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(string option){
  14         try{
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17                 allLines = 1;
  18                 lines.clear();
  19                 labels.clear();
  20
  21                 //allow user to run help
  22                 if(option == "help") { help(); abort = true; }
  23
  24                 else {
  25                         //valid paramters for this command
  26                         string Array[] =  {"fasta","list","line","label","name", "group"};
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string, string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //make sure the user has already run the read.otu command
  40                         if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
  41                                 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
  42                                 abort = true;
  43                         }
  44
  45                         //check for required parameters
  46                         fastafile = validParameter.validFile(parameters, "fasta", true);
  47                         if (fastafile == "not found") { cout << "fasta is a required parameter for the get.oturep command." << endl; abort = true; }
  48                         else if (fastafile == "not open") { abort = true; }
  49
  50                         listfile = validParameter.validFile(parameters, "list", true);
  51                         if (listfile == "not found") { cout << "list is a required parameter for the get.oturep command." << endl; abort = true; }
  52                         else if (listfile == "not open") { abort = true; }
  53
  54                         //check for optional parameter and set defaults
  55                         // ...at some point should added some additional type checking...
  56                         line = validParameter.validFile(parameters, "line", false);
  57                         if (line == "not found") { line = "";  }
  58                         else {
  59                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  60                                 else { allLines = 1;  }
  61                         }
  62
  63                         label = validParameter.validFile(parameters, "label", false);
  64                         if (label == "not found") { label = ""; }
  65                         else {
  66                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  67                                 else { allLines = 1;  }
  68                         }
  69
  70                         //make sure user did not use both the line and label parameters
  71                         if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
  72                         //if the user has not specified any line or labels use the ones from read.otu
  73                         else if ((line == "") && (label == "")) {
  74                                 allLines = globaldata->allLines;
  75                                 labels = globaldata->labels;
  76                                 lines = globaldata->lines;
  77                         }
  78
  79                         namesfile = validParameter.validFile(parameters, "name", true);
  80                         if (namesfile == "not open") { abort = true; }
  81                         else if (namesfile == "not found") { namesfile = ""; }
  82
  83                         groupfile = validParameter.validFile(parameters, "group", true);
  84                         if (groupfile == "not open") { abort = true; }
  85                         else if (groupfile == "not found") { groupfile = ""; }
  86                         else {
  87                                 //read in group map info.
  88                                 groupMap = new GroupMap(groupfile);
  89                                 groupMap->readMap();
  90                         }
  91
  92                         if (abort == false) {
  93
  94                                 if(globaldata->gSparseMatrix != NULL)   {       matrix = globaldata->gSparseMatrix;             }
  95
  96                                 //globaldata->gListVector bin 0 = first name read in distance matrix, globaldata->gListVector bin 1 = second name read in distance matrix
  97                                 if(globaldata->gListVector != NULL)             {
  98
  99                                         vector<string> names;
 100                                         string binnames;
 101                                         //map names to rows in sparsematrix
 102                                         for (int i = 0; i < globaldata->gListVector->size(); i++) {
 103                                                 names.clear();
 104                                                 binnames = globaldata->gListVector->get(i);
 105
 106                                                 splitAtComma(binnames, names);
 107
 108                                                 for (int j = 0; j < names.size(); j++) {
 109                                                         nameToIndex[names[j]] = i;
 110                                                 }
 111
 112                                         }
 113                                 }else { cout << "error, no listvector." << endl; }
 114
 115                                 openInputFile(fastafile, in);
 116                                 fasta = new FastaMap();
 117                         }
 118
 119                 }
 120
 121         }
 122         catch(exception& e) {
 123                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126         catch(...) {
 127                 cout << "An unknown error has occurred in the GetOTURepCommand class function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 128                 exit(1);
 129         }
 130 }
 131
 132 //**********************************************************************************************************************
 133
 134 void GetOTURepCommand::help(){
 135         try {
 136                 cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
 137                 cout << "The get.oturep command parameters are list, fasta, name, group, line and label.  The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
 138                 cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
 139                 cout << "The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
 140                 cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
 141                 cout << "The default value for line and label are all lines in your inputfile." << "\n";
 142                 cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
 143                 cout << "If you provide a groupfile, then it also appends the names of the groups present in that bin." << "\n";
 144                 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
 145         }
 146         catch(exception& e) {
 147                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 148                 exit(1);
 149         }
 150         catch(...) {
