getseqscommand.cpp

   1 /*
   2  *  getseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "counttable.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetSeqsCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
  19         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
  23                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
  24                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
  25                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
  26                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
  27                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
  28                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  29                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  30                 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "GetSeqsCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string GetSeqsCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
  46                 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
  47                 helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
  48                 helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=true. \n";
  49                 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
  50                 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59
  60 //**********************************************************************************************************************
  61 GetSeqsCommand::GetSeqsCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["taxonomy"] = tempOutNames;
  68                 outputTypes["name"] = tempOutNames;
  69                 outputTypes["group"] = tempOutNames;
  70                 outputTypes["alignreport"] = tempOutNames;
  71                 outputTypes["list"] = tempOutNames;
  72                 outputTypes["qfile"] = tempOutNames;
  73         outputTypes["count"] = tempOutNames;
  74                 outputTypes["accnosreport"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 string GetSeqsCommand::getOutputPattern(string type) {
  83     try {
  84         string pattern = "";
  85
  86         if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
  87         else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
  88         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
  89         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  90         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  91         else if (type == "list")        {   pattern = "[filename],[distance],pick,[extension]";    }
  92         else if (type == "qfile")       {   pattern = "[filename],pick,[extension]";    }
  93         else if (type == "accnosreport")      {   pattern = "[filename],pick.accnos.report";    }
  94         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
  95         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  96
  97         return pattern;
  98     }
  99     catch(exception& e) {
 100         m->errorOut(e, "GetSeqsCommand", "getOutputPattern");
 101         exit(1);
 102     }
 103 }
 104 //**********************************************************************************************************************
 105 GetSeqsCommand::GetSeqsCommand(string option)  {
 106         try {
 107                 abort = false; calledHelp = false;
 108
 109                 //allow user to run help
 110                 if(option == "help") { help(); abort = true; calledHelp = true; }
 111                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 112
 113                 else {
 114                         vector<string> myArray = setParameters();
 115
 116                         OptionParser parser(option);
 117                         map<string,string> parameters = parser.getParameters();
 118
 119                         ValidParameters validParameter;
 120                         map<string,string>::iterator it;
 121
 122                         //check to make sure all parameters are valid for command
 123                         for (it = parameters.begin(); it != parameters.end(); it++) {
 124                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 125                         }
 126
 127                         //initialize outputTypes
 128                         vector<string> tempOutNames;
 129                         outputTypes["fasta"] = tempOutNames;
 130                         outputTypes["taxonomy"] = tempOutNames;
 131                         outputTypes["name"] = tempOutNames;
 132                         outputTypes["group"] = tempOutNames;
 133                         outputTypes["alignreport"] = tempOutNames;
 134                         outputTypes["list"] = tempOutNames;
 135                         outputTypes["qfile"] = tempOutNames;
 136                         outputTypes["accnosreport"] = tempOutNames;
 137             outputTypes["count"] = tempOutNames;
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 141
 142                         //if the user changes the input directory command factory will send this info to us in the output parameter
 143                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 144                         if (inputDir == "not found"){   inputDir = "";          }
 145                         else {
 146                                 string path;
 147                                 it = parameters.find("alignreport");
 148                                 //user has given a template 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["alignreport"] = inputDir + it->second;              }
 153                                 }
 154
 155                                 it = parameters.find("fasta");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 161                                 }
 162
 163                                 it = parameters.find("accnos");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 169                                 }
 170
 171                                 it = parameters.find("accnos2");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["accnos2"] = inputDir + it->second;          }
 177                                 }
 178
 179                                 it = parameters.find("list");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 185                                 }
 186
 187                                 it = parameters.find("name");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 193                                 }
 194
 195                                 it = parameters.find("group");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 201                                 }
 202
 203                                 it = parameters.find("taxonomy");
 204                                 //user has given a template file
 205                                 if(it != parameters.end()){
 206                                         path = m->hasPath(it->second);
 207                                         //if the user has not given a path then, add inputdir. else leave path alone.
