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