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