seqerrorcommand.cpp

   1 /*
   2  *  seqerrorcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 7/15/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqerrorcommand.h"
  11 #include "reportfile.h"
  12 #include "qualityscores.h"
  13 #include "refchimeratest.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> SeqErrorCommand::setParameters(){
  17         try {
  18                 CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery);
  19                 CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference);
  20                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile);
  21                 CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport);
  22                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  23                 CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
  24                 CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
  25                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "SeqErrorCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string SeqErrorCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
  43                 helpString += "Example seq.error(...).\n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  45                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
  46                 return helpString;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "SeqErrorCommand", "getHelpString");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 SeqErrorCommand::SeqErrorCommand(){
  55         try {
  56                 abort = true; calledHelp = true;
  57                 vector<string> tempOutNames;
  58                 outputTypes["error.summary"] = tempOutNames;
  59                 outputTypes["error.seq"] = tempOutNames;
  60                 outputTypes["error.quality"] = tempOutNames;
  61                 outputTypes["error.qual.forward"] = tempOutNames;
  62                 outputTypes["error.qual.reverse"] = tempOutNames;
  63                 outputTypes["error.forward"] = tempOutNames;
  64                 outputTypes["error.reverse"] = tempOutNames;
  65                 outputTypes["error.count"] = tempOutNames;
  66                 outputTypes["error.matrix"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
  70                 exit(1);
  71         }
  72 }
  73 //***************************************************************************************************************
  74
  75 SeqErrorCommand::SeqErrorCommand(string option)  {
  76         try {
  77
  78                 abort = false; calledHelp = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; calledHelp = true; }
  82                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  83
  84                 else {
  85                         string temp;
  86                         vector<string> myArray = setParameters();
  87
  88                         OptionParser parser(option);
  89                         map<string,string> parameters = parser.getParameters();
  90
  91                         ValidParameters validParameter;
  92                         map<string,string>::iterator it;
  93
  94                         //check to make sure all parameters are valid for command
  95                         for (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["error.summary"] = tempOutNames;
 102                         outputTypes["error.seq"] = tempOutNames;
 103                         outputTypes["error.quality"] = tempOutNames;
 104                         outputTypes["error.qual.forward"] = tempOutNames;
 105                         outputTypes["error.qual.reverse"] = tempOutNames;
 106                         outputTypes["error.forward"] = tempOutNames;
 107                         outputTypes["error.reverse"] = tempOutNames;
 108                         outputTypes["error.count"] = tempOutNames;
 109                         outputTypes["error.matrix"] = tempOutNames;
 110
 111
 112                         //if the user changes the input directory command factory will send this info to us in the output parameter
 113                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 114                         if (inputDir == "not found"){   inputDir = "";          }
 115                         else {
 116                                 string path;
 117                                 it = parameters.find("fasta");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 123                                 }
 124
 125                                 it = parameters.find("reference");
 126                                 //user has given a template file
 127                                 if(it != parameters.end()){
 128                                         path = m->hasPath(it->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 131                                 }
 132
 133                                 it = parameters.find("name");
 134                                 //user has given a names file
 135                                 if(it != parameters.end()){
 136                                         path = m->hasPath(it->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 139                                 }
 140
 141                                 it = parameters.find("qfile");
 142                                 //user has given a quality score file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 147                                 }
 148
 149                                 it = parameters.find("report");
 150                                 //user has given a alignment report file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["report"] = inputDir + it->second;           }
 155                                 }
 156
 157                         }
 158                         //check for required parameters
 159                         queryFileName = validParameter.validFile(parameters, "fasta", true);
 160                         if (queryFileName == "not found") {
 161                                 queryFileName = m->getFastaFile();
 162                                 if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 163                                 else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 164                         }
 165                         else if (queryFileName == "not open") { abort = true; }
 166
 167                         referenceFileName = validParameter.validFile(parameters, "reference", true);
 168                         if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
 169                         else if (referenceFileName == "not open") { abort = true; }
 170
 171
 172                         //check for optional parameters
 173                         namesFileName = validParameter.validFile(parameters, "name", true);
 174                         if(namesFileName == "not found"){       namesFileName = "";     }
 175                         else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
 176
 177                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 178                         if(qualFileName == "not found"){        qualFileName = "";      }
 179                         else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
 180
 181                         reportFileName = validParameter.validFile(parameters, "report", true);
 182                         if(reportFileName == "not found"){      reportFileName = "";    }
 183                         else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
 184
 185                         if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
 186                                 m->mothurOut("if you use either a qual file or a report file, you have to have both.");
 187                                 m->mothurOutEndLine();
 188                                 abort = true;
 189                         }
 190
 191                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 192                         if (outputDir == "not found"){
 193                                 outputDir = "";
 194                                 outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it
 195                         }
 196
 197                         //check for optional parameter and set defaults
 198                         // ...at some point should added some additional type checking...
