sensspeccommand.cpp

   1 /*
   2  *  sensspeccommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 7/6/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sensspeccommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SensSpecCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
  16                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
  17                 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pcolumn);
  18                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  19                 CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
  20                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
  21                 CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "SensSpecCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string SensSpecCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The sens.spec command....\n";
  39                 return helpString;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "SensSpecCommand", "getHelpString");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 string SensSpecCommand::getOutputPattern(string type) {
  48     try {
  49         string pattern = "";
  50
  51         if (type == "sensspec") {  pattern = "[filename],sensspec"; }
  52         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  53
  54         return pattern;
  55     }
  56     catch(exception& e) {
  57         m->errorOut(e, "SensSpecCommand", "getOutputPattern");
  58         exit(1);
  59     }
  60 }
  61 //**********************************************************************************************************************
  62 SensSpecCommand::SensSpecCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["sensspec"] = tempOutNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
  71                 exit(1);
  72         }
  73 }
  74 //***************************************************************************************************************
  75
  76 SensSpecCommand::SensSpecCommand(string option)  {
  77         try {
  78
  79                 abort = false; calledHelp = false;
  80                 allLines = 1;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; calledHelp = true; }
  84                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  85
  86                 else {
  87                         string temp;
  88
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string,string> parameters = parser.getParameters();
  93
  94                         ValidParameters validParameter;
  95                         map<string,string>::iterator it;
  96
  97                         //check to make sure all parameters are valid for command
  98                         for (it = parameters.begin(); it != parameters.end(); it++) {
  99                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 100                         }
 101
 102                         //initialize outputTypes
 103                         vector<string> tempOutNames;
 104                         outputTypes["sensspec"] = tempOutNames;
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("list");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 117                                 }
 118
 119                                 it = parameters.find("phylip");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 125                                 }
 126
 127                                 it = parameters.find("column");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 133                                 }
 134                         }
 135                         //check for required parameters
 136                         listFile = validParameter.validFile(parameters, "list", true);
 137                         if (listFile == "not found") {
 138                                 listFile = m->getListFile();
 139                                 if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 140                                 else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 141                         }
 142                         else if (listFile == "not open") { abort = true; }
 143                         else { m->setListFile(listFile); }
 144
 145                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 146                         if (phylipfile == "not found") { phylipfile = "";  }
 147                         else if (phylipfile == "not open") { abort = true; }
 148                         else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
 149
 150                         columnfile = validParameter.validFile(parameters, "column", true);
 151                         if (columnfile == "not found") { columnfile = ""; }
 152                         else if (columnfile == "not open") { abort = true; }
 153                         else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
 154
 155                         if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
 156                                 //give priority to column, then phylip
 157                                 columnfile = m->getColumnFile();
 158                                 if (columnfile != "") {  distFile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 159                                 else {
 160                                         phylipfile = m->getPhylipFile();
 161                                         if (phylipfile != "") {  distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 162                                         else {
 163                                                 m->mothurOut("No valid current files. You must provide a phylip or column file."); m->mothurOutEndLine();
 164                                                 abort = true;
 165                                         }
 166                                 }
 167                         }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a sens.spec command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
 168
 169
 170                         //if the user changes the output directory command factory will send this info to us in the output parameter
 171                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 172                         if (outputDir == "not found"){
 173                                 outputDir = "";
 174                                 outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
 175                         }
 176
 177                         //check for optional parameter and set defaults
 178                         // ...at some point should added some additional type checking...
