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 pfastq("fastq", "InputTypes", "", "", "none", "FNGLT", "none","fastq",false,false,true); parameters.push_back(pfastq);
  20         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
  21         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
  22                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
  23                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
  24                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
  25                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
  26                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
  27                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
  28                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  31                 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
  32
  33                 vector<string> myArray;
  34                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  35                 return myArray;
  36         }
  37         catch(exception& e) {
  38                 m->errorOut(e, "GetSeqsCommand", "setParameters");
  39                 exit(1);
  40         }
  41 }
  42 //**********************************************************************************************************************
  43 string GetSeqsCommand::getHelpString(){
  44         try {
  45                 string helpString = "";
  46                 helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality, fastq or alignreport file.\n";
  47                 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
  48                 helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport, fastq and dups.  You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
  49                 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";
  50                 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
  51                 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
  52                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  53                 return helpString;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetSeqsCommand", "getHelpString");
  57                 exit(1);
  58         }
  59 }
  60
  61 //**********************************************************************************************************************
  62 GetSeqsCommand::GetSeqsCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["fasta"] = tempOutNames;
  68         outputTypes["fastq"] = tempOutNames;
  69                 outputTypes["taxonomy"] = tempOutNames;
  70                 outputTypes["name"] = tempOutNames;
  71                 outputTypes["group"] = tempOutNames;
  72                 outputTypes["alignreport"] = tempOutNames;
  73                 outputTypes["list"] = tempOutNames;
  74                 outputTypes["qfile"] = tempOutNames;
  75         outputTypes["count"] = tempOutNames;
  76                 outputTypes["accnosreport"] = tempOutNames;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 string GetSeqsCommand::getOutputPattern(string type) {
  85     try {
  86         string pattern = "";
  87
  88         if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
  89         else if (type == "fastq")       {   pattern = "[filename],pick,[extension]";    }
  90         else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
  91         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
  92         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  93         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  94         else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
  95         else if (type == "qfile")       {   pattern = "[filename],pick,[extension]";    }
  96         else if (type == "accnosreport")      {   pattern = "[filename],pick.accnos.report";    }
  97         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
  98         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  99
 100         return pattern;
 101     }
 102     catch(exception& e) {
 103         m->errorOut(e, "GetSeqsCommand", "getOutputPattern");
 104         exit(1);
 105     }
 106 }
 107 //**********************************************************************************************************************
 108 GetSeqsCommand::GetSeqsCommand(string option)  {
 109         try {
 110                 abort = false; calledHelp = false;
 111
 112                 //allow user to run help
 113                 if(option == "help") { help(); abort = true; calledHelp = true; }
 114                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 115
 116                 else {
 117                         vector<string> myArray = setParameters();
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter;
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         //initialize outputTypes
 131                         vector<string> tempOutNames;
 132                         outputTypes["fasta"] = tempOutNames;
 133             outputTypes["fastq"] = tempOutNames;
 134                         outputTypes["taxonomy"] = tempOutNames;
 135                         outputTypes["name"] = tempOutNames;
 136                         outputTypes["group"] = tempOutNames;
 137                         outputTypes["alignreport"] = tempOutNames;
 138                         outputTypes["list"] = tempOutNames;
 139                         outputTypes["qfile"] = tempOutNames;
 140                         outputTypes["accnosreport"] = tempOutNames;
 141             outputTypes["count"] = tempOutNames;
 142
 143                         //if the user changes the output directory command factory will send this info to us in the output parameter
 144                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 145
 146                         //if the user changes the input directory command factory will send this info to us in the output parameter
 147                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 148                         if (inputDir == "not found"){   inputDir = "";          }
 149                         else {
 150                                 string path;
 151                                 it = parameters.find("alignreport");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 157                                 }
 158
 159                                 it = parameters.find("fasta");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 165                                 }
 166
 167                                 it = parameters.find("accnos");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 173                                 }
 174
 175                                 it = parameters.find("accnos2");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["accnos2"] = inputDir + it->second;          }
 181                                 }
 182
 183                                 it = parameters.find("list");
 184                                 //user has given a template file
 185                                 if(it != parameters.end()){
 186                                         path = m->hasPath(it->second);
 187                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 189                                 }
 190
 191                                 it = parameters.find("name");
 192                                 //user has given a template file
 193                                 if(it != parameters.end()){
 194                                         path = m->hasPath(it->second);
 195                                         //if the user has not given a path then, add inputdir. else leave path alone.
