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
  24                 groupMap = globaldata->gGroupmap;
  25
  26                 //fill filehandles with neccessary ofstreams
  27                 int i;
  28                 ofstream* temp;
  29                 for (i=0; i<groupMap->getNumGroups(); i++) {
  30                         temp = new ofstream;
  31                         filehandles[groupMap->namesOfGroups[i]] = temp;
  32                 }
  33
  34                 //set fileroot
  35                 fileroot = getRootName(globaldata->getListFile());
  36
  37                 //clears file before we start to write to it below
  38                 for (int i=0; i<groupMap->getNumGroups(); i++) {
  39                         remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
  40                 }
  41
  42         }
  43         catch(exception& e) {
  44                 errorOut(e, "SharedCommand", "SharedCommand");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49
  50 int SharedCommand::execute(){
  51         try {
  52
  53                 //lookup.clear();
  54                 int count = 1;
  55                 string errorOff = "no error";
  56
  57                 //read in listfile
  58                 read = new ReadOTUFile(globaldata->inputFileName);
  59                 read->read(&*globaldata);
  60                 delete read;
  61
  62                 input = globaldata->ginput;
  63                 SharedList = globaldata->gSharedList;
  64                 string lastLabel = SharedList->getLabel();
  65                 vector<SharedRAbundVector*> lookup;
  66
  67                 if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {
  68                         mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
  69
  70                         createMisMatchFile();
  71
  72                         //delete memory
  73                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
  74                                 delete it3->second;
  75                         }
  76                         delete SharedList;
  77                         globaldata->gSharedList = NULL;
  78
  79                         return 1;
  80                 }
  81
  82                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  83                 set<string> processedLabels;
  84                 set<string> userLabels = globaldata->labels;
  85                 set<int> userLines = globaldata->lines;
  86
  87
  88                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  89
  90
  91                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  92
  93                                         lookup = SharedList->getSharedRAbundVector();
  94                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
  95
  96                                         printSharedData(lookup); //prints info to the .shared file
  97                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  98
  99                                         processedLabels.insert(SharedList->getLabel());
 100                                         userLabels.erase(SharedList->getLabel());
 101                                         userLines.erase(count);
 102                         }
 103
 104                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 105                                         delete SharedList;
 106                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 107
 108                                         lookup = SharedList->getSharedRAbundVector();
 109                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 110
 111                                         printSharedData(lookup); //prints info to the .shared file
 112                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 113
 114                                         processedLabels.insert(SharedList->getLabel());
 115                                         userLabels.erase(SharedList->getLabel());
 116                         }
 117
 118
 119                         lastLabel = SharedList->getLabel();
 120
 121                         delete SharedList;
 122                         SharedList = input->getSharedListVector(); //get new list vector to process
 123
 124                         count++;
 125                 }
 126
 127                 //output error messages about any remaining user labels
 128                 set<string>::iterator it;
 129                 bool needToRun = false;
 130                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 131                         if (processedLabels.count(lastLabel) != 1) {
 132                                 needToRun = true;
 133                         }
 134                 }
 135
 136                 //run last line if you need to
 137                 if (needToRun == true)  {
 138                         if (SharedList != NULL) {       delete SharedList;      }
 139                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 140
 141                         lookup = SharedList->getSharedRAbundVector();
 142                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 143
 144                         printSharedData(lookup); //prints info to the .shared file
 145                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 146                         delete SharedList;
 147                 }
 148
 149                 globaldata->gSharedList = NULL;
 150
 151                 out.close();
 152
 153                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 154                         delete it3->second;
 155                 }
 156
 157
 158                 return 0;
 159         }
 160         catch(exception& e) {
 161                 errorOut(e, "SharedCommand", "execute");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 167         try {
 168
 169                 //initialize bin values
 170                 for (int i = 0; i < thislookup.size(); i++) {
 171                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 172                         thislookup[i]->print(out);
 173
 174                         RAbundVector rav = thislookup[i]->getRAbundVector();
 175                         openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 176                         rav.print(*(filehandles[thislookup[i]->getGroup()]));
 177                         (*(filehandles[thislookup[i]->getGroup()])).close();
 178                 }
 179
 180         }
 181         catch(exception& e) {
 182                 errorOut(e, "SharedCommand", "printSharedData");
 183                 exit(1);
 184         }
 185 }
 186 //**********************************************************************************************************************
 187 void SharedCommand::createMisMatchFile() {
 188         try {
 189                 ofstream outMisMatch;
 190                 string outputMisMatchName = getRootName(globaldata->inputFileName);
 191
 192                 //you have sequences in your list file that are not in your group file
 193                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 194                         outputMisMatchName += "missing.group";
 195                         mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 196
 197                         openOutputFile(outputMisMatchName, outMisMatch);
 198
 199                         //go through list and if group returns "not found" output it
 200                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 201
 202                                 string names = SharedList->get(i);
 203
 204                                 while (names.find_first_of(',') != -1) {
 205                                         string name = names.substr(0,names.find_first_of(','));
 206                                         names = names.substr(names.find_first_of(',')+1, names.length());
 207                                         string group = groupMap->getGroup(name);
 208
 209                                         if(group == "not found") {      outMisMatch << name << endl;  }
 210                                 }
 211
 212                                 //get last name
 213                                 string group = groupMap->getGroup(names);
 214                                 if(group == "not found") {      outMisMatch << names << endl;  }
 215                         }
 216
 217                         outMisMatch.close();
 218
 219
 220                 }else {//you have sequences in your group file that are not in you list file
 221
 222                         outputMisMatchName += "missing.name";
 223                         mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 224
 225                         map<string, string> namesInList;
 226
 227                         //go through listfile and get names
 228                         for (int i = 0; i < SharedList->getNumSeqs(); i++) {
 229
 230                                 string names = SharedList->get(i);
 231
 232                                 while (names.find_first_of(',') != -1) {
 233                                         string name = names.substr(0,names.find_first_of(','));
 234                                         names = names.substr(names.find_first_of(',')+1, names.length());
 235
 236                                         namesInList[name] = name;
 237                                 }
 238
 239                                 //get last name
 240                                 namesInList[names] = names;
 241                         }
 242
 243                         //get names of sequences in groupfile
 244                         vector<string> seqNames = groupMap->getNamesSeqs();
 245
 246                         map<string, string>::iterator itMatch;
 247
 248                         openOutputFile(outputMisMatchName, outMisMatch);
 249
 250                         //loop through names in seqNames and if they aren't in namesIn list output them
 251                         for (int i = 0; i < seqNames.size(); i++) {
 252
 253                                 itMatch = namesInList.find(seqNames[i]);
 254
 255                                 if (itMatch == namesInList.end()) {
 256
 257                                         outMisMatch << seqNames[i] << endl;
 258                                 }
 259                         }
 260                         outMisMatch.close();
 261                 }
 262
 263         }
 264         catch(exception& e) {
 265                 errorOut(e, "SharedCommand", "createMisMatchFile");
 266                 exit(1);
 267         }
 268 }
 269
 270 //**********************************************************************************************************************
 271
 272 SharedCommand::~SharedCommand(){
 273         //delete list;
 274
 275
 276 }
 277
 278 //**********************************************************************************************************************