 208                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 209                                 }
 210
 211                                 it = parameters.find("qfile");
 212                                 //user has given a template file
 213                                 if(it != parameters.end()){
 214                                         path = m->hasPath(it->second);
 215                                         //if the user has not given a path then, add inputdir. else leave path alone.
 216                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 217                                 }
 218
 219                 it = parameters.find("count");
 220                                 //user has given a template file
 221                                 if(it != parameters.end()){
 222                                         path = m->hasPath(it->second);
 223                                         //if the user has not given a path then, add inputdir. else leave path alone.
 224                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 225                                 }
 226                         }
 227
 228
 229                         //check for required parameters
 230                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 231                         if (accnosfile == "not open") { abort = true; }
 232                         else if (accnosfile == "not found") {
 233                                 accnosfile = m->getAccnosFile();
 234                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 235                                 else {
 236                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 237                                         abort = true;
 238                                 }
 239                         }else { m->setAccnosFile(accnosfile); }
 240
 241                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 242
 243                         fastafile = validParameter.validFile(parameters, "fasta", true);
 244                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 245                         else if (fastafile == "not found") {  fastafile = "";  }
 246                         else { m->setFastaFile(fastafile); }
 247
 248                         namefile = validParameter.validFile(parameters, "name", true);
 249                         if (namefile == "not open") { namefile = ""; abort = true; }
 250                         else if (namefile == "not found") {  namefile = "";  }
 251                         else { m->setNameFile(namefile); }
 252
 253                         groupfile = validParameter.validFile(parameters, "group", true);
 254                         if (groupfile == "not open") { abort = true; }
 255                         else if (groupfile == "not found") {  groupfile = "";  }
 256                         else { m->setGroupFile(groupfile); }
 257
 258                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 259                         if (alignfile == "not open") { abort = true; }
 260                         else if (alignfile == "not found") {  alignfile = "";  }
 261
 262                         listfile = validParameter.validFile(parameters, "list", true);
 263                         if (listfile == "not open") { abort = true; }
 264                         else if (listfile == "not found") {  listfile = "";  }
 265                         else { m->setListFile(listfile); }
 266
 267                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 268                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 269                         else if (taxfile == "not found") {  taxfile = "";  }
 270                         else { m->setTaxonomyFile(taxfile); }
 271
 272                         qualfile = validParameter.validFile(parameters, "qfile", true);
 273                         if (qualfile == "not open") { abort = true; }
 274                         else if (qualfile == "not found") {  qualfile = "";  }
 275                         else { m->setQualFile(qualfile); }
 276
 277                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 278                         if (accnosfile2 == "not open") { abort = true; }
 279                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 280
 281             countfile = validParameter.validFile(parameters, "count", true);
 282             if (countfile == "not open") { countfile = ""; abort = true; }
 283             else if (countfile == "not found") { countfile = "";  }
 284             else { m->setCountTableFile(countfile); }
 285
 286             if ((namefile != "") && (countfile != "")) {
 287                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 288             }
 289
 290             if ((groupfile != "") && (countfile != "")) {
 291                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 292             }
 293
 294
 295                         string usedDups = "true";
 296                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 297                         dups = m->isTrue(temp);
 298
 299                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "") && (countfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
 300
 301             if (countfile == "") {
 302                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 303                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 304                     parser.getNameFile(files);
 305                 }
 306             }
 307                 }
 308
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 312                 exit(1);
 313         }
 314 }
 315 //**********************************************************************************************************************
 316
 317 int GetSeqsCommand::execute(){
 318         try {
 319
 320                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 321
 322                 //get names you want to keep
 323                 names = m->readAccnos(accnosfile);
 324
 325                 if (m->control_pressed) { return 0; }
 326
 327         if (countfile != "") {
 328             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 329                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
 330             }
