getoturepcommand.cpp

   1 /*
   2  *  getoturepcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getoturepcommand.h"
  11
  12 //**********************************************************************************************************************
  13 GetOTURepCommand::GetOTURepCommand(){
  14         try{
  15                 globaldata = GlobalData::getInstance();
  16
  17                 if(globaldata->gSparseMatrix != NULL)   {       matrix = new SparseMatrix(*globaldata->gSparseMatrix);          }
  18
  19                 //listOfNames bin 0 = first name read in distance matrix, listOfNames bin 1 = second name read in distance matrix
  20                 if(globaldata->gListVector != NULL)             {
  21                         listOfNames = new ListVector(*globaldata->gListVector);
  22
  23                         vector<string> names;
  24                         string binnames;
  25                         //map names to rows in sparsematrix
  26                         for (int i = 0; i < listOfNames->size(); i++) {
  27                                 names.clear();
  28                                 binnames = listOfNames->get(i);
  29                                 splitAtComma(binnames, names);
  30
  31                                 for (int j = 0; j < names.size(); j++) {
  32                                         nameToIndex[names[j]] = i;
  33                                 }
  34                         }
  35                 }else { cout << "error, no listvector." << endl; }
  36
  37
  38                 fastafile = globaldata->getFastaFile();
  39                 namesfile = globaldata->getNameFile();
  40                 groupfile = globaldata->getGroupFile();
  41
  42                 if (groupfile != "") {
  43                         //read in group map info.
  44                         groupMap = new GroupMap(groupfile);
  45                         groupMap->readMap();
  46                 }
  47
  48                 openInputFile(fastafile, in);
  49
  50                 fasta = new FastaMap();
  51
  52         }
  53         catch(exception& e) {
  54                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57         catch(...) {
  58                 cout << "An unknown error has occurred in the GetOTURepCommand class function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63
  64 GetOTURepCommand::~GetOTURepCommand(){
  65         delete input;
  66         delete read;
  67         delete fasta;
  68         if (groupfile != "") {
  69                 delete groupMap;
  70         }
  71 }
  72
  73 //**********************************************************************************************************************
  74
  75 int GetOTURepCommand::execute(){
  76         try {
  77                 int count = 1;
  78                 int error;
  79
  80                 //read fastafile
  81                 fasta->readFastaFile(in);
  82
  83                 //set format to list so input can get listvector
  84                 globaldata->setFormat("list");
  85
  86                 //if user gave a namesfile then use it
  87                 if (namesfile != "") {
  88                         readNamesFile();
  89                 }
  90
  91                 //read list file
  92                 read = new ReadOTUFile(globaldata->getListFile());
  93                 read->read(&*globaldata);
  94
  95                 input = globaldata->ginput;
  96                 list = globaldata->gListVector;
  97                 ListVector* lastList = list;
  98
  99                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 100                 set<string> processedLabels;
 101                 set<string> userLabels = globaldata->labels;
 102
 103
 104                 while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 105
 106                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
 107                                         cout << list->getLabel() << '\t' << count << endl;
 108                                         error = process(list);
 109                                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 110
 111                                         processedLabels.insert(list->getLabel());
 112                                         userLabels.erase(list->getLabel());
 113                         }
 114
 115                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
 116                                         cout << lastList->getLabel() << '\t' << count << endl;
 117                                         error = process(lastList);
 118                                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 119
 120                                         processedLabels.insert(lastList->getLabel());
 121                                         userLabels.erase(lastList->getLabel());
 122                         }
 123
 124                         if (count != 1) { delete lastList; }
 125                         lastList = list;
 126
 127                         list = input->getListVector();
 128                         count++;
 129                 }
 130
 131                 //output error messages about any remaining user labels
 132                 set<string>::iterator it;
 133                 bool needToRun = false;
 134                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 135                         cout << "Your file does not include the label "<< *it;
 136                         if (processedLabels.count(lastList->getLabel()) != 1) {
 137                                 cout << ". I will use " << lastList->getLabel() << "." << endl;
 138                                 needToRun = true;
 139                         }else {
 140                                 cout << ". Please refer to " << lastList->getLabel() << "." << endl;
 141                         }
 142                 }
 143
 144                 //run last line if you need to
 145                 if (needToRun == true)  {
 146                         cout << lastList->getLabel() << '\t' << count << endl;
 147                         error = process(lastList);
 148                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 149                 }
 150                 delete lastList;
 151
 152                 delete matrix;
 153                 globaldata->gSparseMatrix = NULL;
 154                 delete list;
 155                 globaldata->gListVector = NULL;
 156
 157                 return 0;
 158         }
 159         catch(exception& e) {
 160                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163         catch(...) {
 164                 cout << "An unknown error has occurred in the GetOTURepCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167
 168 }
 169
 170 //**********************************************************************************************************************
 171 void GetOTURepCommand::readNamesFile() {
 172         try {
 173                 vector<string> dupNames;
 174                 openInputFile(namesfile, inNames);
 175
 176                 string name, names, sequence;
 177
 178                 while(inNames){
 179                         inNames >> name;                        //read from first column  A
 180                         inNames >> names;               //read from second column  A,B,C,D
 181
 182                         dupNames.clear();
 183
 184                         //parse names into vector
 185                         splitAtComma(names, dupNames);
 186
 187                         //store names in fasta map
 188                         sequence = fasta->getSequence(name);
 189                         for (int i = 0; i < dupNames.size(); i++) {
 190                                 fasta->push_back(dupNames[i], sequence);
 191                         }
 192
 193                         gobble(inNames);
