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