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         int startTime = time(NULL);
 216
 217         //create list file with only unique names, saves time and memory by removing redundant names from list file that are not in the distance file.
 218         string newListFile = preProcessList();
 219         if (newListFile != "") { listFile = newListFile; }
 220
 221                 setUpOutput();
 222                 outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
 223                 if(format == "phylip")          {       processPhylip();        }
 224                 else if(format == "column")     {       processColumn();        }
 225
 226         //remove temp file if created
 227         if (newListFile != "") { m->mothurRemove(newListFile); }
 228
 229                 if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
 230
 231         m->mothurOut("It took " + toString(time(NULL) - startTime) + " to run sens.spec."); m->mothurOutEndLine();
 232
 233                 m->mothurOutEndLine();
 234                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 235                 m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
 236                 m->mothurOutEndLine();
 237
 238
 239                 return 0;
 240         }
 241         catch(exception& e) {
 242                 m->errorOut(e, "SensSpecCommand", "execute");
 243                 exit(1);
 244         }
 245 }
 246
 247 //***************************************************************************************************************
 248
 249 int SensSpecCommand::processPhylip(){
 250         try{
 251                 //probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
 252                 string origCutoff = "";
 253                 bool getCutoff = 0;
 254                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 255                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 256
 257                 map<string, int> seqMap;
 258                 string seqList;
 259
 260                 InputData input(listFile, "list");
 261                 ListVector* list = input.getListVector();
 262                 string lastLabel = list->getLabel();
 263
 264                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 265                 set<string> processedLabels;
 266                 set<string> userLabels = labels;
 267
 268
 269                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 270
 271                         if(m->control_pressed){
 272                 for (int i = 0; i < outputNames.size(); i++){   m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
 273             }
 274
 275                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 276
 277                                 processedLabels.insert(list->getLabel());
 278                                 userLabels.erase(list->getLabel());
 279
 280                                 //process
 281                                 fillSeqMap(seqMap, list);
 282                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 283                         }
 284
 285                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 286                                 string saveLabel = list->getLabel();
 287
 288                                 delete list;
 289                                 list = input.getListVector(lastLabel);
 290
 291                                 processedLabels.insert(list->getLabel());
 292                                 userLabels.erase(list->getLabel());
 293
 294                                 //process
 295                                 fillSeqMap(seqMap, list);
 296                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 297
 298                                 //restore real lastlabel to save below
 299                                 list->setLabel(saveLabel);
 300                         }
 301
 302                         lastLabel = list->getLabel();
 303
 304                         delete list;
 305                         list = input.getListVector();
 306                 }
 307
 308
 309                 //output error messages about any remaining user labels
 310                 set<string>::iterator it;
 311                 bool needToRun = false;
 312                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 313                         m->mothurOut("Your file does not include the label " + *it);
 314                         if (processedLabels.count(lastLabel) != 1) {
 315                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 316                                 needToRun = true;
 317                         }else {
 318                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 319                         }
 320                 }
 321
 322                 //run last label if you need to
 323                 if (needToRun == true)  {
 324                         if (list != NULL) {     delete list;    }
 325                         list = input.getListVector(lastLabel);
 326
 327                         //process
 328                         fillSeqMap(seqMap, list);
 329                         process(seqMap, list->getLabel(), getCutoff, origCutoff);
 330
 331                         delete list;
 332                 }
 333
 334                 return 0;
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "SensSpecCommand", "processPhylip");
 338                 exit(1);
 339         }
 340 }
 341
 342 //***************************************************************************************************************
 343
 344 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
 345         try {
 346                 //for each otu
 347                 for(int i=0;i<list->getNumBins();i++){
 348
 349                         if (m->control_pressed) { return 0; }
 350
 351                         string seqList = list->get(i);
 352                         int seqListLength = seqList.length();
 353                         string seqName = "";
 354
 355                         //parse bin by name, mapping each name to its otu number
 356                         for(int j=0;j<seqListLength;j++){
 357
 358                                 if(seqList[j] == ','){
 359                                         seqMap[seqName] = i;
 360                                         seqName = "";
 361                                 }
 362                                 else{
 363                                         seqName += seqList[j];
 364                                 }
 365
 366                         }