 331         }
 332
 333                 //read through the correct file and output lines you want to keep
 334                 if (namefile != "")                     {               readName();                     }
 335                 if (fastafile != "")            {               readFasta();            }
 336                 if (groupfile != "")            {               readGroup();            }
 337         if (countfile != "")            {               readCount();            }
 338                 if (alignfile != "")            {               readAlign();            }
 339                 if (listfile != "")                     {               readList();                     }
 340                 if (taxfile != "")                      {               readTax();                      }
 341                 if (qualfile != "")                     {               readQual();                     }
 342                 if (accnosfile2 != "")          {               compareAccnos();        }
 343
 344         if (m->debug) { runSanityCheck(); }
 345
 346                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 347
 348
 349                 if (outputNames.size() != 0) {
 350                         m->mothurOutEndLine();
 351                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 352                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 353                         m->mothurOutEndLine();
 354
 355                         //set fasta file as new current fastafile
 356                         string current = "";
 357                         itTypes = outputTypes.find("fasta");
 358                         if (itTypes != outputTypes.end()) {
 359                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 360                         }
 361
 362                         itTypes = outputTypes.find("name");
 363                         if (itTypes != outputTypes.end()) {
 364                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 365                         }
 366
 367                         itTypes = outputTypes.find("group");
 368                         if (itTypes != outputTypes.end()) {
 369                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 370                         }
 371
 372                         itTypes = outputTypes.find("list");
 373                         if (itTypes != outputTypes.end()) {
 374                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 375                         }
 376
 377                         itTypes = outputTypes.find("taxonomy");
 378                         if (itTypes != outputTypes.end()) {
 379                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 380                         }
 381
 382                         itTypes = outputTypes.find("qfile");
 383                         if (itTypes != outputTypes.end()) {
 384                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 385                         }
 386
 387             itTypes = outputTypes.find("count");
 388                         if (itTypes != outputTypes.end()) {
 389                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 390                         }
 391                 }
 392
 393                 return 0;
 394         }
 395
 396         catch(exception& e) {
 397                 m->errorOut(e, "GetSeqsCommand", "execute");
 398                 exit(1);
 399         }
 400 }
 401
 402 //**********************************************************************************************************************
 403 int GetSeqsCommand::readFasta(){
 404         try {
 405                 string thisOutputDir = outputDir;
 406                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 407                 map<string, string> variables;
 408         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 409         variables["[extension]"] = m->getExtension(fastafile);
 410                 string outputFileName = getOutputFileName("fasta", variables);
 411                 ofstream out;
 412                 m->openOutputFile(outputFileName, out);
 413
 414
 415                 ifstream in;
 416                 m->openInputFile(fastafile, in);
 417                 string name;
 418
 419                 bool wroteSomething = false;
 420                 int selectedCount = 0;
 421
 422         if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
 423
 424                 while(!in.eof()){
 425
 426                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 427
 428                         Sequence currSeq(in);
 429                         name = currSeq.getName();
 430
 431             if (!dups) {//adjust name if needed
 432                 map<string, string>::iterator it = uniqueMap.find(name);
 433                 if (it != uniqueMap.end()) { currSeq.setName(it->second); }
 434             }
 435
 436             name = currSeq.getName();
 437
 438                         if (name != "") {
 439                                 //if this name is in the accnos file
 440                                 if (names.count(name) != 0) {
 441                                         wroteSomething = true;
 442
 443                                         currSeq.printSequence(out);
 444                                         selectedCount++;
 445
 446                     if (m->debug) { sanity["fasta"].insert(name); }
 447                                 }
 448                         }
 449                         m->gobble(in);
 450                 }
 451                 in.close();
 452                 out.close();
 453
 454
 455                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 456                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 457
 458                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 459
 460                 return 0;
 461
 462         }
 463         catch(exception& e) {
 464                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 465                 exit(1);
 466         }
 467 }
 468 //**********************************************************************************************************************
 469 int GetSeqsCommand::readQual(){
 470         try {
 471                 string thisOutputDir = outputDir;