 196                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 197                                 }
 198
 199                                 it = parameters.find("group");
 200                                 //user has given a template file
 201                                 if(it != parameters.end()){
 202                                         path = m->hasPath(it->second);
 203                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 205                                 }
 206
 207                                 it = parameters.find("taxonomy");
 208                                 //user has given a template file
 209                                 if(it != parameters.end()){
 210                                         path = m->hasPath(it->second);
 211                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 213                                 }
 214
 215                                 it = parameters.find("qfile");
 216                                 //user has given a template file
 217                                 if(it != parameters.end()){
 218                                         path = m->hasPath(it->second);
 219                                         //if the user has not given a path then, add inputdir. else leave path alone.
 220                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 221                                 }
 222
 223                 it = parameters.find("count");
 224                                 //user has given a template file
 225                                 if(it != parameters.end()){
 226                                         path = m->hasPath(it->second);
 227                                         //if the user has not given a path then, add inputdir. else leave path alone.
 228                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 229                                 }
 230
 231                 it = parameters.find("fastq");
 232                                 //user has given a template file
 233                                 if(it != parameters.end()){
 234                                         path = m->hasPath(it->second);
 235                                         //if the user has not given a path then, add inputdir. else leave path alone.
 236                                         if (path == "") {       parameters["fastq"] = inputDir + it->second;            }
 237                                 }
 238                         }
 239
 240
 241                         //check for required parameters
 242                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 243                         if (accnosfile == "not open") { abort = true; }
 244                         else if (accnosfile == "not found") {
 245                                 accnosfile = m->getAccnosFile();
 246                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 247                                 else {
 248                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 249                                         abort = true;
 250                                 }
 251                         }else { m->setAccnosFile(accnosfile); }
 252
 253                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 254
 255                         fastafile = validParameter.validFile(parameters, "fasta", true);
 256                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 257                         else if (fastafile == "not found") {  fastafile = "";  }
 258                         else { m->setFastaFile(fastafile); }
 259
 260                         namefile = validParameter.validFile(parameters, "name", true);
 261                         if (namefile == "not open") { namefile = ""; abort = true; }
 262                         else if (namefile == "not found") {  namefile = "";  }
 263                         else { m->setNameFile(namefile); }
 264
 265                         groupfile = validParameter.validFile(parameters, "group", true);
 266                         if (groupfile == "not open") { abort = true; }
 267                         else if (groupfile == "not found") {  groupfile = "";  }
 268                         else { m->setGroupFile(groupfile); }
 269
 270                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 271                         if (alignfile == "not open") { abort = true; }
 272                         else if (alignfile == "not found") {  alignfile = "";  }
 273
 274                         listfile = validParameter.validFile(parameters, "list", true);
 275                         if (listfile == "not open") { abort = true; }
 276                         else if (listfile == "not found") {  listfile = "";  }
 277                         else { m->setListFile(listfile); }
 278
 279                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 280                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 281                         else if (taxfile == "not found") {  taxfile = "";  }
 282                         else { m->setTaxonomyFile(taxfile); }
 283
 284                         qualfile = validParameter.validFile(parameters, "qfile", true);
 285                         if (qualfile == "not open") { abort = true; }
 286                         else if (qualfile == "not found") {  qualfile = "";  }
 287                         else { m->setQualFile(qualfile); }
 288
 289             fastqfile = validParameter.validFile(parameters, "fastq", true);
 290                         if (fastqfile == "not open") { abort = true; }
 291                         else if (fastqfile == "not found") {  fastqfile = "";  }
 292
 293                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 294                         if (accnosfile2 == "not open") { abort = true; }
 295                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 296
 297             countfile = validParameter.validFile(parameters, "count", true);
