         }
 295
 296                         printSharedData(lookup); //prints info to the .shared file
 297                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 298                         delete SharedList;
 299                 }
 300
 301                 globaldata->gSharedList = NULL;
 302
 303                 out.close();
 304
 305                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 306                         delete it3->second;
 307                 }
 308
 309
 310                 //change format to shared  to speed up commands
 311                 globaldata->setFormat("sharedfile");
 312                 globaldata->setListFile("");
 313                 globaldata->setGroupFile("");
 314                 globaldata->setSharedFile(filename);
 315
 316
 317                 if (m->control_pressed) {
 318                                 delete input;  globaldata->ginput = NULL;
 319                                 remove(filename.c_str());
 320                                 for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
 321                                 return 1;
 322                 }
 323
 324                 m->mothurOutEndLine();
 325                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 326                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 327                 m->mothurOut(filename); m->mothurOutEndLine();
 328                 m->mothurOutEndLine();
 329
 330                 return 0;
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "SharedCommand", "execute");
 334                 exit(1);
 335         }
 336 }
 337 //**********************************************************************************************************************
 338 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 339         try {
 340
 341                 if (order.size() == 0) { //user has not specified an order so do aplabetically
 342                         sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
 343
 344                         globaldata->Groups.clear();
 345
 346                         //initialize bin values
 347                         for (int i = 0; i < thislookup.size(); i++) {
 348                                 out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 349                                 thislookup[i]->print(out);
 350
 351                                 globaldata->Groups.push_back(thislookup[i]->getGroup());
 352
 353                                 RAbundVector rav = thislookup[i]->getRAbundVector();
 354                                 m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 355                                 rav.print(*(filehandles[thislookup[i]->getGroup()]));
 356                                 (*(filehandles[thislookup[i]->getGroup()])).close();
 357                         }
 358                 }else{
 359                         //create a map from groupName to each sharedrabund
 360                         map<string, SharedRAbundVector*> myMap;
 361                         map<string, SharedRAbundVector*>::iterator myIt;
 362
 363                         for (int i = 0; i < thislookup.size(); i++) {
 364                                 myMap[thislookup[i]->getGroup()] = thislookup[i];
 365                         }
 366
 367                         globaldata->Groups.clear();
 368
 369                         //loop through ordered list and print the rabund
 370                         for (int i = 0; i < order.size(); i++) {
 371                                 myIt = myMap.find(order[i]);
 372
 373                                 if(myIt != myMap.end()) { //we found it
 374                                         out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
 375                                         (myIt->second)->print(out);
 376
 377                                         globaldata->Groups.push_back((myIt->second)->getGroup());
 378
 379                                         RAbundVector rav = (myIt->second)->getRAbundVector();
 380                                         m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
 381                                         rav.print(*(filehandles[(myIt->second)->getGroup()]));
 382                                         (*(filehandles[(myIt->second)->getGroup()])).close();
 383                                 }else{
 384                                         m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
 385                                 }
 386                         }
 387
 388                 }
 389
 390         }
 391         catch(exception& e) {
 392                 m->errorOut(e, "SharedCommand", "printSharedData");
 393                 exit(1);
 394         }
 395 }
 396 //**********************************************************************************************************************
 397 int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 398         try {
 399
 400                 vector<SharedRAbundVector*> newLookup;
 401                 for (int i = 0; i < thislookup.size(); i++) {
 402                         SharedRAbundVector* temp = new SharedRAbundVector();
 403                         temp->setLabel(thislookup[i]->getLabel());
 404                         temp->setGroup(thislookup[i]->getGroup());
 405                         newLookup.push_back(temp);
 406                 }
 407
 408                 //for each bin
 409                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 410                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 411
 412                         //look at each sharedRabund and make sure they are not all zero
 413                         bool allZero = true;
 414                         for (int j = 0; j < thislookup.size(); j++) {
 415                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 416                         }
 417
 418                         //if they are not all zero add this bin
 419                         if (!allZero) {
 420                                 for (int j = 0; j < thislookup.size(); j++) {
 421                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 422                                 }
 423                         }
 424                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 425                 }
 426
 427                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 428                 thislookup = newLookup;
 429
 430                 return 0;
 431
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439 int SharedCommand::createMisMatchFile() {
 440         try {
 441                 ofstream outMisMatch;
 442                 string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 443