 472                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 473                 map<string, string> variables;
 474         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
 475         variables["[extension]"] = m->getExtension(qualfile);
 476                 string outputFileName = getOutputFileName("qfile", variables);
 477                 ofstream out;
 478                 m->openOutputFile(outputFileName, out);
 479
 480
 481                 ifstream in;
 482                 m->openInputFile(qualfile, in);
 483                 string name;
 484
 485                 bool wroteSomething = false;
 486                 int selectedCount = 0;
 487
 488         if (m->debug) { set<string> temp; sanity["qual"] = temp; }
 489
 490                 while(!in.eof()){
 491                         string saveName = "";
 492                         string name = "";
 493                         string scores = "";
 494
 495                         in >> name;
 496
 497             if (!dups) {//adjust name if needed
 498                 map<string, string>::iterator it = uniqueMap.find(name);
 499                 if (it != uniqueMap.end()) { name = it->second; }
 500             }
 501
 502                         if (name.length() != 0) {
 503                                 saveName = name.substr(1);
 504                                 while (!in.eof())       {
 505                                         char c = in.get();
 506                                         if (c == 10 || c == 13 || c == -1){     break;  }
 507                                         else { name += c; }
 508                                 }
 509                                 m->gobble(in);
 510                         }
 511
 512                         while(in){
 513                                 char letter= in.get();
 514                                 if(letter == '>'){      in.putback(letter);     break;  }
 515                                 else{ scores += letter; }
 516                         }
 517
 518                         m->gobble(in);
 519
 520                         if (names.count(saveName) != 0) {
 521                                 wroteSomething = true;
 522
 523                                 out << name << endl << scores;
 524                                 selectedCount++;
 525                 if (m->debug) { sanity["qual"].insert(name); }
 526                         }
 527
 528                         m->gobble(in);
 529                 }
 530                 in.close();
 531                 out.close();
 532
 533
 534                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 535                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 536
 537                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
 538
 539
 540                 return 0;
 541
 542         }
 543         catch(exception& e) {
 544                 m->errorOut(e, "GetSeqsCommand", "readQual");
 545                 exit(1);
 546         }
 547 }
 548 //**********************************************************************************************************************
 549 int GetSeqsCommand::readCount(){
 550         try {
 551                 string thisOutputDir = outputDir;
 552                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 553                 map<string, string> variables;
 554                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 555         variables["[extension]"] = m->getExtension(countfile);
 556                 string outputFileName = getOutputFileName("count", variables);
 557
 558                 ofstream out;
 559                 m->openOutputFile(outputFileName, out);
 560
 561                 ifstream in;
 562                 m->openInputFile(countfile, in);
 563
 564                 bool wroteSomething = false;
 565                 int selectedCount = 0;
 566
 567         string headers = m->getline(in); m->gobble(in);
 568         out << headers << endl;
 569
 570         string name, rest; int thisTotal;
 571         while (!in.eof()) {
 572
 573             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 574
 575             in >> name; m->gobble(in);
 576             in >> thisTotal; m->gobble(in);
 577             rest = m->getline(in); m->gobble(in);
 578             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 579
 580             if (names.count(name) != 0) {
 581                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 582                 wroteSomething = true;
 583                 selectedCount+= thisTotal;
 584             }
 585         }
 586         in.close();
 587                 out.close();
 588
 589         //check for groups that have been eliminated
 590         CountTable ct;
 591         if (ct.testGroups(outputFileName)) {
 592             ct.readTable(outputFileName, true, false);
 593             ct.printTable(outputFileName);
 594         }
 595
 596                 if (wroteSomething == false) {  m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 597                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 598
 599                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
 600
 601                 return 0;
 602         }
 603         catch(exception& e) {
 604                 m->errorOut(e, "GetSeqsCommand", "readCount");
 605                 exit(1);
 606         }
 607 }
 608
 609 //**********************************************************************************************************************
 610 int GetSeqsCommand::readList(){
 611         try {
 612                 string thisOutputDir = outputDir;
 613                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 614         map<string, string> variables;
 615                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 616         variables["[extension]"] = m->getExtension(listfile);
 617
 618                 ifstream in;
 619                 m->openInputFile(listfile, in);
 620
 621                 bool wroteSomething = false;
 622                 int selectedCount = 0;
 623
 624         if (m->debug) { set<string> temp; sanity["list"] = temp; }
 625
 626                 while(!in.eof()){
 627
 628                         selectedCount = 0;
 629
 630                         //read in list vector
 631                         ListVector list(in);