 298             if (countfile == "not open") { countfile = ""; abort = true; }
 299             else if (countfile == "not found") { countfile = "";  }
 300             else { m->setCountTableFile(countfile); }
 301
 302             if ((namefile != "") && (countfile != "")) {
 303                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 304             }
 305
 306             if ((groupfile != "") && (countfile != "")) {
 307                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 308             }
 309
 310
 311                         string usedDups = "true";
 312                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 313                         dups = m->isTrue(temp);
 314
 315                         if ((fastqfile == "") && (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, fastq or listfile."); m->mothurOutEndLine(); abort = true; }
 316
 317             if (countfile == "") {
 318                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 319                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 320                     parser.getNameFile(files);
 321                 }
 322             }
 323                 }
 324
 325         }
 326         catch(exception& e) {
 327                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 328                 exit(1);
 329         }
 330 }
 331 //**********************************************************************************************************************
 332
 333 int GetSeqsCommand::execute(){
 334         try {
 335
 336                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 337
 338                 //get names you want to keep
 339                 names = m->readAccnos(accnosfile);
 340
 341                 if (m->control_pressed) { return 0; }
 342
 343         if (countfile != "") {
 344             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 345                 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");
 346             }
 347         }
 348
 349                 //read through the correct file and output lines you want to keep
 350                 if (namefile != "")                     {               readName();                     }
 351                 if (fastafile != "")            {               readFasta();            }
 352         if (fastqfile != "")            {               readFastq();            }
 353                 if (groupfile != "")            {               readGroup();            }
 354         if (countfile != "")            {               readCount();            }
 355                 if (alignfile != "")            {               readAlign();            }
 356                 if (listfile != "")                     {               readList();                     }
 357                 if (taxfile != "")                      {               readTax();                      }
 358                 if (qualfile != "")                     {               readQual();                     }
 359                 if (accnosfile2 != "")          {               compareAccnos();        }
 360
 361         if (m->debug) { runSanityCheck(); }
 362
 363                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 364
 365
 366                 if (outputNames.size() != 0) {
 367                         m->mothurOutEndLine();
 368                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 369                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 370                         m->mothurOutEndLine();
 371
 372                         //set fasta file as new current fastafile
 373                         string current = "";
 374                         itTypes = outputTypes.find("fasta");
 375                         if (itTypes != outputTypes.end()) {
 376                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 377                         }
 378
 379                         itTypes = outputTypes.find("name");
 380                         if (itTypes != outputTypes.end()) {
 381                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 382                         }
 383
 384                         itTypes = outputTypes.find("group");
 385                         if (itTypes != outputTypes.end()) {
 386                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 387                         }
 388
 389                         itTypes = outputTypes.find("list");
 390                         if (itTypes != outputTypes.end()) {
 391                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 392                         }
 393
 394                         itTypes = outputTypes.find("taxonomy");
 395                         if (itTypes != outputTypes.end()) {
 396                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 397                         }
 398
 399                         itTypes = outputTypes.find("qfile");
 400                         if (itTypes != outputTypes.end()) {
 401                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 402                         }
 403
 404             itTypes = outputTypes.find("count");
 405                         if (itTypes != outputTypes.end()) {
 406                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 407                         }
 408                 }
 409
 410                 return 0;
 411         }
 412
 413         catch(exception& e) {
 414                 m->errorOut(e, "GetSeqsCommand", "execute");
 415                 exit(1);
 416         }
 417 }
 418 //**********************************************************************************************************************
 419 int GetSeqsCommand::readFastq(){
 420         try {
 421                 bool wroteSomething = false;
 422                 int selectedCount = 0;
 423
 424                 ifstream in;
 425                 m->openInputFile(fastqfile, in);
 426
 427                 string thisOutputDir = outputDir;
 428                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastqfile);  }
