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                         out.close();
  70                         remove(filename.c_str()); //remove blank shared file you made
  71
  72                         createMisMatchFile();
  73
  74                         //delete memory
  75                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
  76                                 delete it3->second;
  77                         }
  78                         delete SharedList;
  79                         globaldata->gSharedList = NULL;
  80
  81                         return 1;
  82                 }
  83
  84                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  85                 set<string> processedLabels;
  86                 set<string> userLabels = globaldata->labels;
  87
  88
  89                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
  90
  91
  92                         if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  93
  94                                         lookup = SharedList->getSharedRAbundVector();
  95                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
  96
  97                                         printSharedData(lookup); //prints info to the .shared file
  98                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  99
 100                                         processedLabels.insert(SharedList->getLabel());
 101                                         userLabels.erase(SharedList->getLabel());
 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
 125                 //output error messages about any remaining user labels
 126                 set<string>::iterator it;
 127                 bool needToRun = false;
 128                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 129                         if (processedLabels.count(lastLabel) != 1) {
 130                                 needToRun = true;
 131                         }
 132                 }
 133
 134                 //run last label if you need to
 135                 if (needToRun == true)  {
 136                         if (SharedList != NULL) {       delete SharedList;      }
 137                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 138
 139                         lookup = SharedList->getSharedRAbundVector();
 140                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 141
 142                         printSharedData(lookup); //prints info to the .shared file
 143                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 144                         delete SharedList;
 145                 }
 146
 147                 globaldata->gSharedList = NULL;
 148
 149                 out.close();
 150
 151                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 152                         delete it3->second;
 153                 }
 154
 155
 156                 return 0;
 157         }
 158         catch(exception& e) {
 159                 errorOut(e, "SharedCommand", "execute");
 160                 exit(1);
 161         }
 162 }
 163 //**********************************************************************************************************************
 164 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 165         try {
 166
 167                 //initialize bin values
 168                 for (int i = 0; i < thislookup.size(); i++) {
 169                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 170                         thislookup[i]->print(out);
 171
 172                         RAbundVector rav = thislookup[i]->getRAbundVector();
 173                         openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 174                         rav.print(*(filehandles[thislookup[i]->getGroup()]));
 175                         (*(filehandles[thislookup[i]->getGroup()])).close();
 176                 }
 177
 178         }
 179         catch(exception& e) {
 180                 errorOut(e, "SharedCommand", "printSharedData");
 181                 exit(1);
 182         }
 183 }
 184 //**********************************************************************************************************************
 185 void SharedCommand::createMisMatchFile() {
 186         try {
 187                 ofstream outMisMatch;
 188                 string outputMisMatchName = getRootName(globaldata->inputFileName);
 189
 190                 //you have sequences in your list file that are not in your group file
 191                 if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
 192                         outputMisMatchName += "missing.group";
 193                         mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 194
 195                         openOutputFile(outputMisMatchName, outMisMatch);
 196
 197                         //go through list and if group returns "not found" output it
 198                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 199
 200                                 string names = SharedList->get(i);
 201
 202                                 while (names.find_first_of(',') != -1) {
 203                                         string name = names.substr(0,names.find_first_of(','));
 204                                         names = names.substr(names.find_first_of(',')+1, names.length());
 205                                         string group = groupMap->getGroup(name);
 206
 207                                         if(group == "not found") {      outMisMatch << name << endl;  }
 208                                 }
 209
 210                                 //get last name
 211                                 string group = groupMap->getGroup(names);
 212                                 if(group == "not found") {      outMisMatch << names << endl;  }
 213                         }
 214
 215                         outMisMatch.close();
 216
 217
 218                 }else {//you have sequences in your group file that are not in you list file
 219
 220                         outputMisMatchName += "missing.name";
 221                         mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 222
 223                         map<string, string> namesInList;
 224
 225                         //go through listfile and get names
 226                         for (int i = 0; i < SharedList->getNumBins(); i++) {
 227
 228                                 string names = SharedList->get(i);
 229
 230                                 while (names.find_first_of(',') != -1) {
 231                                         string name = names.substr(0,names.find_first_of(','));
 232                                         names = names.substr(names.find_first_of(',')+1, names.length());
 233
 234                                         namesInList[name] = name;
 235                                 }
 236
 237                                 //get last name
 238                                 namesInList[names] = names;
 239                         }
 240
 241                         //get names of sequences in groupfile
 242                         vector<string> seqNames = groupMap->getNamesSeqs();
 243
 244                         map<string, string>::iterator itMatch;
 245
 246                         openOutputFile(outputMisMatchName, outMisMatch);
 247
 248                         //loop through names in seqNames and if they aren't in namesIn list output them
 249                         for (int i = 0; i < seqNames.size(); i++) {
 250
 251                                 itMatch = namesInList.find(seqNames[i]);
 252
 253                                 if (itMatch == namesInList.end()) {
 254
 255                                         outMisMatch << seqNames[i] << endl;
 256                                 }
 257                         }
 258                         outMisMatch.close();
 259                 }
 260
 261         }
 262         catch(exception& e) {
 263                 errorOut(e, "SharedCommand", "createMisMatchFile");
 264                 exit(1);
 265         }
 266 }
 267
 268 //**********************************************************************************************************************
 269
 270 SharedCommand::~SharedCommand(){
 271         //delete list;
 272
 273
 274 }
 275
 276 //**********************************************************************************************************************