 179                         temp = validParameter.validFile(parameters, "hard", false);
 180                         if (temp == "not found"){       hard = 0;       }
 181                         else if(!m->isTrue(temp))       {       hard = 0;       }
 182                         else if(m->isTrue(temp))        {       hard = 1;       }
 183
 184                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
 185                         m->mothurConvert(temp, cutoff);
 186 //                      cout << cutoff << endl;
 187
 188                         temp = validParameter.validFile(parameters, "precision", false);        if (temp == "not found") { temp = "100"; }
 189                         m->mothurConvert(temp, precision);
 190 //                      cout << precision << endl;
 191
 192                         string label = validParameter.validFile(parameters, "label", false);
 193                         if (label == "not found") { label = ""; }
 194                         else {
 195                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 196                                 else { allLines = 1;  }
 197                         }
 198
 199             map<string, string> variables;
 200             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
 201                         sensSpecFileName = getOutputFileName("sensspec",variables);
 202                 }
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
 206                 exit(1);
 207         }
 208 }
 209 //***************************************************************************************************************
 210
 211 int SensSpecCommand::execute(){
 212         try{
 213                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 214
 215                 setUpOutput();
 216                 outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
 217                 if(format == "phylip")          {       processPhylip();        }
 218                 else if(format == "column")     {       processColumn();        }
 219
 220                 if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
 221
 222                 m->mothurOutEndLine();
 223                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 224                 m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
 225                 m->mothurOutEndLine();
 226
 227
 228                 return 0;
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "SensSpecCommand", "execute");
 232                 exit(1);
 233         }
 234 }
 235
 236 //***************************************************************************************************************
 237
 238 int SensSpecCommand::processPhylip(){
 239         try{
 240                 //probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
 241                 string origCutoff = "";
 242                 bool getCutoff = 0;
 243                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 244                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 245
 246                 map<string, int> seqMap;
 247                 string seqList;
 248
 249                 InputData input(listFile, "list");
 250                 ListVector* list = input.getListVector();
 251                 string lastLabel = list->getLabel();
 252
 253                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 254                 set<string> processedLabels;
 255                 set<string> userLabels = labels;
 256
 257
 258                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 259
 260                         if(m->control_pressed){
 261                 for (int i = 0; i < outputNames.size(); i++){   m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
 262             }
 263
 264                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 265
 266                                 processedLabels.insert(list->getLabel());
 267                                 userLabels.erase(list->getLabel());
 268
 269                                 //process
 270                                 fillSeqMap(seqMap, list);
 271                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 272                         }
 273
 274                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 275                                 string saveLabel = list->getLabel();
 276
 277                                 delete list;
 278                                 list = input.getListVector(lastLabel);
 279
 280                                 processedLabels.insert(list->getLabel());
 281                                 userLabels.erase(list->getLabel());
 282
 283                                 //process
 284                                 fillSeqMap(seqMap, list);
 285                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 286
 287                                 //restore real lastlabel to save below
 288                                 list->setLabel(saveLabel);
 289                         }
 290
 291                         lastLabel = list->getLabel();
 292
 293                         delete list;
 294                         list = input.getListVector();
 295                 }
 296
 297
 298                 //output error messages about any remaining user labels
 299                 set<string>::iterator it;
 300                 bool needToRun = false;
 301                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 302                         m->mothurOut("Your file does not include the label " + *it);
 303                         if (processedLabels.count(lastLabel) != 1) {
 304                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 305                                 needToRun = true;