 199                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
 200                         convert(temp, threshold);
 201
 202                         temp = validParameter.validFile(parameters, "ignorechimeras", false);   if (temp == "not found") { temp = "1"; }
 203                         convert(temp, ignoreChimeras);
 204
 205                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 206                         m->setProcessors(temp);
 207                         convert(temp, processors);
 208
 209                         substitutionMatrix.resize(6);
 210                         for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
 211                 }
 212         }
 213         catch(exception& e) {
 214                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
 215                 exit(1);
 216         }
 217 }
 218 //***************************************************************************************************************
 219
 220 int SeqErrorCommand::execute(){
 221         try{
 222                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 223
 224                 maxLength = 2000;
 225
 226                 string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
 227                 m->openOutputFile(errorSummaryFileName, errorSummaryFile);
 228                 outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
 229                 printErrorHeader();
 230
 231                 string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
 232                 m->openOutputFile(errorSeqFileName, errorSeqFile);
 233                 outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
 234
 235                 getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 236
 237                 map<string, int> weights;
 238                 if(namesFileName != ""){        weights = getWeights(); }
 239
 240                 ifstream queryFile;
 241                 m->openInputFile(queryFileName, queryFile);
 242
 243                 ifstream reportFile;
 244                 ifstream qualFile;
 245
 246                 ReportFile report;
 247                 QualityScores quality;
 248                 vector<vector<int> > qualForwardMap;
 249                 vector<vector<int> > qualReverseMap;
 250
 251                 if(qualFileName != "" && reportFileName != ""){
 252                         m->openInputFile(qualFileName, qualFile);
 253                         report = ReportFile(reportFile, reportFileName);
 254
 255                         qualForwardMap.resize(maxLength);
 256                         qualReverseMap.resize(maxLength);
 257                         for(int i=0;i<maxLength;i++){
 258                                 qualForwardMap[i].assign(41,0);
 259                                 qualReverseMap[i].assign(41,0);
 260                         }
 261                 }
 262
 263                 int totalBases = 0;
 264                 int totalMatches = 0;
 265
 266                 vector<int> misMatchCounts(11, 0);
 267                 int maxMismatch = 0;
 268                 int numSeqs = 0;
 269
 270                 map<string, int>::iterator it;
 271                 map<char, vector<int> > qScoreErrorMap;
 272                 qScoreErrorMap['m'].assign(41, 0);
 273                 qScoreErrorMap['s'].assign(41, 0);
 274                 qScoreErrorMap['i'].assign(41, 0);
 275                 qScoreErrorMap['a'].assign(41, 0);
 276
 277                 map<char, vector<int> > errorForward;
 278                 errorForward['m'].assign(maxLength,0);
 279                 errorForward['s'].assign(maxLength,0);
 280                 errorForward['i'].assign(maxLength,0);
 281                 errorForward['d'].assign(maxLength,0);
 282                 errorForward['a'].assign(maxLength,0);
 283
 284                 map<char, vector<int> > errorReverse;
 285                 errorReverse['m'].assign(maxLength,0);
 286                 errorReverse['s'].assign(maxLength,0);
 287                 errorReverse['i'].assign(maxLength,0);
 288                 errorReverse['d'].assign(maxLength,0);
 289                 errorReverse['a'].assign(maxLength,0);
 290
 291
 292                 string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
 293                 RefChimeraTest chimeraTest(referenceSeqs, errorChimeraFileName);
 294                 outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
 295
 296                 vector<string> megaAlignVector(numRefs, "");
 297
 298                 int index = 0;
 299                 bool ignoreSeq = 0;
 300
 301                 while(queryFile){
 302
 303                         if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 304
 305                         Sequence query(queryFile);
 306
 307                         int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
 308                         int closestRefIndex = chimeraTest.getClosestRefIndex();
 309
 310                         if(numParentSeqs > 1 && ignoreChimeras == 1)    {       ignoreSeq = 1;  }
 311                         else                                                                                    {       ignoreSeq = 0;  }
 312
 313                         Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
 314
 315                         if(namesFileName != ""){
 316                                 it = weights.find(query.getName());