 429                 map<string, string> variables;
 430         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastqfile));
 431         variables["[extension]"] = m->getExtension(fastqfile);
 432                 string outputFileName = getOutputFileName("fastq", variables);
 433                 ofstream out;
 434                 m->openOutputFile(outputFileName, out);
 435
 436
 437                 while(!in.eof()){
 438
 439                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
 440
 441                         //read sequence name
 442                         string input = m->getline(in); m->gobble(in);
 443
 444             string outputString = input + "\n";
 445
 446                         if (input[0] == '@') {
 447                 //get rest of lines
 448                 outputString += m->getline(in) + "\n"; m->gobble(in);
 449                 outputString += m->getline(in) + "\n"; m->gobble(in);
 450                 outputString += m->getline(in) + "\n"; m->gobble(in);
 451
 452                 vector<string> splits = m->splitWhiteSpace(input);
 453                 string name = splits[0];
 454                 name = name.substr(1);
 455                 m->checkName(name);
 456
 457                 if (names.count(name) != 0) {
 458                                         wroteSomething = true;
 459                     selectedCount++;
 460                     out << outputString;
 461                 }
 462             }
 463
 464                         m->gobble(in);
 465                 }
 466                 in.close();
 467                 out.close();
 468
 469
 470                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 471                 outputNames.push_back(outputFileName);  outputTypes["fastq"].push_back(outputFileName);
 472
 473                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fastq file."); m->mothurOutEndLine();
 474
 475                 return 0;
 476
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "GetSeqsCommand", "readFastq");
 480                 exit(1);
 481         }
 482 }
 483
 484 //**********************************************************************************************************************
 485 int GetSeqsCommand::readFasta(){
 486         try {
 487                 string thisOutputDir = outputDir;
 488                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 489                 map<string, string> variables;
 490         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 491         variables["[extension]"] = m->getExtension(fastafile);
 492                 string outputFileName = getOutputFileName("fasta", variables);
 493                 ofstream out;
 494                 m->openOutputFile(outputFileName, out);
 495
 496
 497                 ifstream in;
 498                 m->openInputFile(fastafile, in);
 499                 string name;
 500
 501                 bool wroteSomething = false;
 502                 int selectedCount = 0;
 503
 504         if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
 505
 506                 while(!in.eof()){
 507
 508                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 509
 510                         Sequence currSeq(in);
 511                         name = currSeq.getName();
 512
 513             if (!dups) {//adjust name if needed
 514                 map<string, string>::iterator it = uniqueMap.find(name);
 515                 if (it != uniqueMap.end()) { currSeq.setName(it->second); }
 516             }
 517
 518             name = currSeq.getName();
 519
 520                         if (name != "") {
 521                                 //if this name is in the accnos file
 522                                 if (names.count(name) != 0) {
 523                                         wroteSomething = true;
 524
 525                                         currSeq.printSequence(out);
 526                                         selectedCount++;
 527
 528                     if (m->debug) { sanity["fasta"].insert(name); }
 529                                 }
 530                         }
 531                         m->gobble(in);
 532                 }
 533                 in.close();
 534                 out.close();
 535
 536
 537                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 538                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 539
 540                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 541
 542                 return 0;
 543
 544         }
 545         catch(exception& e) {
 546                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 547                 exit(1);
 548         }
 549 }
 550 //**********************************************************************************************************************
 551 int GetSeqsCommand::readQual(){
 552         try {
 553                 string thisOutputDir = outputDir;
 554                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 555                 map<string, string> variables;
 556         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
 557         variables["[extension]"] = m->getExtension(qualfile);
 558                 string outputFileName = getOutputFileName("qfile", variables);
 559                 ofstream out;
 560                 m->openOutputFile(outputFileName, out);
 561
 562
 563                 ifstream in;
 564                 m->openInputFile(qualfile, in);
 565                 string name;
 566
 567                 bool wroteSomething = false;
 568                 int selectedCount = 0;
 569
 570         if (m->debug) { set<string> temp; sanity["qual"] = temp; }
 571
 572                 while(!in.eof()){
 573                         string saveName = "";
 574                         string name = "";
 575                         string scores = "";
 576
 577                         in >> name;
 578
 579             if (!dups) {//adjust name if needed