 151                 cout << "An unknown error has occurred in the GetOTURepCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154 }
 155
 156 //**********************************************************************************************************************
 157
 158 GetOTURepCommand::~GetOTURepCommand(){
 159         if (abort == false) {
 160                 delete input;  globaldata->ginput = NULL;
 161                 delete read;
 162                 delete fasta;
 163                 if (groupfile != "") {
 164                         delete groupMap;  globaldata->gGroupmap = NULL;
 165                 }
 166         }
 167 }
 168
 169 //**********************************************************************************************************************
 170
 171 int GetOTURepCommand::execute(){
 172         try {
 173
 174                 if (abort == true) { return 0; }
 175
 176                 int count = 1;
 177                 int error;
 178
 179                 //read fastafile
 180                 fasta->readFastaFile(in);
 181
 182                 in.close();
 183
 184                 //set format to list so input can get listvector
 185                 globaldata->setFormat("list");
 186
 187                 //if user gave a namesfile then use it
 188                 if (namesfile != "") {
 189                         readNamesFile();
 190                 }
 191
 192                 //read list file
 193                 read = new ReadOTUFile(listfile);
 194                 read->read(&*globaldata);
 195
 196                 input = globaldata->ginput;
 197                 list = globaldata->gListVector;
 198                 ListVector* lastList = list;
 199
 200                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 201                 set<string> processedLabels;
 202                 set<string> userLabels = labels;
 203                 set<int> userLines = lines;
 204
 205
 206                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 207
 208                         if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
 209                                         cout << list->getLabel() << '\t' << count << endl;
 210                                         error = process(list);
 211                                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 212
 213                                         processedLabels.insert(list->getLabel());
 214                                         userLabels.erase(list->getLabel());
 215                                         userLines.erase(count);
 216                         }
 217
 218                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
 219                                         cout << lastList->getLabel() << '\t' << count << endl;
 220                                         error = process(lastList);
 221                                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 222
 223                                         processedLabels.insert(lastList->getLabel());
 224                                         userLabels.erase(lastList->getLabel());
 225                         }
 226
 227                         if (count != 1) { delete lastList; }
 228                         lastList = list;
 229
 230                         list = input->getListVector();
 231                         count++;
 232                 }
 233
 234                 //output error messages about any remaining user labels
 235                 bool needToRun = false;
 236                 for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
 237                         cout << "Your file does not include the label "<< *it;
 238                         if (processedLabels.count(lastList->getLabel()) != 1) {
 239                                 cout << ". I will use " << lastList->getLabel() << "." << endl;
 240                                 needToRun = true;
 241                         }else {
 242                                 cout << ". Please refer to " << lastList->getLabel() << "." << endl;
 243                         }
 244                 }
 245
 246                 //run last line if you need to
 247                 if (needToRun == true)  {
 248                         cout << lastList->getLabel() << '\t' << count << endl;
 249                         error = process(lastList);
 250                         if (error == 1) { return 0; } //there is an error in hte input files, abort command
 251                 }
 252                 delete lastList;
 253
 254                 delete matrix;
 255                 globaldata->gSparseMatrix = NULL;
 256                 delete list;
 257                 globaldata->gListVector = NULL;
 258
 259                 return 0;
 260         }
 261         catch(exception& e) {
 262                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 263                 exit(1);
 264         }
 265         catch(...) {
 266                 cout << "An unknown error has occurred in the GetOTURepCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 267                 exit(1);
 268         }
 269
 270 }
 271
 272 //**********************************************************************************************************************
 273 void GetOTURepCommand::readNamesFile() {
 274         try {
 275                 vector<string> dupNames;
 276                 openInputFile(namesfile, inNames);
 277
 278                 string name, names, sequence;
 279
 280                 while(inNames){
 281                         inNames >> name;                        //read from first column  A
 282                         inNames >> names;               //read from second column  A,B,C,D
 283
 284                         dupNames.clear();
 285
 286                         //parse names into vector
 287                         splitAtComma(names, dupNames);
 288
 289                         //store names in fasta map
 290                         sequence = fasta->getSequence(name);
 291                         for (int i = 0; i < dupNames.size(); i++) {
 292                                 fasta->push_back(dupNames[i], sequence);
 293                         }
 294
 295                         gobble(inNames);
 296                 }
 297                 inNames.close();
 298
 299         }
 300         catch(exception& e) {
 301                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 302                 exit(1);
 303         }
 304         catch(...) {
 305                 cout << "An unknown error has occurred in the GetOTURepCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 306                 exit(1);
 307         }
 308 }
 309 //**********************************************************************************************************************
 310 string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
 311         try{
 312                 vector<string> names;
 313                 map<string, float> sums;
 314                 map<int, string> binMap; //subset of namesToIndex - just member of this bin
 315                 string binnames;
 316                 float min = 10000;