 317                                 minCompare.weight = it->second;
 318                         }
 319                         else{   minCompare.weight = 1;  }
 320
 321                         printErrorData(minCompare, numParentSeqs);
 322
 323                         if(!ignoreSeq){
 324
 325                                 for(int i=0;i<minCompare.sequence.length();i++){
 326                                         char letter = minCompare.sequence[i];
 327
 328                                         errorForward[letter][i] += minCompare.weight;
 329                                         errorReverse[letter][minCompare.total-i-1] += minCompare.weight;
 330                                 }
 331                         }
 332
 333                         if(qualFileName != "" && reportFileName != ""){
 334                                 report = ReportFile(reportFile);
 335
 336 //                              int origLength = report.getQueryLength();
 337                                 int startBase = report.getQueryStart();
 338                                 int endBase = report.getQueryEnd();
 339
 340                                 quality = QualityScores(qualFile);
 341
 342                                 if(!ignoreSeq){
 343                                         quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
 344                                         quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
 345                                         quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
 346                                 }
 347                         }
 348
 349                         if(minCompare.errorRate < threshold && !ignoreSeq){
 350                                 totalBases += (minCompare.total * minCompare.weight);
 351                                 totalMatches += minCompare.matches * minCompare.weight;
 352                                 if(minCompare.mismatches > maxMismatch){
 353                                         maxMismatch = minCompare.mismatches;
 354                                         misMatchCounts.resize(maxMismatch + 1, 0);
 355                                 }
 356                                 misMatchCounts[minCompare.mismatches] += minCompare.weight;
 357                                 numSeqs++;
 358
 359                                 megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
 360                         }
 361
 362                         index++;
 363
 364                         if(index % 1000 == 0){  m->mothurOut(toString(index) + '\n');   }
 365                 }
 366                 queryFile.close();
 367                 errorSummaryFile.close();
 368                 errorSeqFile.close();
 369
 370                 if(qualFileName != "" && reportFileName != ""){
 371                         printErrorQuality(qScoreErrorMap);
 372                         printQualityFR(qualForwardMap, qualReverseMap);
 373                 }
 374
 375                 printErrorFRFile(errorForward, errorReverse);
 376
 377                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 378
 379                 string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
 380                 ofstream errorCountFile;
 381                 m->openOutputFile(errorCountFileName, errorCountFile);
 382                 outputNames.push_back(errorCountFileName);  outputTypes["error.count"].push_back(errorCountFileName);
 383                 m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
 384                 m->mothurOut("Errors\tSequences\n");
 385                 errorCountFile << "Errors\tSequences\n";
 386                 for(int i=0;i<misMatchCounts.size();i++){
 387                         m->mothurOut(toString(i) + '\t' + toString(misMatchCounts[i]) + '\n');
 388                         errorCountFile << i << '\t' << misMatchCounts[i] << endl;
 389                 }
 390                 errorCountFile.close();
 391
 392                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 393
 394                 printSubMatrix();
 395
 396                 string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
 397                 ofstream megAlignmentFile;
 398                 m->openOutputFile(megAlignmentFileName, megAlignmentFile);
 399                 outputNames.push_back(megAlignmentFileName);  outputTypes["error.ref-query"].push_back(megAlignmentFileName);
 400
 401                 for(int i=0;i<numRefs;i++){
 402                         megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
 403                         megAlignmentFile << megaAlignVector[i] << endl;
 404                 }
 405
 406
 407                 m->mothurOutEndLine();
 408                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 409                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 410                 m->mothurOutEndLine();
 411
 412                 return 0;
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "SeqErrorCommand", "execute");
 416                 exit(1);
 417         }
 418 }
 419
 420 //***************************************************************************************************************
 421
 422 void SeqErrorCommand::getReferences(){
 423         try {
 424
 425                 ifstream referenceFile;
 426                 m->openInputFile(referenceFileName, referenceFile);
 427