 580                 map<string, string>::iterator it = uniqueMap.find(name);
 581                 if (it != uniqueMap.end()) { name = it->second; }
 582             }
 583
 584                         if (name.length() != 0) {
 585                                 saveName = name.substr(1);
 586                                 while (!in.eof())       {
 587                                         char c = in.get();
 588                                         if (c == 10 || c == 13 || c == -1){     break;  }
 589                                         else { name += c; }
 590                                 }
 591                                 m->gobble(in);
 592                         }
 593
 594                         while(in){
 595                                 char letter= in.get();
 596                                 if(letter == '>'){      in.putback(letter);     break;  }
 597                                 else{ scores += letter; }
 598                         }
 599
 600                         m->gobble(in);
 601
 602                         if (names.count(saveName) != 0) {
 603                                 wroteSomething = true;
 604
 605                                 out << name << endl << scores;
 606                                 selectedCount++;
 607                 if (m->debug) { sanity["qual"].insert(name); }
 608                         }
 609
 610                         m->gobble(in);
 611                 }
 612                 in.close();
 613                 out.close();
 614
 615
 616                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 617                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 618
 619                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
 620
 621
 622                 return 0;
 623
 624         }
 625         catch(exception& e) {
 626                 m->errorOut(e, "GetSeqsCommand", "readQual");
 627                 exit(1);
 628         }
 629 }
 630 //**********************************************************************************************************************
 631 int GetSeqsCommand::readCount(){
 632         try {
 633                 string thisOutputDir = outputDir;
 634                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 635                 map<string, string> variables;
 636                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 637         variables["[extension]"] = m->getExtension(countfile);
 638                 string outputFileName = getOutputFileName("count", variables);
 639
 640                 ofstream out;
 641                 m->openOutputFile(outputFileName, out);
 642
 643                 ifstream in;
 644                 m->openInputFile(countfile, in);
 645
 646                 bool wroteSomething = false;
 647                 int selectedCount = 0;
 648
 649         string headers = m->getline(in); m->gobble(in);
 650         out << headers << endl;
 651
 652         string name, rest; int thisTotal;
 653         while (!in.eof()) {
 654
 655             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 656
 657             in >> name; m->gobble(in);
 658             in >> thisTotal; m->gobble(in);
 659             rest = m->getline(in); m->gobble(in);
 660             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 661
 662             if (names.count(name) != 0) {
 663                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 664                 wroteSomething = true;
 665                 selectedCount+= thisTotal;
 666             }
 667         }
 668         in.close();
 669                 out.close();
 670
 671         //check for groups that have been eliminated
 672         CountTable ct;
 673         if (ct.testGroups(outputFileName)) {
 674             ct.readTable(outputFileName, true, false);
 675             ct.printTable(outputFileName);
 676         }
 677
 678                 if (wroteSomething == false) {  m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 679                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 680
 681                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
 682
 683                 return 0;
 684         }
 685         catch(exception& e) {
 686                 m->errorOut(e, "GetSeqsCommand", "readCount");
 687                 exit(1);
 688         }
 689 }
 690
 691 //**********************************************************************************************************************
 692 int GetSeqsCommand::readList(){
 693         try {
 694                 string thisOutputDir = outputDir;
 695                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 696         map<string, string> variables;
 697                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 698         variables["[extension]"] = m->getExtension(listfile);
 699                 string outputFileName = getOutputFileName("list", variables);
 700                 ofstream out;
 701                 m->openOutputFile(outputFileName, out);
 702
 703                 ifstream in;
 704                 m->openInputFile(listfile, in);
 705
 706                 bool wroteSomething = false;
 707                 int selectedCount = 0;
 708
 709         if (m->debug) { set<string> temp; sanity["list"] = temp; }
 710
 711                 while(!in.eof()){
 712
 713                         selectedCount = 0;
 714
 715                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 716
 717                         //read in list vector
 718                         ListVector list(in);
 719
 720                         //make a new list vector
 721                         ListVector newList;
 722                         newList.setLabel(list.getLabel());
 723
 724                         //for each bin
 725                         for (int i = 0; i < list.getNumBins(); i++) {
 726
 727                                 //parse out names that are in accnos file
 728                                 string binnames = list.get(i);
 729                 vector<string> bnames;
