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 pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  26                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  27
  28                 vector<string> myArray;
  29                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  30                 return myArray;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "SeqErrorCommand", "setParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 string SeqErrorCommand::getHelpString(){
  39         try {
  40                 string helpString = "";
  41                 helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
  42                 helpString += "Example seq.error(...).\n";
  43                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  44                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SeqErrorCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 SeqErrorCommand::SeqErrorCommand(){
  54         try {
  55                 abort = true; calledHelp = true;
  56                 vector<string> tempOutNames;
  57                 outputTypes["error.summary"] = tempOutNames;
  58                 outputTypes["error.seq"] = tempOutNames;
  59                 outputTypes["error.quality"] = tempOutNames;
  60                 outputTypes["error.qual.forward"] = tempOutNames;
  61                 outputTypes["error.qual.reverse"] = tempOutNames;
  62                 outputTypes["error.forward"] = tempOutNames;
  63                 outputTypes["error.reverse"] = tempOutNames;
  64                 outputTypes["error.count"] = tempOutNames;
  65                 outputTypes["error.matrix"] = tempOutNames;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
  69                 exit(1);
  70         }
  71 }
  72 //***************************************************************************************************************
  73
  74 SeqErrorCommand::SeqErrorCommand(string option)  {
  75         try {
  76
  77                 abort = false; calledHelp = false;
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81
  82                 else {
  83                         string temp;
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter;
  90                         map<string,string>::iterator it;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["error.summary"] = tempOutNames;
 100                         outputTypes["error.seq"] = tempOutNames;
 101                         outputTypes["error.quality"] = tempOutNames;
 102                         outputTypes["error.qual.forward"] = tempOutNames;
 103                         outputTypes["error.qual.reverse"] = tempOutNames;
 104                         outputTypes["error.forward"] = tempOutNames;
 105                         outputTypes["error.reverse"] = tempOutNames;
 106                         outputTypes["error.count"] = tempOutNames;
 107                         outputTypes["error.matrix"] = tempOutNames;
 108
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 112                         if (inputDir == "not found"){   inputDir = "";          }
 113                         else {
 114                                 string path;
 115                                 it = parameters.find("fasta");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 121                                 }
 122
 123                                 it = parameters.find("reference");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 129                                 }
 130
 131                                 it = parameters.find("name");
 132                                 //user has given a names file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 137                                 }
 138
 139                                 it = parameters.find("qfile");
 140                                 //user has given a quality score file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 145                                 }
 146
 147                                 it = parameters.find("report");
 148                                 //user has given a alignment report file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["report"] = inputDir + it->second;           }
 153                                 }
 154
 155                         }
 156                         //check for required parameters
 157                         queryFileName = validParameter.validFile(parameters, "fasta", true);
 158                         if (queryFileName == "not found") {
 159                                 queryFileName = m->getFastaFile();
 160                                 if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 161                                 else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 162                         }
 163                         else if (queryFileName == "not open") { abort = true; }
 164
 165                         referenceFileName = validParameter.validFile(parameters, "reference", true);
 166                         if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
 167                         else if (referenceFileName == "not open") { abort = true; }
 168
 169
 170                         //check for optional parameters
 171                         namesFileName = validParameter.validFile(parameters, "name", true);
 172                         if(namesFileName == "not found"){       namesFileName = "";     }
 173                         else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
 174
 175                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 176                         if(qualFileName == "not found"){        qualFileName = "";      }
 177                         else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
 178
 179                         reportFileName = validParameter.validFile(parameters, "report", true);
 180                         if(reportFileName == "not found"){      reportFileName = "";    }
 181                         else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
 182
 183                         if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
 184                                 m->mothurOut("if you use either a qual file or a report file, you have to have both.");
 185                                 m->mothurOutEndLine();
 186                                 abort = true;
 187                         }
 188
 189                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 190                         if (outputDir == "not found"){
 191                                 outputDir = "";
 192                                 outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it
 193                         }
 194
 195                         //check for optional parameter and set defaults
 196                         // ...at some point should added some additional type checking...