 428                 int numAmbigSeqs = 0;
 429
 430                 int maxStartPos = 0;
 431                 int minEndPos = 100000;
 432
 433                 while(referenceFile){
 434                         Sequence currentSeq(referenceFile);
 435                         int numAmbigs = currentSeq.getAmbigBases();
 436                         if(numAmbigs > 0){      numAmbigSeqs++; }
 437
 438 //                      int startPos = currentSeq.getStartPos();
 439 //                      if(startPos > maxStartPos)      {       maxStartPos = startPos; }
 440 //
 441 //                      int endPos = currentSeq.getEndPos();
 442 //                      if(endPos < minEndPos)          {       minEndPos = endPos;             }
 443                         referenceSeqs.push_back(currentSeq);
 444
 445                         m->gobble(referenceFile);
 446                 }
 447                 referenceFile.close();
 448                 numRefs = referenceSeqs.size();
 449
 450
 451                 for(int i=0;i<numRefs;i++){
 452                         referenceSeqs[i].padToPos(maxStartPos);
 453                         referenceSeqs[i].padFromPos(minEndPos);
 454                 }
 455
 456                 if(numAmbigSeqs != 0){
 457                         m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
 458                 }
 459
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "SeqErrorCommand", "getReferences");
 463                 exit(1);
 464         }
 465 }
 466
 467 //***************************************************************************************************************
 468
 469 Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 470         try {
 471                 if(query.getAlignLength() != reference.getAlignLength()){
 472                         m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
 473                 }
 474                 int alignLength = query.getAlignLength();
 475
 476                 string q = query.getAligned();
 477                 string r = reference.getAligned();
 478
 479                 int started = 0;
 480                 Compare errors;
 481
 482                 for(int i=0;i<alignLength;i++){
 483                         if(r[i] != 'N' && q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){                  //      no missing data and no double gaps
 484                                 started = 1;
 485
 486                                 if(q[i] == 'A'){
 487                                         if(r[i] == 'A'){        errors.AA++;    errors.matches++;       errors.sequence += 'm'; }
 488                                         if(r[i] == 'T'){        errors.AT++;    errors.sequence += 's'; }
 489                                         if(r[i] == 'G'){        errors.AG++;    errors.sequence += 's'; }
 490                                         if(r[i] == 'C'){        errors.AC++;    errors.sequence += 's'; }
 491                                         if(r[i] == '-'){        errors.Ai++;    errors.sequence += 'i'; }
 492                                 }
 493                                 else if(q[i] == 'T'){
 494                                         if(r[i] == 'A'){        errors.TA++;    errors.sequence += 's'; }
 495                                         if(r[i] == 'T'){        errors.TT++;    errors.matches++;       errors.sequence += 'm'; }
 496                                         if(r[i] == 'G'){        errors.TG++;    errors.sequence += 's'; }
 497                                         if(r[i] == 'C'){        errors.TC++;    errors.sequence += 's'; }
 498                                         if(r[i] == '-'){        errors.Ti++;    errors.sequence += 'i'; }
 499                                 }
 500                                 else if(q[i] == 'G'){
 501                                         if(r[i] == 'A'){        errors.GA++;    errors.sequence += 's'; }
 502                                         if(r[i] == 'T'){        errors.GT++;    errors.sequence += 's'; }
 503                                         if(r[i] == 'G'){        errors.GG++;    errors.matches++;       errors.sequence += 'm'; }
 504                                         if(r[i] == 'C'){        errors.GC++;    errors.sequence += 's'; }
 505                                         if(r[i] == '-'){        errors.Gi++;    errors.sequence += 'i'; }
 506                                 }
 507                                 else if(q[i] == 'C'){
 508                                         if(r[i] == 'A'){        errors.CA++;    errors.sequence += 's'; }
 509                                         if(r[i] == 'T'){        errors.CT++;    errors.sequence += 's'; }
 510                                         if(r[i] == 'G'){        errors.CG++;    errors.sequence += 's'; }
 511                                         if(r[i] == 'C'){        errors.CC++;    errors.matches++;       errors.sequence += 'm'; }
 512                                         if(r[i] == '-'){        errors.Ci++;    errors.sequence += 'i'; }
 513                                 }
 514                                 else if(q[i] == 'N'){
 515                                         if(r[i] == 'A'){        errors.NA++;    errors.sequence += 'a'; }
 516                                         if(r[i] == 'T'){        errors.NT++;    errors.sequence += 'a'; }