 367                         seqMap[seqName] = i;
 368                 }
 369
 370                 return 0;
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "SensSpecCommand", "fillSeqMap");
 374                 exit(1);
 375         }
 376 }
 377 //***************************************************************************************************************
 378 int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
 379         try {
 380                 int numSeqs = 0;
 381
 382                 //for each otu
 383                 for(int i=0;i<list->getNumBins();i++){
 384
 385                         if (m->control_pressed) { return 0; }
 386
 387                         vector<string> seqNameVector;
 388                         string bin = list->get(i);
 389                         m->splitAtComma(bin, seqNameVector);
 390
 391                         numSeqs += seqNameVector.size();
 392
 393                         for(int j=0;j<seqNameVector.size();j++){
 394                                 string seqPairString = "";
 395                                 for(int k=0;k<j;k++){
 396                                         if(seqNameVector[j] < seqNameVector[k]) {       seqPairString = seqNameVector[j] + '\t' + seqNameVector[k];     }
 397                                         else                                                                    {       seqPairString = seqNameVector[k] + '\t' + seqNameVector[j];     }
 398                                         seqPairSet.insert(seqPairString);
 399                                 }
 400                         }
 401                 }
 402
 403                 return numSeqs;
 404         }
 405         catch(exception& e) {
 406                 m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
 407                 exit(1);
 408         }
 409 }
 410 //***************************************************************************************************************
 411 int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCutoff, string& origCutoff){
 412         try {
 413
 414                 int lNumSeqs = seqMap.size();
 415                 int pNumSeqs = 0;
 416
 417                 ifstream phylipFile;
 418                 m->openInputFile(distFile, phylipFile);
 419                 phylipFile >> pNumSeqs;
 420                 if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
 421
 422                 string seqName;
 423                 double distance;
 424                 vector<int> otuIndices(lNumSeqs, -1);
 425
 426                 truePositives = 0;
 427                 falsePositives = 0;
 428                 trueNegatives = 0;
 429                 falseNegatives = 0;
 430
 431                 if(getCutoff == 1){
 432                         if(label != "unique"){
 433                                 origCutoff = label;
 434                                 convert(label, cutoff);
 435                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 436                         }
 437                         else{
 438                                 origCutoff = "unique";
 439                                 cutoff = 0.0000;
 440                         }
 441                 }
 442
 443                 m->mothurOut(label); m->mothurOutEndLine();
 444
 445                 for(int i=0;i<pNumSeqs;i++){
 446
 447                         if (m->control_pressed) { return 0; }
 448
 449                         phylipFile >> seqName;
 450                         otuIndices[i] = seqMap[seqName];
 451
 452                         for(int j=0;j<i;j++){
 453                                 phylipFile >> distance;
 454
 455                                 if(distance <= cutoff){
 456                                         if(otuIndices[i] == otuIndices[j])      {       truePositives++;        }
 457                                         else                                                            {       falseNegatives++;       }
 458                                 }
 459                                 else{
 460                                         if(otuIndices[i] == otuIndices[j])      {       falsePositives++;       }
 461                                         else                                                            {       trueNegatives++;        }
 462                                 }
 463                         }
 464                 }
 465                 phylipFile.close();
 466
 467                 outputStatistics(label, origCutoff);
 468
 469                 return 0;
 470         }
 471         catch(exception& e) {
 472                 m->errorOut(e, "SensSpecCommand", "process");
 473                 exit(1);
 474         }
 475 }
 476 //***************************************************************************************************************
 477 int SensSpecCommand::process(set<string>& seqPairSet, string label, bool& getCutoff, string& origCutoff, int numSeqs){
 478         try {
 479                 int numDists = (numSeqs * (numSeqs-1) / 2);
 480
 481                 ifstream columnFile;
 482                 m->openInputFile(distFile, columnFile);
 483                 string seqNameA, seqNameB, seqPairString;
 484                 double distance;
 485
 486                 truePositives = 0;
 487                 falsePositives = 0;
 488                 trueNegatives = numDists;
 489                 falseNegatives = 0;
 490
 491                 if(getCutoff == 1){
 492                         if(label != "unique"){
 493                                 origCutoff = label;
 494                                 convert(label, cutoff);
 495                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 496                         }
 497                         else{
 498                                 origCutoff = "unique";
 499                                 cutoff = 0.0000;
 500                         }
 501                 }
 502
 503                 m->mothurOut(label); m->mothurOutEndLine();
 504
 505                 while(columnFile){
 506                         columnFile >> seqNameA >> seqNameB >> distance;
 507                         if(seqNameA < seqNameB) {       seqPairString = seqNameA + '\t' + seqNameB;     }
 508                         else                                    {       seqPairString = seqNameB + '\t' + seqNameA;     }
 509
 510                         set<string>::iterator it = seqPairSet.find(seqPairString);
 511
 512                         if(distance <= cutoff){
 513                                 if(it != seqPairSet.end()){