 730                 m->splitAtComma(binnames, bnames);
 731
 732                                 string newNames = "";
 733                 for (int i = 0; i < bnames.size(); i++) {
 734                                         string name = bnames[i];
 735                                         //if that name is in the .accnos file, add it
 736                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
 737                                 }
 738
 739                                 //if there are names in this bin add to new list
 740                                 if (newNames != "") {
 741                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 742                                         newList.push_back(newNames);
 743                                 }
 744                         }
 745
 746                         //print new listvector
 747                         if (newList.getNumBins() != 0) {
 748                                 wroteSomething = true;
 749                                 newList.print(out);
 750                         }
 751
 752                         m->gobble(in);
 753                 }
 754                 in.close();
 755                 out.close();
 756
 757                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 758                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 759
 760                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 761
 762                 return 0;
 763
 764         }
 765         catch(exception& e) {
 766                 m->errorOut(e, "GetSeqsCommand", "readList");
 767                 exit(1);
 768         }
 769 }
 770 //**********************************************************************************************************************
 771 int GetSeqsCommand::readName(){
 772         try {
 773                 string thisOutputDir = outputDir;
 774                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 775         map<string, string> variables;
 776                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 777         variables["[extension]"] = m->getExtension(namefile);
 778                 string outputFileName = getOutputFileName("name", variables);
 779                 ofstream out;
 780                 m->openOutputFile(outputFileName, out);
 781
 782
 783                 ifstream in;
 784                 m->openInputFile(namefile, in);
 785                 string name, firstCol, secondCol;
 786
 787                 bool wroteSomething = false;
 788                 int selectedCount = 0;
 789
 790         if (m->debug) { set<string> temp; sanity["name"] = temp; }
 791         if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
 792
 793                 while(!in.eof()){
 794
 795                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 796
 797                         in >> firstCol;                 m->gobble(in);
 798                         in >> secondCol;
 799
 800                         string hold = "";
 801                         if (dups) { hold = secondCol; }
 802
 803                         vector<string> parsedNames;
 804                         m->splitAtComma(secondCol, parsedNames);
 805
 806                         vector<string> validSecond;
 807                         for (int i = 0; i < parsedNames.size(); i++) {
 808                                 if (names.count(parsedNames[i]) != 0) {
 809                                         validSecond.push_back(parsedNames[i]);
 810                     if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
 811                                 }
 812                         }
 813
 814                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 815                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
 816                                 out << firstCol << '\t' << hold << endl;
 817                                 wroteSomething = true;
 818                                 selectedCount += parsedNames.size();
 819                 if (m->debug) { sanity["name"].insert(firstCol); }
 820                         }else {
 821
 822                                 selectedCount += validSecond.size();
 823
 824                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 825                                 if (names.count(firstCol) != 0) {
 826
 827                                         wroteSomething = true;
 828
 829                                         out << firstCol << '\t';
 830
 831                                         //you know you have at least one valid second since first column is valid
 832                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 833                                         out << validSecond[validSecond.size()-1] << endl;
 834
 835                     if (m->debug) { sanity["name"].insert(firstCol); }
 836
 837
 838                                 //make first name in set you come to first column and then add the remaining names to second column
 839                                 }else {
 840
 841                                         //you want part of this row
 842                                         if (validSecond.size() != 0) {
 843
 844                                                 wroteSomething = true;
 845
 846                                                 out << validSecond[0] << '\t';
 847                         //we are changing the unique name in the fasta file
 848                         uniqueMap[firstCol] = validSecond[0];
 849
 850                                                 //you know you have at least one valid second since first column is valid
 851                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 852                                                 out << validSecond[validSecond.size()-1] << endl;
 853
 854                         if (m->debug) { sanity["name"].insert(validSecond[0]); }
 855                                         }
 856                                 }