 517                                         if(r[i] == 'G'){        errors.NG++;    errors.sequence += 'a'; }
 518                                         if(r[i] == 'C'){        errors.NC++;    errors.sequence += 'a'; }
 519                                         if(r[i] == '-'){        errors.Ni++;    errors.sequence += 'a'; }
 520                                 }
 521                                 else if(q[i] == '-' && r[i] != '-'){
 522                                         if(r[i] == 'A'){        errors.dA++;    errors.sequence += 'd'; }
 523                                         if(r[i] == 'T'){        errors.dT++;    errors.sequence += 'd'; }
 524                                         if(r[i] == 'G'){        errors.dG++;    errors.sequence += 'd'; }
 525                                         if(r[i] == 'C'){        errors.dC++;    errors.sequence += 'd'; }
 526                                 }
 527                                 errors.total++;
 528
 529                         }
 530                         else if(q[i] == '.' && r[i] != '.'){            //      reference extends beyond query
 531                                 if(started == 1){       break;  }
 532                         }
 533                         else if(q[i] != '.' && r[i] == '.'){            //      query extends beyond reference
 534                                 if(started == 1){       break;  }
 535                         }
 536                         else if(q[i] == '.' && r[i] == '.'){            //      both are missing data
 537                                 if(started == 1){       break;  }
 538                         }
 539
 540                 }
 541                 errors.mismatches = errors.total-errors.matches;
 542                 errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total;
 543                 errors.queryName = query.getName();
 544                 errors.refName = reference.getName();
 545
 546                 return errors;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "SeqErrorCommand", "getErrors");
 550                 exit(1);
 551         }
 552 }
 553
 554 //***************************************************************************************************************
 555
 556 map<string, int> SeqErrorCommand::getWeights(){
 557         ifstream nameFile;
 558         m->openInputFile(namesFileName, nameFile);
 559
 560         string seqName;
 561         string redundantSeqs;
 562         map<string, int> nameCountMap;
 563
 564         while(nameFile){
 565                 nameFile >> seqName >> redundantSeqs;
 566                 nameCountMap[seqName] = m->getNumNames(redundantSeqs);
 567                 m->gobble(nameFile);
 568         }
 569         return nameCountMap;
 570 }
 571
 572
 573 //***************************************************************************************************************
 574
 575 void SeqErrorCommand::printErrorHeader(){
 576         try {
 577                 errorSummaryFile << "query\treference\tweight\t";
 578                 errorSummaryFile << "AA\tAT\tAG\tAC\tTA\tTT\tTG\tTC\tGA\tGT\tGG\tGC\tCA\tCT\tCG\tCC\tNA\tNT\tNG\tNC\tAi\tTi\tGi\tCi\tNi\tdA\tdT\tdG\tdC\t";
 579                 errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\tnumparents\n";
 580
 581                 errorSummaryFile << setprecision(6);
 582                 errorSummaryFile.setf(ios::fixed);
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "SeqErrorCommand", "printErrorHeader");
 586                 exit(1);
 587         }
 588 }
 589
 590 //***************************************************************************************************************
 591
 592 void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs){
 593         try {
 594
 595                 errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
 596                 errorSummaryFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
 597                 errorSummaryFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
 598                 errorSummaryFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
 599                 errorSummaryFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
 600                 errorSummaryFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
 601                 errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t';
 602                 errorSummaryFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
 603
 604                 errorSummaryFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t';                  //insertions
 605                 errorSummaryFile << error.dA + error.dT + error.dG + error.dC << '\t';                  //deletions
 606                 errorSummaryFile << error.mismatches - (error.Ai + error.Ti + error.Gi + error.Ci) - (error.dA + error.dT + error.dG + error.dC) - (error.NA + error.NT + error.NG + error.NC + error.Ni) << '\t';      //substitutions
 607                 errorSummaryFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t';       //ambiguities
 608                 errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << '\t' << numParentSeqs << endl;
 609
 610                 errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
 611
 612                 int a=0;                int t=1;                int g=2;                int c=3;
 613                 int gap=4;              int n=5;
 614
 615                 if(numParentSeqs == 1 || ignoreChimeras == 0){
