matrixoutputcommand.cpp

   1 /*
   2  *  matrixoutputcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "matrixoutputcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22 //**********************************************************************************************************************
  23 vector<string> MatrixOutputCommand::getValidParameters(){
  24         try {
  25                 string Array[] =  {"label","calc","groups","outputdir","inputdir", "output"};
  26                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "MatrixOutputCommand", "getValidParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 MatrixOutputCommand::MatrixOutputCommand(){
  36         try {
  37                 abort = true;
  38                 //initialize outputTypes
  39                 vector<string> tempOutNames;
  40                 outputTypes["phylip"] = tempOutNames;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 vector<string> MatrixOutputCommand::getRequiredParameters(){
  49         try {
  50                 vector<string> myArray;
  51                 return myArray;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "MatrixOutputCommand", "getRequiredParameters");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59 vector<string> MatrixOutputCommand::getRequiredFiles(){
  60         try {
  61                 string Array[] =  {"shared"};
  62                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  63                 return myArray;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "MatrixOutputCommand", "getRequiredFiles");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71
  72 MatrixOutputCommand::MatrixOutputCommand(string option)  {
  73         try {
  74                 globaldata = GlobalData::getInstance();
  75                 abort = false;
  76                 allLines = 1;
  77                 labels.clear();
  78                 Groups.clear();
  79                 Estimators.clear();
  80
  81                 //allow user to run help
  82                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  83
  84                 else {
  85                         //valid paramters for this command
  86                         string Array[] =  {"label","calc","groups","outputdir","inputdir", "output"};
  87                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters  = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93
  94                         //check to make sure all parameters are valid for command
  95                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  96                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["phylip"] = tempOutNames;
 102
 103                         //if the user changes the output directory command factory will send this info to us in the output parameter
 104                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 105                                 outputDir = "";
 106                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 107                         }
 108
 109                         //make sure the user has already run the read.otu command
 110                         if (globaldata->getSharedFile() == "") {
 111                                 if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
 112                                 else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
 113                         }
 114
 115                         //check for optional parameter and set defaults
 116                         // ...at some point should added some additional type checking...
 117                         label = validParameter.validFile(parameters, "label", false);
 118                         if (label == "not found") { label = ""; }
 119                         else {
 120                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 121                                 else { allLines = 1;  }
 122                         }
 123
 124                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
 125                         if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
 126
 127                         //if the user has not specified any labels use the ones from read.otu
 128                         if (label == "") {
 129                                 allLines = globaldata->allLines;
 130                                 labels = globaldata->labels;
 131                         }
 132
 133                         groups = validParameter.validFile(parameters, "groups", false);
 134                         if (groups == "not found") { groups = ""; }
 135                         else {
 136                                 m->splitAtDash(groups, Groups);
 137                                 globaldata->Groups = Groups;
 138                         }
 139
 140                         calc = validParameter.validFile(parameters, "calc", false);
 141                         if (calc == "not found") { calc = "jclass-thetayc";  }
 142                         else {
 143                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 144                         }
 145                         m->splitAtDash(calc, Estimators);
 146
 147                         if (abort == false) {
 148
 149                                 validCalculator = new ValidCalculators();
 150
 151                                 int i;
 152                                 for (i=0; i<Estimators.size(); i++) {
 153                                         if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
 154                                                 if (Estimators[i] == "jabund") {
 155                                                         matrixCalculators.push_back(new JAbund());
 156                                                 }else if (Estimators[i] == "sorabund") {
 157                                                         matrixCalculators.push_back(new SorAbund());
 158                                                 }else if (Estimators[i] == "jclass") {
 159                                                         matrixCalculators.push_back(new Jclass());
 160                                                 }else if (Estimators[i] == "sorclass") {
 161                                                         matrixCalculators.push_back(new SorClass());
 162                                                 }else if (Estimators[i] == "jest") {
 163                                                         matrixCalculators.push_back(new Jest());
 164                                                 }else if (Estimators[i] == "sorest") {
 165                                                         matrixCalculators.push_back(new SorEst());
 166                                                 }else if (Estimators[i] == "thetayc") {
 167                                                         matrixCalculators.push_back(new ThetaYC());
 168                                                 }else if (Estimators[i] == "thetan") {
 169                                                         matrixCalculators.push_back(new ThetaN());
 170                                                 }else if (Estimators[i] == "morisitahorn") {
 171                                                         matrixCalculators.push_back(new MorHorn());
 172                                                 }else if (Estimators[i] == "braycurtis") {
 173                                                         matrixCalculators.push_back(new BrayCurtis());
 174                                                 }
 175                                         }
 176                                 }
 177
 178                         }
 179                 }
 180
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 184                 exit(1);
 185         }
 186 }
 187
 188 //**********************************************************************************************************************
 189
 190 void MatrixOutputCommand::help(){
 191         try {
 192                 m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
 193                 m->mothurOut("The dist.shared command parameters are groups, calc, output and label.  No parameters are required.\n");
 194                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
 195                 m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
 196                 m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
 197                 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
 198                 m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
 199                 m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
 200                 m->mothurOut("The default value for calc is jclass and thetayc.\n");
 201                 validCalculator->printCalc("matrix", cout);
 202                 m->mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
 203                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "MatrixOutputCommand", "help");
 207                 exit(1);
 208         }
 209 }
 210
 211
 212 //**********************************************************************************************************************
 213
 214 MatrixOutputCommand::~MatrixOutputCommand(){
 215         if (abort == false) {
 216                 delete input; globaldata->ginput = NULL;
 217                 delete read;
 218                 delete validCalculator;
 219         }
 220 }
 221