 632
 633                         //make a new list vector
 634                         ListVector newList;
 635                         newList.setLabel(list.getLabel());
 636
 637             variables["[distance]"] = list.getLabel();
 638             string outputFileName = getOutputFileName("list", variables);
 639
 640                         ofstream out;
 641                         m->openOutputFile(outputFileName, out);
 642                         outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 643
 644             vector<string> binLabels = list.getLabels();
 645             vector<string> newBinLabels;
 646
 647             if (m->control_pressed) { in.close(); out.close();  return 0; }
 648
 649                         //for each bin
 650                         for (int i = 0; i < list.getNumBins(); i++) {
 651
 652                                 //parse out names that are in accnos file
 653                                 string binnames = list.get(i);
 654                 vector<string> bnames;
 655                 m->splitAtComma(binnames, bnames);
 656
 657                                 string newNames = "";
 658                 for (int i = 0; i < bnames.size(); i++) {
 659                                         string name = bnames[i];
 660                                         //if that name is in the .accnos file, add it
 661                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
 662                                 }
 663
 664                                 //if there are names in this bin add to new list
 665                                 if (newNames != "") {
 666                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 667                                         newList.push_back(newNames);
 668                     newBinLabels.push_back(binLabels[i]);
 669                                 }
 670                         }
 671
 672                         //print new listvector
 673                         if (newList.getNumBins() != 0) {
 674                                 wroteSomething = true;
 675                                 newList.setLabels(newBinLabels);
 676                 newList.printHeaders(out);
 677                                 newList.print(out);
 678                         }
 679
 680                         m->gobble(in);
 681             out.close();
 682                 }
 683                 in.close();
 684
 685
 686                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 687
 688                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 689
 690                 return 0;
 691
 692         }
 693         catch(exception& e) {
 694                 m->errorOut(e, "GetSeqsCommand", "readList");
 695                 exit(1);
 696         }
 697 }
 698 //**********************************************************************************************************************
 699 int GetSeqsCommand::readName(){
 700         try {
 701                 string thisOutputDir = outputDir;
 702                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 703         map<string, string> variables;
 704                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 705         variables["[extension]"] = m->getExtension(namefile);
 706                 string outputFileName = getOutputFileName("name", variables);
 707                 ofstream out;
 708                 m->openOutputFile(outputFileName, out);
 709
 710
 711                 ifstream in;
 712                 m->openInputFile(namefile, in);
 713                 string name, firstCol, secondCol;
 714
 715                 bool wroteSomething = false;
 716                 int selectedCount = 0;
 717
 718         if (m->debug) { set<string> temp; sanity["name"] = temp; }
 719         if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
 720
 721                 while(!in.eof()){
 722
 723                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 724
 725                         in >> firstCol;                 m->gobble(in);
 726                         in >> secondCol;
 727
 728                         string hold = "";
 729                         if (dups) { hold = secondCol; }
 730
 731                         vector<string> parsedNames;
 732                         m->splitAtComma(secondCol, parsedNames);
 733
 734                         vector<string> validSecond;
 735                         for (int i = 0; i < parsedNames.size(); i++) {
 736                                 if (names.count(parsedNames[i]) != 0) {
 737                                         validSecond.push_back(parsedNames[i]);
 738                     if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
 739                                 }
 740                         }
 741
 742                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 743                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
 744                                 out << firstCol << '\t' << hold << endl;
 745                                 wroteSomething = true;
 746                                 selectedCount += parsedNames.size();
 747                 if (m->debug) { sanity["name"].insert(firstCol); }
 748                         }else {
 749
 750                                 selectedCount += validSecond.size();
 751
 752                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 753                                 if (names.count(firstCol) != 0) {
 754
 755                                         wroteSomething = true;
 756
 757                                         out << firstCol << '\t';
 758
 759                                         //you know you have at least one valid second since first column is valid
 760                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 761                                         out << validSecond[validSecond.size()-1] << endl;
 762
 763                     if (m->debug) { sanity["name"].insert(firstCol); }
 764
 765
 766                                 //make first name in set you come to first column and then add the remaining names to second column
 767                                 }else {
 768
 769                                         //you want part of this row