 306                         }else {
 307                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 308                         }
 309                 }
 310
 311                 //run last label if you need to
 312                 if (needToRun == true)  {
 313                         if (list != NULL) {     delete list;    }
 314                         list = input.getListVector(lastLabel);
 315
 316                         //process
 317                         fillSeqMap(seqMap, list);
 318                         process(seqMap, list->getLabel(), getCutoff, origCutoff);
 319
 320                         delete list;
 321                 }
 322
 323                 return 0;
 324         }
 325         catch(exception& e) {
 326                 m->errorOut(e, "SensSpecCommand", "processPhylip");
 327                 exit(1);
 328         }
 329 }
 330
 331 //***************************************************************************************************************
 332
 333 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
 334         try {
 335                 //for each otu
 336                 for(int i=0;i<list->getNumBins();i++){
 337
 338                         if (m->control_pressed) { return 0; }
 339
 340                         string seqList = list->get(i);
 341                         int seqListLength = seqList.length();
 342                         string seqName = "";
 343
 344                         //parse bin by name, mapping each name to its otu number
 345                         for(int j=0;j<seqListLength;j++){
 346
 347                                 if(seqList[j] == ','){
 348                                         seqMap[seqName] = i;
 349                                         seqName = "";
 350                                 }
 351                                 else{
 352                                         seqName += seqList[j];
 353                                 }
 354
 355                         }
 356                         seqMap[seqName] = i;
 357                 }
 358
 359                 return 0;
 360         }
 361         catch(exception& e) {
 362                 m->errorOut(e, "SensSpecCommand", "fillSeqMap");
 363                 exit(1);
 364         }
 365 }
 366 //***************************************************************************************************************
 367 int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
 368         try {
 369                 int numSeqs = 0;
 370
 371                 //for each otu
 372                 for(int i=0;i<list->getNumBins();i++){
 373
 374                         if (m->control_pressed) { return 0; }
 375
 376                         vector<string> seqNameVector;
 377                         string bin = list->get(i);
 378                         m->splitAtComma(bin, seqNameVector);
 379
 380                         numSeqs += seqNameVector.size();
 381
 382                         for(int j=0;j<seqNameVector.size();j++){
 383                                 string seqPairString = "";
 384                                 for(int k=0;k<j;k++){
 385                                         if(seqNameVector[j] < seqNameVector[k]) {       seqPairString = seqNameVector[j] + '\t' + seqNameVector[k];     }
 386                                         else                                                                    {       seqPairString = seqNameVector[k] + '\t' + seqNameVector[j];     }
 387                                         seqPairSet.insert(seqPairString);
 388                                 }
 389                         }
 390                 }
 391
 392                 return numSeqs;
 393         }
 394         catch(exception& e) {
 395                 m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
 396                 exit(1);
 397         }
 398 }
 399 //***************************************************************************************************************
 400 int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCutoff, string& origCutoff){
 401         try {
 402
 403                 int lNumSeqs = seqMap.size();
 404                 int pNumSeqs = 0;
 405
 406                 ifstream phylipFile;
 407                 m->openInputFile(distFile, phylipFile);
 408                 phylipFile >> pNumSeqs;
 409                 if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
 410
 411                 string seqName;
 412                 double distance;
 413                 vector<int> otuIndices(lNumSeqs, -1);
 414
 415                 truePositives = 0;
 416                 falsePositives = 0;
 417                 trueNegatives = 0;
 418                 falseNegatives = 0;
 419
 420                 if(getCutoff == 1){
 421                         if(label != "unique"){
 422                                 origCutoff = label;
 423                                 convert(label, cutoff);
 424                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 425                         }
 426                         else{
 427                                 origCutoff = "unique";
 428                                 cutoff = 0.0000;
 429                         }
 430                 }
 431
 432                 m->mothurOut(label); m->mothurOutEndLine();
 433
 434                 for(int i=0;i<pNumSeqs;i++){
 435
 436                         if (m->control_pressed) { return 0; }
 437
 438                         phylipFile >> seqName;
 439                         otuIndices[i] = seqMap[seqName];
 440
 441                         for(int j=0;j<i;j++){
 442                                 phylipFile >> distance;
 443