 222 //**********************************************************************************************************************
 223
 224 int MatrixOutputCommand::execute(){
 225         try {
 226
 227                 if (abort == true) {    return 0;       }
 228
 229                 //if the users entered no valid calculators don't execute command
 230                 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
 231
 232                 //you have groups
 233                 read = new ReadOTUFile(globaldata->inputFileName);
 234                 read->read(&*globaldata);
 235
 236                 input = globaldata->ginput;
 237                 lookup = input->getSharedRAbundVectors();
 238                 string lastLabel = lookup[0]->getLabel();
 239
 240                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 241                 set<string> processedLabels;
 242                 set<string> userLabels = labels;
 243
 244                 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0;}
 245
 246                 numGroups = lookup.size();
 247
 248                 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); return 0;  }
 249
 250                 //as long as you are not at the end of the file or done wih the lines you want
 251                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 252
 253                         if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 254
 255                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 256                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 257                                 process(lookup);
 258
 259                                 processedLabels.insert(lookup[0]->getLabel());
 260                                 userLabels.erase(lookup[0]->getLabel());
 261                         }
 262
 263                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 264                                 string saveLabel = lookup[0]->getLabel();
 265
 266                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 267                                 lookup = input->getSharedRAbundVectors(lastLabel);
 268
 269                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 270                                 process(lookup);
 271
 272                                 processedLabels.insert(lookup[0]->getLabel());
 273                                 userLabels.erase(lookup[0]->getLabel());
 274
 275                                 //restore real lastlabel to save below
 276                                 lookup[0]->setLabel(saveLabel);
 277                         }
 278
 279                         lastLabel = lookup[0]->getLabel();
 280
 281                         //get next line to process
 282                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 283                         lookup = input->getSharedRAbundVectors();
 284                 }
 285
 286                 if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 287
 288                 //output error messages about any remaining user labels
 289                 set<string>::iterator it;
 290                 bool needToRun = false;
 291                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 292                         m->mothurOut("Your file does not include the label " + *it);
 293                         if (processedLabels.count(lastLabel) != 1) {
 294                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 295                                 needToRun = true;
 296                         }else {
 297                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 298                         }
 299                 }
 300
 301                 if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 302
 303                 //run last label if you need to
 304                 if (needToRun == true)  {
 305                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  }
 306                         lookup = input->getSharedRAbundVectors(lastLabel);
 307
 308                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 309                         process(lookup);
 310                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 311                 }
 312
 313                 if (m->control_pressed) { outputTypes.clear();  delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 314
 315                 //reset groups parameter
 316                 globaldata->Groups.clear();
 317
 318                 m->mothurOutEndLine();
 319                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 320                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 321                 m->mothurOutEndLine();
 322
 323
 324                 return 0;
 325         }
 326         catch(exception& e) {
 327                 m->errorOut(e, "MatrixOutputCommand", "execute");
 328                 exit(1);
 329         }
 330 }
 331 /***********************************************************/
 332 void MatrixOutputCommand::printSims(ostream& out) {
 333         try {
 334
 335                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 336
 337                 //output num seqs
 338                 out << simMatrix.size() << endl;
 339
 340                 if (output == "lt") {
 341                         for (int m = 0; m < simMatrix.size(); m++)      {
 342                                 out << lookup[m]->getGroup() << '\t';
 343                                 for (int n = 0; n < m; n++)     {
 344                                         out << simMatrix[m][n] << '\t';
 345                                 }
 346                                 out << endl;
 347                         }
 348                 }else{
 349                         for (int m = 0; m < simMatrix.size(); m++)      {
 350                                 out << lookup[m]->getGroup() << '\t';
 351                                 for (int n = 0; n < simMatrix[m].size(); n++)   {
 352                                         out << simMatrix[m][n] << '\t';
 353                                 }
 354                                 out << endl;
 355                         }
 356                 }
 357         }
 358         catch(exception& e) {
 359                 m->errorOut(e, "MatrixOutputCommand", "printSims");
 360                 exit(1);
 361         }
 362 }
 363 /***********************************************************/
 364 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 365         try {
 366
 367                                 EstOutput data;
 368                                 vector<SharedRAbundVector*> subset;
 369
 370                                 //for each calculator
 371                                 for(int i = 0 ; i < matrixCalculators.size(); i++) {
 372
 373                                         //initialize simMatrix
 374                                         simMatrix.clear();
 375                                         simMatrix.resize(numGroups);
 376                                         for (int p = 0; p < simMatrix.size(); p++)      {
 377                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 378                                                         simMatrix[p].push_back(0.0);
 379                                                 }
 380                                         }
 381
 382                                         for (int k = 0; k < thisLookup.size(); k++) {
 383                                                 for (int l = k; l < thisLookup.size(); l++) {
 384                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 385                                                                 //get estimated similarity between 2 groups
 386
 387                                                                 if (m->control_pressed) { return 0; }
 388
 389                                                                 subset.clear(); //clear out old pair of sharedrabunds
 390                                                                 //add new pair of sharedrabunds
 391                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 392
 393                                                                 data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 394                                                                 //save values in similarity matrix
 395                                                                 simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
 396                                                                 simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
 397                                                         }
 398                                                 }
 399                                         }
 400
 401                                         exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
 402                                         m->openOutputFile(exportFileName, out);
 403                                         outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
 404
 405                                         printSims(out);
 406                                         out.close();
 407
 408                                 }
 409
 410                                 return 0;
 411
 412         }
 413         catch(exception& e) {
 414                 m->errorOut(e, "MatrixOutputCommand", "process");
 415                 exit(1);
 416         }
 417 }
 418 /***********************************************************/
 419
 420
 421