 770                                         if (validSecond.size() != 0) {
 771
 772                                                 wroteSomething = true;
 773
 774                                                 out << validSecond[0] << '\t';
 775                         //we are changing the unique name in the fasta file
 776                         uniqueMap[firstCol] = validSecond[0];
 777
 778                                                 //you know you have at least one valid second since first column is valid
 779                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 780                                                 out << validSecond[validSecond.size()-1] << endl;
 781
 782                         if (m->debug) { sanity["name"].insert(validSecond[0]); }
 783                                         }
 784                                 }
 785                         }
 786                         m->gobble(in);
 787                 }
 788                 in.close();
 789                 out.close();
 790
 791                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 792                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 793
 794                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 795
 796                 return 0;
 797
 798         }
 799         catch(exception& e) {
 800                 m->errorOut(e, "GetSeqsCommand", "readName");
 801                 exit(1);
 802         }
 803 }
 804
 805 //**********************************************************************************************************************
 806 int GetSeqsCommand::readGroup(){
 807         try {
 808                 string thisOutputDir = outputDir;
 809                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 810                 map<string, string> variables;
 811                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 812         variables["[extension]"] = m->getExtension(groupfile);
 813                 string outputFileName = getOutputFileName("group", variables);
 814                 ofstream out;
 815                 m->openOutputFile(outputFileName, out);
 816
 817
 818                 ifstream in;
 819                 m->openInputFile(groupfile, in);
 820                 string name, group;
 821
 822                 bool wroteSomething = false;
 823                 int selectedCount = 0;
 824
 825         if (m->debug) { set<string> temp; sanity["group"] = temp; }
 826
 827                 while(!in.eof()){
 828
 829                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 830
 831
 832                         in >> name;                             //read from first column
 833                         in >> group;                    //read from second column
 834
 835
 836                         //if this name is in the accnos file
 837                         if (names.count(name) != 0) {
 838                                 wroteSomething = true;
 839
 840                                 out << name << '\t' << group << endl;
 841                                 selectedCount++;
 842
 843                 if (m->debug) {  sanity["group"].insert(name); }
 844                         }
 845
 846                         m->gobble(in);
 847                 }
 848                 in.close();
 849                 out.close();
 850
 851                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 852                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 853
 854                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 855
 856
 857                 return 0;
 858
 859         }
 860         catch(exception& e) {
 861                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 862                 exit(1);
 863         }
 864 }
 865 //**********************************************************************************************************************
 866 int GetSeqsCommand::readTax(){
 867         try {
 868                 string thisOutputDir = outputDir;
 869                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 870                 map<string, string> variables;
 871                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
 872         variables["[extension]"] = m->getExtension(taxfile);
 873                 string outputFileName = getOutputFileName("taxonomy", variables);
 874                 ofstream out;
 875                 m->openOutputFile(outputFileName, out);
 876
 877                 ifstream in;
 878                 m->openInputFile(taxfile, in);
 879                 string name, tax;
 880
 881                 bool wroteSomething = false;
 882                 int selectedCount = 0;
 883
 884         if (m->debug) { set<string> temp; sanity["tax"] = temp; }
 885
 886                 while(!in.eof()){
 887
 888                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 889
 890                         in >> name;                             //read from first column
 891                         in >> tax;                      //read from second column
 892
 893             if (!dups) {//adjust name if needed
 894                 map<string, string>::iterator it = uniqueMap.find(name);
 895                 if (it != uniqueMap.end()) { name = it->second; }
 896             }
 897
 898                         //if this name is in the accnos file
 899                         if (names.count(name) != 0) {
 900                                 wroteSomething = true;
 901
 902                                 out << name << '\t' << tax << endl;
 903                                 selectedCount++;
 904
 905                 if (m->debug) { sanity["tax"].insert(name); }
 906                         }
 907
 908                         m->gobble(in);
 909                 }
 910                 in.close();
 911                 out.close();
 912
 913                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 914                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 915
 916                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 917
 918                 return 0;
 919
 920         }
 921         catch(exception& e) {
 922                 m->errorOut(e, "GetSeqsCommand", "readTax");
 923                 exit(1);
 924         }
 925 }