 857                         }
 858                         m->gobble(in);
 859                 }
 860                 in.close();
 861                 out.close();
 862
 863                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 864                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 865
 866                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 867
 868                 return 0;
 869
 870         }
 871         catch(exception& e) {
 872                 m->errorOut(e, "GetSeqsCommand", "readName");
 873                 exit(1);
 874         }
 875 }
 876
 877 //**********************************************************************************************************************
 878 int GetSeqsCommand::readGroup(){
 879         try {
 880                 string thisOutputDir = outputDir;
 881                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 882                 map<string, string> variables;
 883                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 884         variables["[extension]"] = m->getExtension(groupfile);
 885                 string outputFileName = getOutputFileName("group", variables);
 886                 ofstream out;
 887                 m->openOutputFile(outputFileName, out);
 888
 889
 890                 ifstream in;
 891                 m->openInputFile(groupfile, in);
 892                 string name, group;
 893
 894                 bool wroteSomething = false;
 895                 int selectedCount = 0;
 896
 897         if (m->debug) { set<string> temp; sanity["group"] = temp; }
 898
 899                 while(!in.eof()){
 900
 901                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 902
 903
 904                         in >> name;                             //read from first column
 905                         in >> group;                    //read from second column
 906
 907
 908                         //if this name is in the accnos file
 909                         if (names.count(name) != 0) {
 910                                 wroteSomething = true;
 911
 912                                 out << name << '\t' << group << endl;
 913                                 selectedCount++;
 914
 915                 if (m->debug) {  sanity["group"].insert(name); }
 916                         }
 917
 918                         m->gobble(in);
 919                 }
 920                 in.close();
 921                 out.close();
 922
 923                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 924                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 925
 926                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 927
 928
 929                 return 0;
 930
 931         }
 932         catch(exception& e) {
 933                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 934                 exit(1);
 935         }
 936 }
 937 //**********************************************************************************************************************
 938 int GetSeqsCommand::readTax(){
 939         try {
 940                 string thisOutputDir = outputDir;
 941                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 942                 map<string, string> variables;
 943                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
 944         variables["[extension]"] = m->getExtension(taxfile);
 945                 string outputFileName = getOutputFileName("taxonomy", variables);
 946                 ofstream out;
 947                 m->openOutputFile(outputFileName, out);
 948
 949                 ifstream in;
 950                 m->openInputFile(taxfile, in);
 951                 string name, tax;
 952
 953                 bool wroteSomething = false;
 954                 int selectedCount = 0;
 955
 956         if (m->debug) { set<string> temp; sanity["tax"] = temp; }
 957
 958                 while(!in.eof()){
 959
 960                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 961
 962                         in >> name;                             //read from first column
 963                         in >> tax;                      //read from second column
 964
 965             if (!dups) {//adjust name if needed
 966                 map<string, string>::iterator it = uniqueMap.find(name);
 967                 if (it != uniqueMap.end()) { name = it->second; }
 968             }
 969
 970                         //if this name is in the accnos file
 971                         if (names.count(name) != 0) {
 972                                 wroteSomething = true;
 973
 974                                 out << name << '\t' << tax << endl;
 975                                 selectedCount++;
 976
 977                 if (m->debug) { sanity["tax"].insert(name); }
 978                         }
 979
 980                         m->gobble(in);
 981                 }
 982                 in.close();
 983                 out.close();
 984
 985                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 986                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 987
 988                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 989
 990                 return 0;
 991
 992         }
 993         catch(exception& e) {
 994                 m->errorOut(e, "GetSeqsCommand", "readTax");
 995                 exit(1);
 996         }
 997 }
 998 //**********************************************************************************************************************
 999 //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
1000 int GetSeqsCommand::readAlign(){
1001         try {
1002                 string thisOutputDir = outputDir;
1003                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
1004         map<string, string> variables;
1005                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
1006                 string outputFileName = getOutputFileName("alignreport", variables);
1007                 ofstream out;