 197                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
 198                         convert(temp, threshold);
 199
 200                         temp = validParameter.validFile(parameters, "ignorechimeras", false);   if (temp == "not found") { temp = "1"; }
 201                         convert(temp, ignoreChimeras);
 202
 203                         substitutionMatrix.resize(6);
 204                         for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
 205                 }
 206         }
 207         catch(exception& e) {
 208                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
 209                 exit(1);
 210         }
 211 }
 212 //***************************************************************************************************************
 213
 214 int SeqErrorCommand::execute(){
 215         try{
 216                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 217
 218                 maxLength = 2000;
 219
 220                 string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
 221                 m->openOutputFile(errorSummaryFileName, errorSummaryFile);
 222                 outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
 223                 printErrorHeader();
 224
 225                 string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
 226                 m->openOutputFile(errorSeqFileName, errorSeqFile);
 227                 outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
 228
 229                 getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 230
 231                 map<string, int> weights;
 232                 if(namesFileName != ""){        weights = getWeights(); }
 233
 234                 ifstream queryFile;
 235                 m->openInputFile(queryFileName, queryFile);
 236
 237                 ifstream reportFile;
 238                 ifstream qualFile;
 239
 240                 ReportFile report;
 241                 QualityScores quality;
 242                 vector<vector<int> > qualForwardMap;
 243                 vector<vector<int> > qualReverseMap;
 244
 245                 if(qualFileName != "" && reportFileName != ""){
 246                         m->openInputFile(qualFileName, qualFile);
 247                         report = ReportFile(reportFile, reportFileName);
 248
 249                         qualForwardMap.resize(maxLength);
 250                         qualReverseMap.resize(maxLength);
 251                         for(int i=0;i<maxLength;i++){
 252                                 qualForwardMap[i].assign(41,0);
 253                                 qualReverseMap[i].assign(41,0);
 254                         }
 255                 }
 256
 257                 int totalBases = 0;
 258                 int totalMatches = 0;
 259
 260                 vector<int> misMatchCounts(11, 0);
 261                 int maxMismatch = 0;
 262                 int numSeqs = 0;
 263
 264                 map<string, int>::iterator it;
 265                 map<char, vector<int> > qScoreErrorMap;
 266                 qScoreErrorMap['m'].assign(41, 0);
 267                 qScoreErrorMap['s'].assign(41, 0);
 268                 qScoreErrorMap['i'].assign(41, 0);
 269                 qScoreErrorMap['a'].assign(41, 0);
 270
 271                 map<char, vector<int> > errorForward;
 272                 errorForward['m'].assign(maxLength,0);
 273                 errorForward['s'].assign(maxLength,0);
 274                 errorForward['i'].assign(maxLength,0);
 275                 errorForward['d'].assign(maxLength,0);
 276                 errorForward['a'].assign(maxLength,0);
 277
 278                 map<char, vector<int> > errorReverse;
 279                 errorReverse['m'].assign(maxLength,0);
 280                 errorReverse['s'].assign(maxLength,0);
 281                 errorReverse['i'].assign(maxLength,0);
 282                 errorReverse['d'].assign(maxLength,0);
 283                 errorReverse['a'].assign(maxLength,0);
 284
 285
 286                 string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
 287                 RefChimeraTest chimeraTest(referenceSeqs, errorChimeraFileName);
 288                 outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
 289
 290                 vector<string> megaAlignVector(numRefs, "");
 291
 292                 int index = 0;
 293                 bool ignoreSeq = 0;
 294
 295                 while(queryFile){
 296
 297                         if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 298
 299                         Sequence query(queryFile);
 300
 301                         int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
 302                         int closestRefIndex = chimeraTest.getClosestRefIndex();
 303
 304                         if(numParentSeqs > 1 && ignoreChimeras == 1)    {       ignoreSeq = 1;  }
 305                         else                                                                                    {       ignoreSeq = 0;  }
 306
 307                         Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
 308
 309                         if(namesFileName != ""){
 310                                 it = weights.find(query.getName());
 311                                 minCompare.weight = it->second;
 312                         }