 926 //**********************************************************************************************************************
 927 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 928 int GetSeqsCommand::readAlign(){
 929         try {
 930                 string thisOutputDir = outputDir;
 931                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 932         map<string, string> variables;
 933                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
 934                 string outputFileName = getOutputFileName("alignreport", variables);
 935                 ofstream out;
 936                 m->openOutputFile(outputFileName, out);
 937
 938
 939                 ifstream in;
 940                 m->openInputFile(alignfile, in);
 941                 string name, junk;
 942
 943                 bool wroteSomething = false;
 944                 int selectedCount = 0;
 945
 946                 //read column headers
 947                 for (int i = 0; i < 16; i++) {
 948                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 949                         else                    {       break;                  }
 950                 }
 951                 out << endl;
 952
 953                 while(!in.eof()){
 954
 955                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 956
 957
 958                         in >> name;                             //read from first column
 959
 960             if (!dups) {//adjust name if needed
 961                 map<string, string>::iterator it = uniqueMap.find(name);
 962                 if (it != uniqueMap.end()) { name = it->second; }
 963             }
 964
 965                         //if this name is in the accnos file
 966                         if (names.count(name) != 0) {
 967                                 wroteSomething = true;
 968                                 selectedCount++;
 969
 970                                 out << name << '\t';
 971
 972                                 //read rest
 973                                 for (int i = 0; i < 15; i++) {
 974                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 975                                         else                    {       break;                  }
 976                                 }
 977                                 out << endl;
 978
 979                         }else {//still read just don't do anything with it
 980                                 //read rest
 981                                 for (int i = 0; i < 15; i++) {
 982                                         if (!in.eof())  {       in >> junk;             }
 983                                         else                    {       break;                  }
 984                                 }
 985                         }
 986
 987                         m->gobble(in);
 988                 }
 989                 in.close();
 990                 out.close();
 991
 992                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 993                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 994
 995                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
 996
 997                 return 0;
 998
 999         }
1000         catch(exception& e) {
1001                 m->errorOut(e, "GetSeqsCommand", "readAlign");
1002                 exit(1);
1003         }
1004 }
1005 //**********************************************************************************************************************
1006 //just looking at common mistakes.
1007 int GetSeqsCommand::runSanityCheck(){
1008         try {
1009         string thisOutputDir = outputDir;
1010         if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
1011         string filename = outputDir + "get.seqs.debug.report";
1012
1013         ofstream out;
1014                 m->openOutputFile(filename, out);
1015
1016
1017         //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
1018         if (fastafile != "") {
1019             if (namefile != "") { //compare with fasta
1020                 if (sanity["fasta"] != sanity["name"]) { //create mismatch file
1021                     createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
1022                 }
1023             }
1024             if (qualfile != "") {
1025                 if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
1026                     createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
1027                 }
1028             }
1029             if (taxfile != "") {
1030                 if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
1031                     createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
1032                 }
1033             }
1034         }
1035
1036         //compare dupnames, groups and list if given to make sure they match
1037         if (namefile != "") {
1038             if (groupfile != "") {
1039                 if (sanity["dupname"] != sanity["group"]) { //create mismatch file
1040                     createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
1041                 }
1042             }
1043             if (listfile != "") {
1044                 if (sanity["dupname"] != sanity["list"]) { //create mismatch file
1045                     createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
1046                 }
1047             }
1048         }else{
1049
1050             if ((groupfile != "") && (fastafile != "")) {
1051                 if (sanity["fasta"] != sanity["group"]) { //create mismatch file
1052                     createMisMatchFile(out, fastafile, groupfile, sanity["fasta"], sanity["group"]);
1053                 }
1054             }
1055         }
1056
1057         out.close();
1058
1059         if (m->isBlank(filename)) { m->mothurRemove(filename); }
1060         else { m->mothurOut("\n[DEBUG]: " + filename + " contains the file mismatches.\n");outputNames.push_back(filename); outputTypes["debug"].push_back(filename); }
1061
1062         return 0;
1063     }
1064         catch(exception& e) {
1065                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1066                 exit(1);
1067         }
1068 }
1069 //**********************************************************************************************************************
1070 //just looking at common mistakes.