 444                                 if(distance <= cutoff){
 445                                         if(otuIndices[i] == otuIndices[j])      {       truePositives++;        }
 446                                         else                                                            {       falseNegatives++;       }
 447                                 }
 448                                 else{
 449                                         if(otuIndices[i] == otuIndices[j])      {       falsePositives++;       }
 450                                         else                                                            {       trueNegatives++;        }
 451                                 }
 452                         }
 453                 }
 454                 phylipFile.close();
 455
 456                 outputStatistics(label, origCutoff);
 457
 458                 return 0;
 459         }
 460         catch(exception& e) {
 461                 m->errorOut(e, "SensSpecCommand", "process");
 462                 exit(1);
 463         }
 464 }
 465 //***************************************************************************************************************
 466 int SensSpecCommand::process(set<string>& seqPairSet, string label, bool& getCutoff, string& origCutoff, int numSeqs){
 467         try {
 468                 int numDists = (numSeqs * (numSeqs-1) / 2);
 469
 470                 ifstream columnFile;
 471                 m->openInputFile(distFile, columnFile);
 472                 string seqNameA, seqNameB, seqPairString;
 473                 double distance;
 474
 475                 truePositives = 0;
 476                 falsePositives = 0;
 477                 trueNegatives = numDists;
 478                 falseNegatives = 0;
 479
 480                 if(getCutoff == 1){
 481                         if(label != "unique"){
 482                                 origCutoff = label;
 483                                 convert(label, cutoff);
 484                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 485                         }
 486                         else{
 487                                 origCutoff = "unique";
 488                                 cutoff = 0.0000;
 489                         }
 490                 }
 491
 492                 m->mothurOut(label); m->mothurOutEndLine();
 493
 494                 while(columnFile){
 495                         columnFile >> seqNameA >> seqNameB >> distance;
 496                         if(seqNameA < seqNameB) {       seqPairString = seqNameA + '\t' + seqNameB;     }
 497                         else                                    {       seqPairString = seqNameB + '\t' + seqNameA;     }
 498
 499                         set<string>::iterator it = seqPairSet.find(seqPairString);
 500
 501                         if(distance <= cutoff){
 502                                 if(it != seqPairSet.end()){
 503                                         truePositives++;
 504                                         seqPairSet.erase(it);
 505                                 }
 506                                 else{
 507                                         falseNegatives++;
 508                                 }
 509                                 trueNegatives--;
 510                         }
 511                         else if(it != seqPairSet.end()){
 512                                 falsePositives++;
 513                                 trueNegatives--;
 514                                 seqPairSet.erase(it);
 515                         }
 516
 517                         m->gobble(columnFile);
 518                 }
 519                 falsePositives += seqPairSet.size();
 520
 521                 outputStatistics(label, origCutoff);
 522
 523
 524                 return 0;
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "SensSpecCommand", "process");
 528                 exit(1);
 529         }
 530 }
 531 //***************************************************************************************************************
 532
 533 int SensSpecCommand::processColumn(){
 534         try{
 535                 string origCutoff = "";
 536                 bool getCutoff = 0;
 537                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 538                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 539
 540                 set<string> seqPairSet;
 541                 int numSeqs = 0;
 542
 543                 InputData input(listFile, "list");
 544                 ListVector* list = input.getListVector();
 545                 string lastLabel = list->getLabel();
 546
 547                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 548                 set<string> processedLabels;
 549                 set<string> userLabels = labels;
 550
 551
 552                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 553
 554                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
 555
 556                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 557
 558                                 processedLabels.insert(list->getLabel());
 559                                 userLabels.erase(list->getLabel());
 560
 561                                 //process
 562                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 563                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 564                         }
 565
 566                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 567                                 string saveLabel = list->getLabel();
 568
 569                                 delete list;
 570                                 list = input.getListVector(lastLabel);
 571