 317                 string minName;
 318                 map<string, string> groups;
 319                 map<string, string>::iterator groupIt;
 320
 321                 binnames = thisList->get(bin);
 322
 323                 //parse names into vector
 324                 splitAtComma(binnames, names);
 325
 326                 //if you have a groupfile
 327                 if(groupfile != "") {
 328                         //find the groups that are in this bin
 329                         for (int i = 0; i < names.size(); i++) {
 330                                 string groupName = groupMap->getGroup(names[i]);
 331                                 if (groupName == "not found") {
 332                                         cout << names[i] << " is missing from your group file. Please correct. " << endl;
 333                                         groupError = true;
 334                                 }else{
 335                                         groups[groupName] = groupName;
 336                                 }
 337                         }
 338
 339                         //turn the groups into a string
 340                         for(groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { group += groupIt->first + "-"; }
 341
 342                         //rip off last dash
 343                         group = group.substr(0, group.length()-1);
 344                 }
 345
 346                 //if only 1 sequence in bin then that's the rep
 347                 if (names.size() == 1) { return names[0]; }
 348                 else {
 349                         //fill binMap
 350                         for (int i = 0; i < names.size(); i++) {
 351                                 for (map<string, int>::iterator it = nameToIndex.begin(); it != nameToIndex.end(); it++) {
 352
 353                                         if (it->first == names[i]) {
 354                                                 binMap[it->second] = it->first;
 355
 356                                                 //initialize sums map
 357                                                 sums[it->first] = 0.0;
 358                                                 break;
 359                                         }
 360                                 }
 361                         }
 362
 363                         //go through each cell in the sparsematrix
 364                         for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
 365                                 //is this a distance between 2 members of this bin
 366                                 map<int, string>::iterator it = binMap.find(currentCell->row);
 367                                 map<int, string>::iterator it2 = binMap.find(currentCell->column);
 368
 369                                 //sum the distance of the sequences in the bin to eachother
 370                                 if ((it != binMap.end()) && (it2 != binMap.end())) {
 371                                         //this is a cell that repesents the distance between to of this bins members
 372                                         sums[it->second] += currentCell->dist;
 373                                         sums[it2->second] += currentCell->dist;
 374                                 }
 375                         }
 376
 377                         //smallest sum is the representative
 378                         for (map<string, float>::iterator it4 = sums.begin(); it4 != sums.end(); it4++) {
 379                                 if (it4->second < min) {
 380                                         min = it4->second;
 381                                         minName = it4->first;
 382                                 }
 383
 384                         }
 385
 386                         return minName;
 387                 }
 388
 389         }
 390         catch(exception& e) {
 391                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 392                 exit(1);
 393         }
 394         catch(...) {
 395                 cout << "An unknown error has occurred in the GetOTURepCommand class function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 396                 exit(1);
 397         }
 398 }
 399
 400 //**********************************************************************************************************************
 401 int GetOTURepCommand::process(ListVector* processList) {
 402         try{
 403                                 string nameRep, name, sequence;
 404
 405                                 //create output file
 406                                 string outputFileName = getRootName(listfile) + processList->getLabel() + ".rep.fasta";
 407                                 openOutputFile(outputFileName, out);
 408
 409                                 //for each bin in the list vector
 410                                 for (int i = 0; i < processList->size(); i++) {
 411                                         string groups;
 412                                         nameRep = FindRep(i, groups, processList);
 413
 414                                         //print out name and sequence for that bin
 415                                         sequence = fasta->getSequence(nameRep);
 416
 417                                         if (sequence != "not found") {
 418                                                 if (groupfile == "") {
 419                                                         nameRep = nameRep + "|" + toString(i+1);
 420                                                         out << ">" << nameRep << endl;
 421                                                         out << sequence << endl;
 422                                                 }else {
 423                                                         nameRep = nameRep + "|" + groups + "|" + toString(i+1);
 424                                                         out << ">" << nameRep << endl;
 425                                                         out << sequence << endl;
 426                                                 }
 427                                         }else {
 428                                                 cout << nameRep << " is missing from your fasta or name file. Please correct. " << endl;
 429                                                 remove(outputFileName.c_str());
 430                                                 return 1;
 431                                         }
 432                                 }
 433
 434                                 out.close();
 435                                 return 0;
 436
 437         }
 438         catch(exception& e) {
 439                 cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 440                 exit(1);
 441         }
 442         catch(...) {
 443                 cout << "An unknown error has occurred in the GetOTURepCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 444                 exit(1);
 445         }
 446 }
 447
 448 //**********************************************************************************************************************
 449
 450
 451
 452
 453