 616                         substitutionMatrix[a][a] += error.weight * error.AA;
 617                         substitutionMatrix[a][t] += error.weight * error.TA;
 618                         substitutionMatrix[a][g] += error.weight * error.GA;
 619                         substitutionMatrix[a][c] += error.weight * error.CA;
 620                         substitutionMatrix[a][gap] += error.weight * error.dA;
 621                         substitutionMatrix[a][n] += error.weight * error.NA;
 622
 623                         substitutionMatrix[t][a] += error.weight * error.AT;
 624                         substitutionMatrix[t][t] += error.weight * error.TT;
 625                         substitutionMatrix[t][g] += error.weight * error.GT;
 626                         substitutionMatrix[t][c] += error.weight * error.CT;
 627                         substitutionMatrix[t][gap] += error.weight * error.dT;
 628                         substitutionMatrix[t][n] += error.weight * error.NT;
 629
 630                         substitutionMatrix[g][a] += error.weight * error.AG;
 631                         substitutionMatrix[g][t] += error.weight * error.TG;
 632                         substitutionMatrix[g][g] += error.weight * error.GG;
 633                         substitutionMatrix[g][c] += error.weight * error.CG;
 634                         substitutionMatrix[g][gap] += error.weight * error.dG;
 635                         substitutionMatrix[g][n] += error.weight * error.NG;
 636
 637                         substitutionMatrix[c][a] += error.weight * error.AC;
 638                         substitutionMatrix[c][t] += error.weight * error.TC;
 639                         substitutionMatrix[c][g] += error.weight * error.GC;
 640                         substitutionMatrix[c][c] += error.weight * error.CC;
 641                         substitutionMatrix[c][gap] += error.weight * error.dC;
 642                         substitutionMatrix[c][n] += error.weight * error.NC;
 643
 644                         substitutionMatrix[gap][a] += error.weight * error.Ai;
 645                         substitutionMatrix[gap][t] += error.weight * error.Ti;
 646                         substitutionMatrix[gap][g] += error.weight * error.Gi;
 647                         substitutionMatrix[gap][c] += error.weight * error.Ci;
 648                         substitutionMatrix[gap][n] += error.weight * error.Ni;
 649                 }
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "SeqErrorCommand", "printErrorData");
 653                 exit(1);
 654         }
 655 }
 656
 657 //***************************************************************************************************************
 658
 659 void SeqErrorCommand::printSubMatrix(){
 660         try {
 661                 string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
 662                 ofstream subMatrixFile;
 663                 m->openOutputFile(subMatrixFileName, subMatrixFile);
 664                 outputNames.push_back(subMatrixFileName);  outputTypes["error.matrix"].push_back(subMatrixFileName);
 665                 vector<string> bases(6);
 666                 bases[0] = "A";
 667                 bases[1] = "T";
 668                 bases[2] = "G";
 669                 bases[3] = "C";
 670                 bases[4] = "Gap";
 671                 bases[5] = "N";
 672                 vector<int> refSums(5,1);
 673
 674                 for(int i=0;i<5;i++){
 675                         subMatrixFile << "\tr" << bases[i];
 676
 677                         for(int j=0;j<6;j++){
 678                                 refSums[i] += substitutionMatrix[i][j];
 679                         }
 680                 }
 681                 subMatrixFile << endl;
 682
 683                 for(int i=0;i<6;i++){
 684                         subMatrixFile << 'q' << bases[i];
 685                         for(int j=0;j<5;j++){
 686                                 subMatrixFile << '\t' << substitutionMatrix[j][i];
 687                         }
 688                         subMatrixFile << endl;
 689                 }
 690
 691                 subMatrixFile << "total";
 692                 for(int i=0;i<5;i++){
 693                         subMatrixFile << '\t' << refSums[i];
 694                 }
 695                 subMatrixFile << endl;
 696                 subMatrixFile.close();
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "SeqErrorCommand", "printSubMatrix");
 700                 exit(1);
 701         }
 702 }
 703 //***************************************************************************************************************
 704
 705 void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
 706         try{
 707                 string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward";
 708                 ofstream errorForwardFile;
 709                 m->openOutputFile(errorForwardFileName, errorForwardFile);
 710                 outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
 711
 712                 errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
 713                 for(int i=0;i<maxLength;i++){
 714                         float match = (float)errorForward['m'][i];
 715                         float subst = (float)errorForward['s'][i];
 716                         float insert = (float)errorForward['i'][i];
 717                         float del = (float)errorForward['d'][i];
