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 //**********************************************************************************************************************
  13
  14 SharedCommand::SharedCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 //getting output filename
  19                 filename = globaldata->inputFileName;
  20                 filename = getRootName(filename);
  21                 filename = filename + "shared";
  22                 openOutputFile(filename, out);
  23                 pickedGroups = false;
  24
  25                 groupMap = globaldata->gGroupmap;
  26
  27                 //if hte user has not specified any groups then use them all
  28                 if (globaldata->Groups.size() == 0) {
  29                         groups = groupMap->namesOfGroups;
  30                 }else{ //they have specified groups
  31                         groups = globaldata->Groups;
  32                         pickedGroups = true;
  33                 }
  34
  35                 //fill filehandles with neccessary ofstreams
  36                 int i;
  37                 ofstream* temp;
  38                 for (i=0; i<groups.size(); i++) {
  39                         temp = new ofstream;
  40                         filehandles[groups[i]] = temp;
  41                 }
  42
  43                 //set fileroot
  44                 fileroot = getRootName(globaldata->getListFile());
  45
  46                 //clears file before we start to write to it below
  47                 for (int i=0; i<groups.size(); i++) {
  48                         remove((fileroot + groups[i] + ".rabund").c_str());
  49                 }
  50
  51         }
  52         catch(exception& e) {
  53                 errorOut(e, "SharedCommand", "SharedCommand");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 int SharedCommand::execute(){
  60         try {
  61
  62                 //lookup.clear();
  63                 string errorOff = "no error";
  64                 //errorOff = "";
  65
  66                 //read in listfile
  67                 read = new ReadOTUFile(globaldata->inputFileName);
  68                 read->read(&*globaldata);
  69                 delete read;
  70
  71                 input = globaldata->ginput;
  72                 SharedList = globaldata->gSharedList;
  73                 string lastLabel = SharedList->getLabel();
  74                 vector<SharedRAbundVector*> lookup;
  75
  76                 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
  77                         mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
  78
  79                         out.close();
  80                         remove(filename.c_str()); //remove blank shared file you made
  81
  82                         createMisMatchFile();
  83
  84                         //delete memory
  85                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
  86                                 delete it3->second;
  87                         }
  88                         delete SharedList;
  89                         globaldata->gSharedList = NULL;
  90
  91                         return 1;
  92                 }
  93
  94                 //if user has specified groups make new groupfile for them
  95                 if (globaldata->Groups.size() != 0) { //make new group file
  96                         string groups = "";
  97                         for (int i = 0; i < globaldata->Groups.size(); i++) {
  98                                 groups += globaldata->Groups[i] + ".";
  99                         }
 100
 101                         string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
 102                         ofstream outGroups;
 103                         openOutputFile(newGroupFile, outGroups);
 104
 105                         vector<string> names = groupMap->getNamesSeqs();
 106                         string groupName;
 107                         for (int i = 0; i < names.size(); i++) {
 108                                 groupName = groupMap->getGroup(names[i]);
 109                                 if (isValidGroup(groupName, globaldata->Groups)) {
 110                                         outGroups << names[i] << '\t' << groupName << endl;
 111                                 }
 112                         }
 113                         outGroups.close();
 114                 }
 115
 116                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 117                 set<string> processedLabels;
 118                 set<string> userLabels = globaldata->labels;
 119
 120                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 121
 122                         if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
 123
 124                                         lookup = SharedList->getSharedRAbundVector();
 125                                         if (pickedGroups) { //check for otus with no seqs in them
 126                                                 eliminateZeroOTUS(lookup);
 127                                         }
 128                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 129
 130                                         printSharedData(lookup); //prints info to the .shared file
 131                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 132
 133                                         processedLabels.insert(SharedList->getLabel());
 134                                         userLabels.erase(SharedList->getLabel());
 135                         }
 136
 137                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 138                                         string saveLabel = SharedList->getLabel();
 139
 140                                         delete SharedList;
 141                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 142
 143                                         lookup = SharedList->getSharedRAbundVector();
 144                                         if (pickedGroups) { //check for otus with no seqs in them
 145                                                 eliminateZeroOTUS(lookup);
 146                                         }
 147                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 148
 149                                         printSharedData(lookup); //prints info to the .shared file
 150                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 151
 152                                         processedLabels.insert(SharedList->getLabel());
 153                                         userLabels.erase(SharedList->getLabel());
 154
 155                                         //restore real lastlabel to save below
 156                                         SharedList->setLabel(saveLabel);
 157                         }
 158
 159
 160                         lastLabel = SharedList->getLabel();
 161
 162                         delete SharedList;
 163                         SharedList = input->getSharedListVector(); //get new list vector to process
 164                 }
 165
 166                 //output error messages about any remaining user labels
 167                 set<string>::iterator it;
 168                 bool needToRun = false;
 169                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 170                         if (processedLabels.count(lastLabel) != 1) {
 171                                 needToRun = true;
 172                         }
 173                 }
 174
 175                 //run last label if you need to
 176                 if (needToRun == true)  {
 177                         if (SharedList != NULL) {       delete SharedList;      }
 178                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 179
 180                         lookup = SharedList->getSharedRAbundVector();
 181                         if (pickedGroups) { //check for otus with no seqs in them
 182                                 eliminateZeroOTUS(lookup);
 183                         }
 184                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 185
 186                         printSharedData(lookup); //prints info to the .shared file
 187                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 188                         delete SharedList;