 313                         else{   minCompare.weight = 1;  }
 314
 315                         printErrorData(minCompare, numParentSeqs);
 316
 317                         if(!ignoreSeq){
 318
 319                                 for(int i=0;i<minCompare.total;i++){
 320                                         char letter = minCompare.sequence[i];
 321
 322                                         errorForward[letter][i] += minCompare.weight;
 323                                         errorReverse[letter][minCompare.total-i-1] += minCompare.weight;
 324                                 }
 325                         }
 326
 327                         if(qualFileName != "" && reportFileName != ""){
 328                                 report = ReportFile(reportFile);
 329
 330 //                              int origLength = report.getQueryLength();
 331                                 int startBase = report.getQueryStart();
 332                                 int endBase = report.getQueryEnd();
 333
 334                                 quality = QualityScores(qualFile);
 335
 336                                 if(!ignoreSeq){
 337                                         quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
 338                                         quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
 339                                         quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
 340                                 }
 341                         }
 342
 343                         if(minCompare.errorRate < threshold && !ignoreSeq){
 344                                 totalBases += (minCompare.total * minCompare.weight);
 345                                 totalMatches += minCompare.matches * minCompare.weight;
 346                                 if(minCompare.mismatches > maxMismatch){
 347                                         maxMismatch = minCompare.mismatches;
 348                                         misMatchCounts.resize(maxMismatch + 1, 0);
 349                                 }
 350                                 misMatchCounts[minCompare.mismatches] += minCompare.weight;
 351                                 numSeqs++;
 352
 353                                 megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
 354                         }
 355
 356                         index++;
 357
 358                         if(index % 1000 == 0){  m->mothurOut(toString(index) + '\n');   }
 359                 }
 360                 queryFile.close();
 361                 errorSummaryFile.close();
 362                 errorSeqFile.close();
 363
 364                 if(qualFileName != "" && reportFileName != ""){
 365                         printErrorQuality(qScoreErrorMap);
 366                         printQualityFR(qualForwardMap, qualReverseMap);
 367                 }
 368
 369                 printErrorFRFile(errorForward, errorReverse);
 370
 371                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 372
 373                 string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
 374                 ofstream errorCountFile;
 375                 m->openOutputFile(errorCountFileName, errorCountFile);
 376                 outputNames.push_back(errorCountFileName);  outputTypes["error.count"].push_back(errorCountFileName);
 377                 m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
 378                 m->mothurOut("Errors\tSequences\n");
 379                 errorCountFile << "Errors\tSequences\n";
 380                 for(int i=0;i<misMatchCounts.size();i++){
 381                         m->mothurOut(toString(i) + '\t' + toString(misMatchCounts[i]) + '\n');
 382                         errorCountFile << i << '\t' << misMatchCounts[i] << endl;
 383                 }
 384                 errorCountFile.close();
 385
 386                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 387
 388                 printSubMatrix();
 389
 390                 string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
 391                 ofstream megAlignmentFile;
 392                 m->openOutputFile(megAlignmentFileName, megAlignmentFile);
 393                 outputNames.push_back(megAlignmentFileName);  outputTypes["error.ref-query"].push_back(megAlignmentFileName);
 394
 395                 for(int i=0;i<numRefs;i++){
 396                         megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
 397                         megAlignmentFile << megaAlignVector[i] << endl;
 398                 }
 399
 400
 401                 m->mothurOutEndLine();
 402                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 403                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 404                 m->mothurOutEndLine();
 405
 406                 return 0;
 407         }
 408         catch(exception& e) {
 409                 m->errorOut(e, "SeqErrorCommand", "execute");
 410                 exit(1);
 411         }
 412 }
 413
 414 //***************************************************************************************************************
 415
 416 void SeqErrorCommand::getReferences(){
 417         try {
 418
 419                 ifstream referenceFile;
 420                 m->openInputFile(referenceFileName, referenceFile);
 421
 422                 int numAmbigSeqs = 0;