 514                                         truePositives++;
 515                                         seqPairSet.erase(it);
 516                                 }
 517                                 else{
 518                                         falseNegatives++;
 519                                 }
 520                                 trueNegatives--;
 521                         }
 522                         else if(it != seqPairSet.end()){
 523                                 falsePositives++;
 524                                 trueNegatives--;
 525                                 seqPairSet.erase(it);
 526                         }
 527
 528                         m->gobble(columnFile);
 529                 }
 530                 falsePositives += seqPairSet.size();
 531
 532                 outputStatistics(label, origCutoff);
 533
 534
 535                 return 0;
 536         }
 537         catch(exception& e) {
 538                 m->errorOut(e, "SensSpecCommand", "process");
 539                 exit(1);
 540         }
 541 }
 542 //***************************************************************************************************************
 543
 544 int SensSpecCommand::processColumn(){
 545         try{
 546                 string origCutoff = "";
 547                 bool getCutoff = 0;
 548                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 549                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 550
 551                 set<string> seqPairSet;
 552                 int numSeqs = 0;
 553
 554                 InputData input(listFile, "list");
 555                 ListVector* list = input.getListVector();
 556                 string lastLabel = list->getLabel();
 557
 558                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 559                 set<string> processedLabels;
 560                 set<string> userLabels = labels;
 561
 562
 563                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 564
 565                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
 566
 567                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 568
 569                                 processedLabels.insert(list->getLabel());
 570                                 userLabels.erase(list->getLabel());
 571
 572                                 //process
 573                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 574                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 575                         }
 576
 577                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 578                                 string saveLabel = list->getLabel();
 579
 580                                 delete list;
 581                                 list = input.getListVector(lastLabel);
 582
 583                                 processedLabels.insert(list->getLabel());
 584                                 userLabels.erase(list->getLabel());
 585
 586                                 //process
 587                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 588                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 589
 590                                 //restore real lastlabel to save below
 591                                 list->setLabel(saveLabel);
 592                         }
 593
 594                         lastLabel = list->getLabel();
 595
 596                         delete list;
 597                         list = input.getListVector();
 598                 }
 599
 600
 601                 //output error messages about any remaining user labels
 602                 set<string>::iterator it;
 603                 bool needToRun = false;
 604                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 605                         m->mothurOut("Your file does not include the label " + *it);
 606                         if (processedLabels.count(lastLabel) != 1) {
 607                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 608                                 needToRun = true;
 609                         }else {
 610                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 611                         }
 612                 }
 613
 614                 //run last label if you need to
 615                 if (needToRun == true)  {
 616                         if (list != NULL) {     delete list;    }
 617                         list = input.getListVector(lastLabel);
 618
 619                         //process
 620                         numSeqs = fillSeqPairSet(seqPairSet, list);
 621                         delete list;
 622                         process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 623                 }
 624
 625                 return 0;
 626         }
 627         catch(exception& e) {
 628                 m->errorOut(e, "SensSpecCommand", "processColumn");
 629                 exit(1);
 630         }
 631 }
 632
 633 //***************************************************************************************************************
 634
 635 void SensSpecCommand::setUpOutput(){
 636         try{
 637                 ofstream sensSpecFile;
 638                 m->openOutputFile(sensSpecFileName, sensSpecFile);
 639
 640                 sensSpecFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
 641
 642                 sensSpecFile.close();
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "SensSpecCommand", "setUpOutput");
 646                 exit(1);
 647         }
 648 }
 649
 650 //***************************************************************************************************************
 651
 652 void SensSpecCommand::outputStatistics(string label, string cutoff){
 653         try{
 654                 double tp = (double) truePositives;
 655                 double fp = (double) falsePositives;
 656                 double tn = (double) trueNegatives;
 657                 double fn = (double) falseNegatives;
 658
 659                 double p = tp + fn;
 660                 double n = fp + tn;
 661                 double pPrime = tp + fp;
 662                 double nPrime = tn + fn;
 663
 664                 double sensitivity = tp / p;
 665                 double specificity = tn / n;
 666                 double positivePredictiveValue = tp / pPrime;
 667                 double negativePredictiveValue = tn / nPrime;
 668                 double falseDiscoveryRate = fp / pPrime;
 669
 670                 double accuracy = (tp + tn) / (p + n);