 194                 }
 195                 inNames.close();
 196
 197         }
 198         catch(exception& e) {
 199                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202         catch(...) {
 203                 cout << "An unknown error has occurred in the GetOTURepCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206 }
 207 //**********************************************************************************************************************
 208 string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
 209         try{
 210                 vector<string> names;
 211                 map<string, float> sums;
 212                 map<string, float>::iterator it4;
 213                 map<int, string> binMap; //subset of namesToIndex - just member of this bin
 214                 string binnames;
 215                 float min = 10000;
 216                 string minName;
 217                 map<string, string> groups;
 218                 map<string, string>::iterator groupIt;
 219
 220                 binnames = thisList->get(bin);
 221
 222                 //parse names into vector
 223                 splitAtComma(binnames, names);
 224
 225                 //if you have a groupfile
 226                 if(groupfile != "") {
 227                         //find the groups that are in this bin
 228                         for (int i = 0; i < names.size(); i++) {
 229                                 string groupName = groupMap->getGroup(names[i]);
 230                                 if (groupName == "not found") {
 231                                         cout << names[i] << " is missing from your group file. Please correct. " << endl;
 232                                         groupError = true;
 233                                 }else{
 234                                         groups[groupName] = groupName;
 235                                 }
 236                         }
 237
 238                         //turn the groups into a string
 239                         for(groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { group += groupIt->first + "-"; }
 240
 241                         //rip off last dash
 242                         group = group.substr(0, group.length()-1);
 243                 }
 244
 245                 //if only 1 sequence in bin then that's the rep
 246                 if (names.size() == 1) { return names[0]; }
 247                 else {
 248                         //fill binMap
 249                         for (int i = 0; i < names.size(); i++) {
 250                                 for (it3 = nameToIndex.begin(); it3 != nameToIndex.end(); it3++) {
 251
 252                                         if (it3->first == names[i]) {
 253                                                 binMap[it3->second] = it3->first;
 254
 255                                                 //initialize sums map
 256                                                 sums[it3->first] = 0.0;
 257                                                 break;
 258                                         }
 259                                 }
 260                         }
 261
 262                         //go through each cell in the sparsematrix
 263                         for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 264                                 //is this a distance between 2 members of this bin
 265                                 it = binMap.find(currentCell->row);
 266                                 it2 = binMap.find(currentCell->column);
 267
 268                                 //sum the distance of the sequences in the bin to eachother
 269                                 if ((it != binMap.end()) && (it2 != binMap.end())) {
 270                                         //this is a cell that repesents the distance between to of this bins members
 271                                         sums[it->second] += currentCell->dist;
 272                                         sums[it2->second] += currentCell->dist;
 273                                 }
 274                         }
 275
 276                         //smallest sum is the representative
 277                         for (it4 = sums.begin(); it4 != sums.end(); it4++) {
 278                                 if (it4->second < min) {
 279                                         min = it4->second;
 280                                         minName = it4->first;
 281                                 }
 282
 283                         }
 284
 285                         return minName;
 286                 }
 287
 288         }
 289         catch(exception& e) {
 290                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293         catch(...) {
 294                 cout << "An unknown error has occurred in the GetOTURepCommand class function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297 }
 298
 299 //**********************************************************************************************************************
 300 int GetOTURepCommand::process(ListVector* processList) {
 301         try{
 302                                 string nameRep, name, sequence;
 303
 304                                 //create output file
 305                                 string outputFileName = getRootName(globaldata->getListFile()) + processList->getLabel() + ".rep.fasta";
 306                                 openOutputFile(outputFileName, out);
 307
 308                                 //for each bin in the list vector
 309                                 for (int i = 0; i < processList->size(); i++) {
 310                                         string groups;
 311                                         nameRep = FindRep(i, groups, processList);
 312
 313                                         //print out name and sequence for that bin
 314                                         sequence = fasta->getSequence(nameRep);
 315
 316                                         if (sequence != "not found") {
 317                                                 if (groupfile == "") {
 318                                                         nameRep = nameRep + "|" + toString(i+1);
 319                                                         out << ">" << nameRep << endl;
 320                                                         out << sequence << endl;
 321                                                 }else {
 322                                                         nameRep = nameRep + "|" + groups + "|" + toString(i+1);
 323                                                         out << ">" << nameRep << endl;
 324                                                         out << sequence << endl;
 325                                                 }
 326                                         }else {
 327                                                 cout << nameRep << " is missing from your fasta or name file. Please correct. " << endl;
 328                                                 remove(outputFileName.c_str());
 329                                                 return 1;
 330                                         }
 331                                 }
 332
 333                                 out.close();
 334                                 return 0;
 335
 336         }
 337         catch(exception& e) {
 338                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 339                 exit(1);
 340         }
 341         catch(...) {
 342                 cout << "An unknown error has occurred in the GetOTURepCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 343                 exit(1);
 344         }
 345 }
 346
 347 //**********************************************************************************************************************
 348
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 352