 189                 }
 190
 191                 globaldata->gSharedList = NULL;
 192
 193                 out.close();
 194
 195                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 196                         delete it3->second;
 197                 }
 198
 199
 200                 return 0;
 201         }
 202         catch(exception& e) {
 203                 errorOut(e, "SharedCommand", "execute");
 204                 exit(1);
 205         }
 206 }
 207 //**********************************************************************************************************************
 208 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 209         try {
 210
 211                 //initialize bin values
 212                 for (int i = 0; i < thislookup.size(); i++) {
 213 //cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() <<  endl;
 214                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 215                         thislookup[i]->print(out);
 216
 217                         RAbundVector rav = thislookup[i]->getRAbundVector();
 218                         openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 219                         rav.print(*(filehandles[thislookup[i]->getGroup()]));
 220                         (*(filehandles[thislookup[i]->getGroup()])).close();
 221                 }
 222
 223         }
 224         catch(exception& e) {
 225                 errorOut(e, "SharedCommand", "printSharedData");
 226                 exit(1);
 227         }
 228 }
 229 //**********************************************************************************************************************
 230 void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 231         try {
 232
 233                 vector<SharedRAbundVector*> newLookup;
 234                 for (int i = 0; i < thislookup.size(); i++) {
 235                         SharedRAbundVector* temp = new SharedRAbundVector();
 236                         temp->setLabel(thislookup[i]->getLabel());
 237                         temp->setGroup(thislookup[i]->getGroup());
 238                         newLookup.push_back(temp);
 239                 }
 240
 241                 //for each bin
 242                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 243
 244                         //look at each sharedRabund and make sure they are not all zero
 245                         bool allZero = true;
 246                         for (int j = 0; j < thislookup.size(); j++) {
 247                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 248                         }
 249
 250                         //if they are not all zero add this bin
 251                         if (!allZero) {
 252                                 for (int j = 0; j < thislookup.size(); j++) {
 253                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 254                                 }
 255                         }
 256                         //else{  cout << "bin # " << i << " is all zeros" << endl;  }
 257                 }
 258
 259                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 260                 thislookup = newLookup;
 261
 262
 263         }
 264         catch(exception& e) {
 265                 errorOut(e, "SharedCommand", "eliminateZeroOTUS");
 266                 exit(1);
 267         }
 268 }
 269 //**********************************************************************************************************************
 270 void SharedCommand::createMisMatchFile() {
 271         try {
 272                 ofstream outMisMatch;
 273                 string outputMisMatchName = getRootName(globaldata->inputFileName);
 274
 275                 //you have sequences in your list file that are not in your group file
 276                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 277                         outputMisMatchName += "missing.group";
 278                         mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 279
 280                         openOutputFile(outputMisMatchName, outMisMatch);
 281
 282                         //go through list and if group returns "not found" output it
 283                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 284
 285                                 string names = SharedList->get(i);
 286
 287                                 while (names.find_first_of(',') != -1) {
 288                                         string name = names.substr(0,names.find_first_of(','));
 289                                         names = names.substr(names.find_first_of(',')+1, names.length());
 290                                         string group = groupMap->getGroup(name);
 291         cout << name << endl;
 292                                         if(group == "not found") {      outMisMatch << name << endl;  }
 293                                 }
 294         cout << names << endl;
 295                                 //get last name
 296                                 string group = groupMap->getGroup(names);
 297                                 if(group == "not found") {      outMisMatch << names << endl;  }
 298                         }
 299
 300                         outMisMatch.close();
 301
 302
 303                 }else {//you have sequences in your group file that are not in you list file
 304
 305                         outputMisMatchName += "missing.name";
 306                         mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 307
 308                         map<string, string> namesInList;
 309
 310                         //go through listfile and get names
 311                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 312
 313                                 string names = SharedList->get(i);
 314
 315                                 while (names.find_first_of(',') != -1) {
 316                                         string name = names.substr(0,names.find_first_of(','));
 317                                         names = names.substr(names.find_first_of(',')+1, names.length());
 318
 319                                         namesInList[name] = name;
 320                                 }
 321
 322                                 //get last name
 323                                 namesInList[names] = names;
 324                         }
 325
 326                         //get names of sequences in groupfile
 327                         vector<string> seqNames = groupMap->getNamesSeqs();
 328
 329                         map<string, string>::iterator itMatch;
 330
 331                         openOutputFile(outputMisMatchName, outMisMatch);
 332
 333                         //loop through names in seqNames and if they aren't in namesIn list output them
 334                         for (int i = 0; i < seqNames.size(); i++) {
 335
 336                                 itMatch = namesInList.find(seqNames[i]);
 337
 338                                 if (itMatch == namesInList.end()) {
 339
 340                                         outMisMatch << seqNames[i] << endl;
 341                                 }
 342                         }
 343                         outMisMatch.close();
 344                 }
 345
 346         }
 347         catch(exception& e) {
 348                 errorOut(e, "SharedCommand", "createMisMatchFile");
 349                 exit(1);
 350         }
 351 }
 352
 353 //**********************************************************************************************************************
 354
 355 SharedCommand::~SharedCommand(){
 356         //delete list;
 357
 358
 359 }
 360
 361 //**********************************************************************************************************************
 362
 363 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
 364         try {
 365                 for (int i = 0; i < groups.size(); i++) {
 366                         if (groupname == groups[i]) { return true; }
 367                 }
 368
 369                 return false;
 370         }
 371         catch(exception& e) {
 372                 errorOut(e, "SharedCommand", "isValidGroup");
 373                 exit(1);
 374         }
 375 }
 376 /************************************************************/
 377
 378