 671                 double matthewsCorrCoef = (tp * tn - fp * fn) / sqrt(p * n * pPrime * nPrime);  if(p == 0 || n == 0){   matthewsCorrCoef = 0;   }
 672                 double f1Score = 2.0 * tp / (p + pPrime);
 673
 674
 675                 if(p == 0)                      {       sensitivity = 0;        matthewsCorrCoef = 0;   }
 676                 if(n == 0)                      {       specificity = 0;        matthewsCorrCoef = 0;   }
 677                 if(p + n == 0)          {       accuracy = 0;                                                           }
 678                 if(p + pPrime == 0)     {       f1Score = 0;                                                            }
 679                 if(pPrime == 0)         {       positivePredictiveValue = 0;    falseDiscoveryRate = 0; matthewsCorrCoef = 0;   }
 680                 if(nPrime == 0)         {       negativePredictiveValue = 0;    matthewsCorrCoef = 0;                                                   }
 681
 682                 ofstream sensSpecFile;
 683                 m->openOutputFileAppend(sensSpecFileName, sensSpecFile);
 684
 685                 sensSpecFile << label << '\t' << cutoff << '\t';
 686                 sensSpecFile << truePositives << '\t' << trueNegatives << '\t' << falsePositives << '\t' << falseNegatives << '\t';
 687                 sensSpecFile << setprecision(4);
 688                 sensSpecFile << sensitivity << '\t' << specificity << '\t' << positivePredictiveValue << '\t' << negativePredictiveValue << '\t';
 689                 sensSpecFile << falseDiscoveryRate << '\t' << accuracy << '\t' << matthewsCorrCoef << '\t' << f1Score << endl;
 690
 691                 sensSpecFile.close();
 692         }
 693         catch(exception& e) {
 694                 m->errorOut(e, "SensSpecCommand", "outputStatistics");
 695                 exit(1);
 696         }
 697 }
 698 //***************************************************************************************************************
 699
 700 string SensSpecCommand::preProcessList(){
 701     try {
 702         set<string> uniqueNames;
 703         //get unique names from distance file
 704         if (format == "phylip") {
 705
 706             ifstream phylipFile;
 707             m->openInputFile(distFile, phylipFile);
 708             string numTest;
 709             int pNumSeqs;
 710                         phylipFile >> numTest;
 711
 712                         if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
 713             else {
 714                 m->mothurConvert(numTest, pNumSeqs);
 715             }
 716             phylipFile >> pNumSeqs; m->gobble(phylipFile);
 717
 718             string seqName;
 719             double distance;
 720
 721             for(int i=0;i<pNumSeqs;i++){
 722
 723                 if (m->control_pressed) { return ""; }
 724
 725                 phylipFile >> seqName;
 726                 uniqueNames.insert(seqName);
 727
 728                 for(int j=0;j<i;j++){
 729                     phylipFile >> distance;
 730                 }
 731                 m->gobble(phylipFile);
 732             }
 733             phylipFile.close();
 734         }else {
 735             ifstream columnFile;
 736             m->openInputFile(distFile, columnFile);
 737             string seqNameA, seqNameB;
 738             double distance;
 739
 740             while(columnFile){
 741                 if (m->control_pressed) { return ""; }
 742                 columnFile >> seqNameA >> seqNameB >> distance;
 743                 uniqueNames.insert(seqNameA); uniqueNames.insert(seqNameB);
 744                 m->gobble(columnFile);
 745             }
 746             columnFile.close();
 747         }
 748
 749         //read list file, if numSeqs > unique names then remove redundant names
 750         string newListFile = listFile + ".temp";
 751         ofstream out;
 752         m->openOutputFile(newListFile, out);
 753         ifstream in;
 754                 m->openInputFile(listFile, in);
 755
 756                 bool wroteSomething = false;
 757
 758                 while(!in.eof()){
 759
 760                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(newListFile);  return ""; }
 761
 762                         //read in list vector
 763                         ListVector list(in);
 764
 765             //listfile is already unique
 766             if (list.getNumSeqs() == uniqueNames.size()) { in.close(); out.close(); m->mothurRemove(newListFile);  return ""; }
 767
 768                         //make a new list vector
 769                         ListVector newList;
 770                         newList.setLabel(list.getLabel());
 771
 772                         //for each bin
 773                         for (int i = 0; i < list.getNumBins(); i++) {
 774
 775                                 //parse out names that are in accnos file
 776                                 string binnames = list.get(i);
 777                 vector<string> bnames;
 778                 m->splitAtComma(binnames, bnames);
 779
 780                                 string newNames = "";
 781                 for (int i = 0; i < bnames.size(); i++) {
 782                                         string name = bnames[i];
 783                                         //if that name is in the .accnos file, add it
 784                                         if (uniqueNames.count(name) != 0) {  newNames += name + ",";  }
 785                                 }
 786
 787                                 //if there are names in this bin add to new list
 788                                 if (newNames != "") {
 789                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 790                                         newList.push_back(newNames);
 791                                 }
 792                         }
 793
 794                         //print new listvector
 795                         if (newList.getNumBins() != 0) {
 796                                 wroteSomething = true;
 797                                 newList.print(out);
 798                         }
 799
 800                         m->gobble(in);
 801                 }
 802                 in.close();
 803                 out.close();
 804
 805         if (wroteSomething) { return newListFile; }
 806         return "";
 807     }
 808     catch(exception& e) {
 809         m->errorOut(e, "SensSpecCommand", "preProcessList");
 810         exit(1);
 811     }
 812 }
 813
 814
 815 //***************************************************************************************************************
 816
 817
 818