1071 int GetSeqsCommand::createMisMatchFile(ofstream& out, string filename1, string filename2, set<string> set1, set<string> set2){
1072         try {
1073         out << "****************************************" << endl << endl;
1074         out << "Names unique to " << filename1 << ":\n";
1075
1076         //remove names in set1 that are also in set2
1077         for (set<string>::iterator it = set1.begin(); it != set1.end();) {
1078             string name = *it;
1079
1080             if (set2.count(name) == 0)  { out << name << endl;  } //name unique to set1
1081             else                        { set2.erase(name);     } //you are in both so erase
1082             set1.erase(it++);
1083         }
1084
1085         out << "\nNames unique to " << filename2 << ":\n";
1086         //output results
1087         for (set<string>::iterator it = set2.begin(); it != set2.end(); it++) {  out << *it << endl;  }
1088
1089         out << "****************************************" << endl << endl;
1090
1091         return 0;
1092     }
1093         catch(exception& e) {
1094                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1095                 exit(1);
1096         }
1097 }
1098 //**********************************************************************************************************************
1099
1100 int GetSeqsCommand::compareAccnos(){
1101         try {
1102
1103                 string thisOutputDir = outputDir;
1104                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
1105         map<string, string> variables;
1106                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile));
1107                 string outputFileName = getOutputFileName("accnosreport", variables);
1108
1109                 ofstream out;
1110                 m->openOutputFile(outputFileName, out);
1111
1112                 ifstream in;
1113                 m->openInputFile(accnosfile2, in);
1114                 string name;
1115
1116                 set<string> namesAccnos2;
1117                 set<string> namesDups;
1118                 set<string> namesAccnos = names;
1119
1120                 map<string, int> nameCount;
1121
1122                 if (namefile != "") {
1123                         ifstream inName;
1124                         m->openInputFile(namefile, inName);
1125
1126
1127                         while(!inName.eof()){
1128
1129                                 if (m->control_pressed) { inName.close(); return 0; }
1130
1131                                 string thisname, repnames;
1132
1133                                 inName >> thisname;             m->gobble(inName);              //read from first column
1134                                 inName >> repnames;                     //read from second column
1135
1136                                 int num = m->getNumNames(repnames);
1137                                 nameCount[thisname] = num;
1138
1139                                 m->gobble(inName);
1140                         }
1141                         inName.close();
1142                 }
1143
1144                 while(!in.eof()){
1145                         in >> name;
1146
1147                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
1148                                 int pos = name.find_last_of('_');
1149                                 string tempName = name;
1150                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
1151                                 if (namesAccnos.count(tempName) == 0){
1152                                         namesAccnos2.insert(name);
1153                                 }else { //you are in both so erase
1154                                         namesAccnos.erase(name);
1155                                         namesDups.insert(name);
1156                                 }
1157                         }else { //you are in both so erase
1158                                 namesAccnos.erase(name);
1159                                 namesDups.insert(name);
1160                         }
1161
1162                         m->gobble(in);
1163                 }
1164                 in.close();
1165
1166                 out << "Names in both files : " + toString(namesDups.size()) << endl;
1167                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
1168
1169                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
1170                         out << (*it);
1171                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1172                         out << endl;
1173                 }
1174
1175                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
1176                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
1177
1178                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
1179                         out << (*it);
1180                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1181                         out << endl;
1182                 }
1183
1184                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
1185                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
1186
1187                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
1188                         out << (*it);
1189                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1190                         out << endl;
1191                 }
1192
1193                 out.close();
1194
1195                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
1196
1197                 return 0;
1198
1199         }
1200         catch(exception& e) {
1201                 m->errorOut(e, "GetSeqsCommand", "compareAccnos");
1202                 exit(1);
1203         }
1204 }
1205
1206
1207 //**********************************************************************************************************************
1208