 423
 424                 int maxStartPos = 0;
 425                 int minEndPos = 100000;
 426
 427                 while(referenceFile){
 428                         Sequence currentSeq(referenceFile);
 429                         int numAmbigs = currentSeq.getAmbigBases();
 430                         if(numAmbigs > 0){      numAmbigSeqs++; }
 431
 432                         int startPos = currentSeq.getStartPos();
 433                         if(startPos > maxStartPos)      {       maxStartPos = startPos; }
 434
 435                         int endPos = currentSeq.getEndPos();
 436                         if(endPos < minEndPos)          {       minEndPos = endPos;             }
 437                         referenceSeqs.push_back(currentSeq);
 438                         m->gobble(referenceFile);
 439                 }
 440                 referenceFile.close();
 441                 numRefs = referenceSeqs.size();
 442
 443
 444                 for(int i=0;i<numRefs;i++){
 445                         referenceSeqs[i].padToPos(maxStartPos);
 446                         referenceSeqs[i].padFromPos(minEndPos);
 447                 }
 448
 449                 if(numAmbigSeqs != 0){
 450                         m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
 451                 }
 452
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "SeqErrorCommand", "getReferences");
 456                 exit(1);
 457         }
 458 }
 459
 460 //***************************************************************************************************************
 461
 462 Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 463         try {
 464                 if(query.getAlignLength() != reference.getAlignLength()){
 465                         m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
 466                 }
 467                 int alignLength = query.getAlignLength();
 468
 469                 string q = query.getAligned();
 470                 string r = reference.getAligned();
 471
 472                 int started = 0;
 473                 Compare errors;
 474
 475                 for(int i=0;i<alignLength;i++){
 476                         if(r[i] != 'N' && q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){                  //      no missing data and no double gaps
 477                                 started = 1;
 478
 479                                 if(q[i] == 'A'){
 480                                         if(r[i] == 'A'){        errors.AA++;    errors.matches++;       errors.sequence += 'm'; }
 481                                         if(r[i] == 'T'){        errors.AT++;    errors.sequence += 's'; }
 482                                         if(r[i] == 'G'){        errors.AG++;    errors.sequence += 's'; }
 483                                         if(r[i] == 'C'){        errors.AC++;    errors.sequence += 's'; }
 484                                         if(r[i] == '-'){        errors.Ai++;    errors.sequence += 'i'; }
 485                                 }
 486                                 else if(q[i] == 'T'){
 487                                         if(r[i] == 'A'){        errors.TA++;    errors.sequence += 's'; }
 488                                         if(r[i] == 'T'){        errors.TT++;    errors.matches++;       errors.sequence += 'm'; }
 489                                         if(r[i] == 'G'){        errors.TG++;    errors.sequence += 's'; }
 490                                         if(r[i] == 'C'){        errors.TC++;    errors.sequence += 's'; }
 491                                         if(r[i] == '-'){        errors.Ti++;    errors.sequence += 'i'; }
 492                                 }
 493                                 else if(q[i] == 'G'){
 494                                         if(r[i] == 'A'){        errors.GA++;    errors.sequence += 's'; }
 495                                         if(r[i] == 'T'){        errors.GT++;    errors.sequence += 's'; }
 496                                         if(r[i] == 'G'){        errors.GG++;    errors.matches++;       errors.sequence += 'm'; }
 497                                         if(r[i] == 'C'){        errors.GC++;    errors.sequence += 's'; }
 498                                         if(r[i] == '-'){        errors.Gi++;    errors.sequence += 'i'; }
 499                                 }
 500                                 else if(q[i] == 'C'){
 501                                         if(r[i] == 'A'){        errors.CA++;    errors.sequence += 's'; }
 502                                         if(r[i] == 'T'){        errors.CT++;    errors.sequence += 's'; }
 503                                         if(r[i] == 'G'){        errors.CG++;    errors.sequence += 's'; }
 504                                         if(r[i] == 'C'){        errors.CC++;    errors.matches++;       errors.sequence += 'm'; }
 505                                         if(r[i] == '-'){        errors.Ci++;    errors.sequence += 'i'; }
 506                                 }
 507                                 else if(q[i] == 'N'){
 508                                         if(r[i] == 'A'){        errors.NA++;    errors.sequence += 'a'; }
 509                                         if(r[i] == 'T'){        errors.NT++;    errors.sequence += 'a'; }