 718                         float amb = (float)errorForward['a'][i];
 719                         float total = match + subst + insert + del + amb;
 720                         if(total == 0){ break;  }
 721                         errorForwardFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
 722                 }
 723                 errorForwardFile.close();
 724
 725                 string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
 726                 ofstream errorReverseFile;
 727                 m->openOutputFile(errorReverseFileName, errorReverseFile);
 728                 outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
 729
 730                 errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
 731                 for(int i=0;i<maxLength;i++){
 732                         float match = (float)errorReverse['m'][i];
 733                         float subst = (float)errorReverse['s'][i];
 734                         float insert = (float)errorReverse['i'][i];
 735                         float del = (float)errorReverse['d'][i];
 736                         float amb = (float)errorReverse['a'][i];
 737                         float total = match + subst + insert + del + amb;
 738                         if(total == 0){ break;  }
 739                         errorReverseFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
 740                 }
 741                 errorReverseFile.close();
 742         }
 743         catch(exception& e) {
 744                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 745                 exit(1);
 746         }
 747 }
 748
 749 //***************************************************************************************************************
 750
 751 void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
 752         try{
 753
 754                 string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
 755                 ofstream errorQualityFile;
 756                 m->openOutputFile(errorQualityFileName, errorQualityFile);
 757                 outputNames.push_back(errorQualityFileName);  outputTypes["error.quality"].push_back(errorQualityFileName);
 758
 759                 errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
 760                 for(int i=0;i<41;i++){
 761                         errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
 762                 }
 763                 errorQualityFile.close();
 764         }
 765         catch(exception& e) {
 766                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 767                 exit(1);
 768         }
 769 }
 770
 771
 772 //***************************************************************************************************************
 773
 774 void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
 775
 776         try{
 777                 int numRows = 0;
 778                 int numColumns = qualForwardMap[0].size();
 779
 780                 for(int i=0;i<qualForwardMap.size();i++){
 781                         for(int j=0;j<numColumns;j++){
 782                                 if(qualForwardMap[i][j] != 0){
 783                                         if(numRows < i)         {       numRows = i+20;         }
 784                                 }
 785                         }
 786                 }
 787
 788                 string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward";
 789                 ofstream qualityForwardFile;
 790                 m->openOutputFile(qualityForwardFileName, qualityForwardFile);
 791                 outputNames.push_back(qualityForwardFileName);  outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
 792
 793                 for(int i=0;i<numColumns;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
 794
 795                 for(int i=0;i<numRows;i++){
 796                         qualityForwardFile << i+1;
 797                         for(int j=0;j<numColumns;j++){
 798                                 qualityForwardFile << '\t' << qualForwardMap[i][j];
 799                         }
 800
 801                         qualityForwardFile << endl;
 802                 }
 803                 qualityForwardFile.close();
 804
 805
 806                 string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse";
 807                 ofstream qualityReverseFile;
 808                 m->openOutputFile(qualityReverseFileName, qualityReverseFile);
 809                 outputNames.push_back(qualityReverseFileName);  outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
 810
 811                 for(int i=0;i<numColumns;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
 812                 for(int i=0;i<numRows;i++){
 813
 814                         qualityReverseFile << i+1;
 815                         for(int j=0;j<numColumns;j++){
 816                                 qualityReverseFile << '\t' << qualReverseMap[i][j];
 817                         }
 818                         qualityReverseFile << endl;
 819                 }
 820                 qualityReverseFile.close();
 821         }
 822         catch(exception& e) {
 823                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 824                 exit(1);
 825         }
 826
 827 }
 828
 829 //***************************************************************************************************************