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