 444                 //you have sequences in your list file that are not in your group file
 445                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 446                         outputMisMatchName += "missing.group";
 447                         m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 448
 449                         m->openOutputFile(outputMisMatchName, outMisMatch);
 450
 451                         map<string, string> listNames;
 452                         map<string, string>::iterator itList;
 453
 454                         //go through list and if group returns "not found" output it
 455                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 456                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 457
 458                                 string names = SharedList->get(i);
 459
 460                                 while (names.find_first_of(',') != -1) {
 461                                         string name = names.substr(0,names.find_first_of(','));
 462                                         names = names.substr(names.find_first_of(',')+1, names.length());
 463                                         string group = groupMap->getGroup(name);
 464
 465                                         if(group == "not found") {      outMisMatch << name << endl;  }
 466
 467                                         itList = listNames.find(name);
 468                                         if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 469                                         else { listNames[name] = name; }
 470                                 }
 471
 472                                 //get last name
 473                                 string group = groupMap->getGroup(names);
 474                                 if(group == "not found") {      outMisMatch << names << endl;  }
 475
 476                                 itList = listNames.find(names);
 477                                 if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 478                                 else { listNames[names] = names; }
 479
 480                         }
 481
 482                         outMisMatch.close();
 483
 484
 485                 }else {//you have sequences in your group file that are not in you list file
 486
 487                         outputMisMatchName += "missing.name";
 488                         m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 489
 490                         map<string, string> namesInList;
 491                         map<string, string>::iterator itList;
 492
 493                         //go through listfile and get names
 494                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 495                                 if (m->control_pressed) {  return 0; }
 496
 497
 498                                 string names = SharedList->get(i);
 499
 500                                 while (names.find_first_of(',') != -1) {
 501                                         string name = names.substr(0,names.find_first_of(','));
 502                                         names = names.substr(names.find_first_of(',')+1, names.length());
 503
 504                                         itList = namesInList.find(name);
 505                                         if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 506
 507                                         namesInList[name] = name;
 508
 509                                 }
 510
 511                                 itList = namesInList.find(names);
 512                                 if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 513
 514                                 //get last name
 515                                 namesInList[names] = names;
 516                         }
 517
 518                         //get names of sequences in groupfile
 519                         vector<string> seqNames = groupMap->getNamesSeqs();
 520
 521                         map<string, string>::iterator itMatch;
 522
 523                         m->openOutputFile(outputMisMatchName, outMisMatch);
 524
 525                         //loop through names in seqNames and if they aren't in namesIn list output them
 526                         for (int i = 0; i < seqNames.size(); i++) {
 527                                 if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; }
 528
 529                                 itMatch = namesInList.find(seqNames[i]);
 530
 531                                 if (itMatch == namesInList.end()) {
 532
 533                                         outMisMatch << seqNames[i] << endl;
 534                                 }
 535                         }
 536                         outMisMatch.close();
 537                 }
 538
 539                 return 0;
 540         }
 541         catch(exception& e) {
 542                 m->errorOut(e, "SharedCommand", "createMisMatchFile");
 543                 exit(1);
 544         }
 545 }
 546
 547 //**********************************************************************************************************************
 548
 549 SharedCommand::~SharedCommand(){
 550         //delete list;
 551
 552
 553 }
 554 //**********************************************************************************************************************
 555 int SharedCommand::readOrderFile() {
 556         try {
 557                 //remove old names
 558                 order.clear();
 559
 560                 ifstream in;
 561                 m->openInputFile(globaldata->getOrderGroupFile(), in);
 562                 string thisGroup;
 563
 564                 while(!in.eof()){
 565                         in >> thisGroup; m->gobble(in);
 566
 567                         order.push_back(thisGroup);
 568
 569                         if (m->control_pressed) { order.clear(); break; }
 570                 }
 571                 in.close();
 572
 573                 return 0;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "SharedCommand", "readOrderFile");
 577                 exit(1);
 578         }
 579 }
 580 //**********************************************************************************************************************
 581
 582 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 583         try {
 584                 for (int i = 0; i < groups.size(); i++) {
 585                         if (groupname == groups[i]) { return true; }
 586                 }
 587
 588                 return false;
 589         }
 590         catch(exception& e) {
 591                 m->errorOut(e, "SharedCommand", "isValidGroup");
 592                 exit(1);
 593         }
 594 }
 595 /************************************************************/
 596
 597