 510                                         if(r[i] == 'G'){        errors.NG++;    errors.sequence += 'a'; }
 511                                         if(r[i] == 'C'){        errors.NC++;    errors.sequence += 'a'; }
 512                                         if(r[i] == '-'){        errors.Ni++;    errors.sequence += 'a'; }
 513                                 }
 514                                 else if(q[i] == '-' && r[i] != '-'){
 515                                         if(r[i] == 'A'){        errors.dA++;    errors.sequence += 'd'; }
 516                                         if(r[i] == 'T'){        errors.dT++;    errors.sequence += 'd'; }
 517                                         if(r[i] == 'G'){        errors.dG++;    errors.sequence += 'd'; }
 518                                         if(r[i] == 'C'){        errors.dC++;    errors.sequence += 'd'; }
 519                                 }
 520                                 errors.total++;
 521
 522                         }
 523                         else if(q[i] == '.' && r[i] != '.'){            //      reference extends beyond query
 524                                 if(started == 1){       break;  }
 525                         }
 526                         else if(q[i] != '.' && r[i] == '.'){            //      query extends beyond reference
 527                                 if(started == 1){       break;  }
 528                         }
 529                         else if(q[i] == '.' && r[i] == '.'){            //      both are missing data
 530                                 if(started == 1){       break;  }
 531                         }
 532
 533                 }
 534                 errors.mismatches = errors.total-errors.matches;
 535                 errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total;
 536                 errors.queryName = query.getName();
 537                 errors.refName = reference.getName();
 538
 539                 return errors;
 540         }
 541         catch(exception& e) {
 542                 m->errorOut(e, "SeqErrorCommand", "getErrors");
 543                 exit(1);
 544         }
 545 }
 546
 547 //***************************************************************************************************************
 548
 549 map<string, int> SeqErrorCommand::getWeights(){
 550         ifstream nameFile;
 551         m->openInputFile(namesFileName, nameFile);
 552
 553         string seqName;
 554         string redundantSeqs;
 555         map<string, int> nameCountMap;
 556
 557         while(nameFile){
 558                 nameFile >> seqName >> redundantSeqs;
 559                 nameCountMap[seqName] = m->getNumNames(redundantSeqs);
 560                 m->gobble(nameFile);
 561         }
 562         return nameCountMap;
 563 }
 564
 565
 566 //***************************************************************************************************************
 567
 568 void SeqErrorCommand::printErrorHeader(){
 569         try {
 570                 errorSummaryFile << "query\treference\tweight\t";
 571                 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";
 572                 errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\tnumparents\n";
 573
 574                 errorSummaryFile << setprecision(6);
 575                 errorSummaryFile.setf(ios::fixed);
 576         }
 577         catch(exception& e) {
 578                 m->errorOut(e, "SeqErrorCommand", "printErrorHeader");
 579                 exit(1);
 580         }
 581 }
 582
 583 //***************************************************************************************************************
 584
 585 void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs){
 586         try {
 587
 588                 errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
 589                 errorSummaryFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
 590                 errorSummaryFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
 591                 errorSummaryFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
 592                 errorSummaryFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
 593                 errorSummaryFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
 594                 errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t';
 595                 errorSummaryFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
 596
 597                 errorSummaryFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t';                  //insertions
 598                 errorSummaryFile << error.dA + error.dT + error.dG + error.dC << '\t';                  //deletions
 599                 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
 600                 errorSummaryFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t';       //ambiguities
 601                 errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << '\t' << numParentSeqs << endl;
 602
 603                 errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
 604
 605                 int a=0;                int t=1;                int g=2;                int c=3;
 606                 int gap=4;              int n=5;
 607
 608                 if(numParentSeqs == 1 || ignoreChimeras == 0){
 609                         substitutionMatrix[a][a] += error.weight * error.AA;