 572                                 processedLabels.insert(list->getLabel());
 573                                 userLabels.erase(list->getLabel());
 574
 575                                 //process
 576                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 577                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 578
 579                                 //restore real lastlabel to save below
 580                                 list->setLabel(saveLabel);
 581                         }
 582
 583                         lastLabel = list->getLabel();
 584
 585                         delete list;
 586                         list = input.getListVector();
 587                 }
 588
 589
 590                 //output error messages about any remaining user labels
 591                 set<string>::iterator it;
 592                 bool needToRun = false;
 593                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 594                         m->mothurOut("Your file does not include the label " + *it);
 595                         if (processedLabels.count(lastLabel) != 1) {
 596                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 597                                 needToRun = true;
 598                         }else {
 599                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 600                         }
 601                 }
 602
 603                 //run last label if you need to
 604                 if (needToRun == true)  {
 605                         if (list != NULL) {     delete list;    }
 606                         list = input.getListVector(lastLabel);
 607
 608                         //process
 609                         numSeqs = fillSeqPairSet(seqPairSet, list);
 610                         delete list;
 611                         process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 612                 }
 613
 614                 return 0;
 615         }
 616         catch(exception& e) {
 617                 m->errorOut(e, "SensSpecCommand", "processColumn");
 618                 exit(1);
 619         }
 620 }
 621
 622 //***************************************************************************************************************
 623
 624 void SensSpecCommand::setUpOutput(){
 625         try{
 626                 ofstream sensSpecFile;
 627                 m->openOutputFile(sensSpecFileName, sensSpecFile);
 628
 629                 sensSpecFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
 630
 631                 sensSpecFile.close();
 632         }
 633         catch(exception& e) {
 634                 m->errorOut(e, "SensSpecCommand", "setUpOutput");
 635                 exit(1);
 636         }
 637 }
 638
 639 //***************************************************************************************************************
 640
 641 void SensSpecCommand::outputStatistics(string label, string cutoff){
 642         try{
 643                 double tp = (double) truePositives;
 644                 double fp = (double) falsePositives;
 645                 double tn = (double) trueNegatives;
 646                 double fn = (double) falseNegatives;
 647
 648                 double p = tp + fn;
 649                 double n = fp + tn;
 650                 double pPrime = tp + fp;
 651                 double nPrime = tn + fn;
 652
 653                 double sensitivity = tp / p;
 654                 double specificity = tn / n;
 655                 double positivePredictiveValue = tp / pPrime;
 656                 double negativePredictiveValue = tn / nPrime;
 657                 double falseDiscoveryRate = fp / pPrime;
 658
 659                 double accuracy = (tp + tn) / (p + n);
 660                 double matthewsCorrCoef = (tp * tn - fp * fn) / sqrt(p * n * pPrime * nPrime);  if(p == 0 || n == 0){   matthewsCorrCoef = 0;   }
 661                 double f1Score = 2.0 * tp / (p + pPrime);
 662
 663
 664                 if(p == 0)                      {       sensitivity = 0;        matthewsCorrCoef = 0;   }
 665                 if(n == 0)                      {       specificity = 0;        matthewsCorrCoef = 0;   }
 666                 if(p + n == 0)          {       accuracy = 0;                                                           }
 667                 if(p + pPrime == 0)     {       f1Score = 0;                                                            }
 668                 if(pPrime == 0)         {       positivePredictiveValue = 0;    falseDiscoveryRate = 0; matthewsCorrCoef = 0;   }
 669                 if(nPrime == 0)         {       negativePredictiveValue = 0;    matthewsCorrCoef = 0;                                                   }
 670
 671                 ofstream sensSpecFile;
 672                 m->openOutputFileAppend(sensSpecFileName, sensSpecFile);
 673
 674                 sensSpecFile << label << '\t' << cutoff << '\t';
 675                 sensSpecFile << truePositives << '\t' << trueNegatives << '\t' << falsePositives << '\t' << falseNegatives << '\t';
 676                 sensSpecFile << setprecision(4);
 677                 sensSpecFile << sensitivity << '\t' << specificity << '\t' << positivePredictiveValue << '\t' << negativePredictiveValue << '\t';
 678                 sensSpecFile << falseDiscoveryRate << '\t' << accuracy << '\t' << matthewsCorrCoef << '\t' << f1Score << endl;
 679
 680                 sensSpecFile.close();
 681         }
 682         catch(exception& e) {
 683                 m->errorOut(e, "SensSpecCommand", "outputStatistics");
 684                 exit(1);
 685         }
 686 }
 687
 688 //***************************************************************************************************************
 689
 690
 691