 610                         substitutionMatrix[a][t] += error.weight * error.TA;
 611                         substitutionMatrix[a][g] += error.weight * error.GA;
 612                         substitutionMatrix[a][c] += error.weight * error.CA;
 613                         substitutionMatrix[a][gap] += error.weight * error.dA;
 614                         substitutionMatrix[a][n] += error.weight * error.NA;
 615
 616                         substitutionMatrix[t][a] += error.weight * error.AT;
 617                         substitutionMatrix[t][t] += error.weight * error.TT;
 618                         substitutionMatrix[t][g] += error.weight * error.GT;
 619                         substitutionMatrix[t][c] += error.weight * error.CT;
 620                         substitutionMatrix[t][gap] += error.weight * error.dT;
 621                         substitutionMatrix[t][n] += error.weight * error.NT;
 622
 623                         substitutionMatrix[g][a] += error.weight * error.AG;
 624                         substitutionMatrix[g][t] += error.weight * error.TG;
 625                         substitutionMatrix[g][g] += error.weight * error.GG;
 626                         substitutionMatrix[g][c] += error.weight * error.CG;
 627                         substitutionMatrix[g][gap] += error.weight * error.dG;
 628                         substitutionMatrix[g][n] += error.weight * error.NG;
 629
 630                         substitutionMatrix[c][a] += error.weight * error.AC;
 631                         substitutionMatrix[c][t] += error.weight * error.TC;
 632                         substitutionMatrix[c][g] += error.weight * error.GC;
 633                         substitutionMatrix[c][c] += error.weight * error.CC;
 634                         substitutionMatrix[c][gap] += error.weight * error.dC;
 635                         substitutionMatrix[c][n] += error.weight * error.NC;
 636
 637                         substitutionMatrix[gap][a] += error.weight * error.Ai;
 638                         substitutionMatrix[gap][t] += error.weight * error.Ti;
 639                         substitutionMatrix[gap][g] += error.weight * error.Gi;
 640                         substitutionMatrix[gap][c] += error.weight * error.Ci;
 641                         substitutionMatrix[gap][n] += error.weight * error.Ni;
 642                 }
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "SeqErrorCommand", "printErrorData");
 646                 exit(1);
 647         }
 648 }
 649
 650 //***************************************************************************************************************
 651
 652 void SeqErrorCommand::printSubMatrix(){
 653         try {
 654                 string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
 655                 ofstream subMatrixFile;
 656                 m->openOutputFile(subMatrixFileName, subMatrixFile);
 657                 outputNames.push_back(subMatrixFileName);  outputTypes["error.matrix"].push_back(subMatrixFileName);
 658                 vector<string> bases(6);
 659                 bases[0] = "A";
 660                 bases[1] = "T";
 661                 bases[2] = "G";
 662                 bases[3] = "C";
 663                 bases[4] = "Gap";
 664                 bases[5] = "N";
 665                 vector<int> refSums(5,1);
 666
 667                 for(int i=0;i<5;i++){
 668                         subMatrixFile << "\tr" << bases[i];
 669
 670                         for(int j=0;j<6;j++){
 671                                 refSums[i] += substitutionMatrix[i][j];
 672                         }
 673                 }
 674                 subMatrixFile << endl;
 675
 676                 for(int i=0;i<6;i++){
 677                         subMatrixFile << 'q' << bases[i];
 678                         for(int j=0;j<5;j++){
 679                                 subMatrixFile << '\t' << substitutionMatrix[j][i];
 680                         }
 681                         subMatrixFile << endl;
 682                 }
 683
 684                 subMatrixFile << "total";
 685                 for(int i=0;i<5;i++){
 686                         subMatrixFile << '\t' << refSums[i];
 687                 }
 688                 subMatrixFile << endl;
 689                 subMatrixFile.close();
 690         }
 691         catch(exception& e) {
 692                 m->errorOut(e, "SeqErrorCommand", "printSubMatrix");
 693                 exit(1);
 694         }
 695 }
 696 //***************************************************************************************************************
 697
 698 void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
 699         try{
 700                 string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward";
 701                 ofstream errorForwardFile;
 702                 m->openOutputFile(errorForwardFileName, errorForwardFile);
 703                 outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
 704
 705                 errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
 706                 for(int i=0;i<maxLength;i++){
 707                         float match = (float)errorForward['m'][i];
 708                         float subst = (float)errorForward['s'][i];
 709                         float insert = (float)errorForward['i'][i];
 710                         float del = (float)errorForward['d'][i];
 711                         float amb = (float)errorForward['a'][i];
 712                         float total = match + subst + insert + del + amb;
 713                         if(total == 0){ break;  }
 714                         errorForwardFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
 715                 }
 716                 errorForwardFile.close();
 717
 718                 string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
 719                 ofstream errorReverseFile;
 720                 m->openOutputFile(errorReverseFileName, errorReverseFile);
 721                 outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
 722
 723                 errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
 724                 for(int i=0;i<maxLength;i++){
 725                         float match = (float)errorReverse['m'][i];
 726                         float subst = (float)errorReverse['s'][i];
 727                         float insert = (float)errorReverse['i'][i];
 728                         float del = (float)errorReverse['d'][i];
 729                         float amb = (float)errorReverse['a'][i];
 730                         float total = match + subst + insert + del + amb;
 731                         if(total == 0){ break;  }
 732                         errorReverseFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
 733                 }
 734                 errorReverseFile.close();
 735         }
 736         catch(exception& e) {
 737                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 738                 exit(1);
 739         }
 740 }
 741
 742 //***************************************************************************************************************
 743
 744 void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
 745         try{
 746
 747                 string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
 748                 ofstream errorQualityFile;
 749                 m->openOutputFile(errorQualityFileName, errorQualityFile);
 750                 outputNames.push_back(errorQualityFileName);  outputTypes["error.quality"].push_back(errorQualityFileName);
 751
 752                 errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
 753                 for(int i=0;i<41;i++){
 754                         errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
 755                 }
 756                 errorQualityFile.close();
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 760                 exit(1);
 761         }
 762 }
 763
 764
 765 //***************************************************************************************************************
 766
 767 void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
 768
 769         try{
 770                 int numRows = 0;
 771                 int numColumns = qualForwardMap[0].size();
 772
 773                 for(int i=0;i<qualForwardMap.size();i++){
 774                         for(int j=0;j<numColumns;j++){
 775                                 if(qualForwardMap[i][j] != 0){
 776                                         if(numRows < i)         {       numRows = i+20;         }
 777                                 }
 778                         }
 779                 }
 780
 781                 string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward";
 782                 ofstream qualityForwardFile;
 783                 m->openOutputFile(qualityForwardFileName, qualityForwardFile);
 784                 outputNames.push_back(qualityForwardFileName);  outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
 785
 786                 for(int i=0;i<numColumns;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
 787
 788                 for(int i=0;i<numRows;i++){
 789                         qualityForwardFile << i+1;
 790                         for(int j=0;j<numColumns;j++){
 791                                 qualityForwardFile << '\t' << qualForwardMap[i][j];
 792                         }
 793
 794                         qualityForwardFile << endl;
 795                 }
 796                 qualityForwardFile.close();
 797
 798
 799                 string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse";
 800                 ofstream qualityReverseFile;
 801                 m->openOutputFile(qualityReverseFileName, qualityReverseFile);
 802                 outputNames.push_back(qualityReverseFileName);  outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
 803
 804                 for(int i=0;i<numColumns;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
 805                 for(int i=0;i<numRows;i++){
 806
 807                         qualityReverseFile << i+1;
 808                         for(int j=0;j<numColumns;j++){
 809                                 qualityReverseFile << '\t' << qualReverseMap[i][j];
 810                         }
 811                         qualityReverseFile << endl;
 812                 }
 813                 qualityReverseFile.close();
 814         }
 815         catch(exception& e) {
 816                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
 817                 exit(1);
 818         }
 819
 820 }
 821
 822 //***************************************************************************************************************