1008                 m->openOutputFile(outputFileName, out);
1009
1010
1011                 ifstream in;
1012                 m->openInputFile(alignfile, in);
1013                 string name, junk;
1014
1015                 bool wroteSomething = false;
1016                 int selectedCount = 0;
1017
1018                 //read column headers
1019                 for (int i = 0; i < 16; i++) {
1020                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
1021                         else                    {       break;                  }
1022                 }
1023                 out << endl;
1024
1025                 while(!in.eof()){
1026
1027                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
1028
1029
1030                         in >> name;                             //read from first column
1031
1032             if (!dups) {//adjust name if needed
1033                 map<string, string>::iterator it = uniqueMap.find(name);
1034                 if (it != uniqueMap.end()) { name = it->second; }
1035             }
1036
1037                         //if this name is in the accnos file
1038                         if (names.count(name) != 0) {
1039                                 wroteSomething = true;
1040                                 selectedCount++;
1041
1042                                 out << name << '\t';
1043
1044                                 //read rest
1045                                 for (int i = 0; i < 15; i++) {
1046                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
1047                                         else                    {       break;                  }
1048                                 }
1049                                 out << endl;
1050
1051                         }else {//still read just don't do anything with it
1052                                 //read rest
1053                                 for (int i = 0; i < 15; i++) {
1054                                         if (!in.eof())  {       in >> junk;             }
1055                                         else                    {       break;                  }
1056                                 }
1057                         }
1058
1059                         m->gobble(in);
1060                 }
1061                 in.close();
1062                 out.close();
1063
1064                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
1065                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
1066
1067                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
1068
1069                 return 0;
1070
1071         }
1072         catch(exception& e) {
1073                 m->errorOut(e, "GetSeqsCommand", "readAlign");
1074                 exit(1);
1075         }
1076 }
1077 //**********************************************************************************************************************
1078 //just looking at common mistakes.
1079 int GetSeqsCommand::runSanityCheck(){
1080         try {
1081         string thisOutputDir = outputDir;
1082         if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
1083         string filename = outputDir + "get.seqs.debug.report";
1084
1085         ofstream out;
1086                 m->openOutputFile(filename, out);
1087
1088
1089         //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
1090         if (fastafile != "") {
1091             if (namefile != "") { //compare with fasta
1092                 if (sanity["fasta"] != sanity["name"]) { //create mismatch file
1093                     createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
1094                 }
1095             }
1096             if (qualfile != "") {
1097                 if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
1098                     createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
1099                 }
1100             }
1101             if (taxfile != "") {
1102                 if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
1103                     createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
1104                 }
1105             }
1106         }
1107
1108         //compare dupnames, groups and list if given to make sure they match
1109         if (namefile != "") {
1110             if (groupfile != "") {
1111                 if (sanity["dupname"] != sanity["group"]) { //create mismatch file
1112                     createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
1113                 }
1114             }
1115             if (listfile != "") {
1116                 if (sanity["dupname"] != sanity["list"]) { //create mismatch file
1117                     createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
1118                 }
1119             }
1120         }else{
1121
1122             if ((groupfile != "") && (fastafile != "")) {
1123                 if (sanity["fasta"] != sanity["group"]) { //create mismatch file
1124                     createMisMatchFile(out, fastafile, groupfile, sanity["fasta"], sanity["group"]);
1125                 }
1126             }
1127         }
1128
1129         out.close();
1130
1131         if (m->isBlank(filename)) { m->mothurRemove(filename); }
1132         else { m->mothurOut("\n[DEBUG]: " + filename + " contains the file mismatches.\n");outputNames.push_back(filename); outputTypes["debug"].push_back(filename); }
1133
1134         return 0;
1135     }
1136         catch(exception& e) {
1137                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1138                 exit(1);
1139         }
1140 }
1141 //**********************************************************************************************************************
1142 //just looking at common mistakes.
1143 int GetSeqsCommand::createMisMatchFile(ofstream& out, string filename1, string filename2, set<string> set1, set<string> set2){
1144         try {
1145         out << "****************************************" << endl << endl;
1146         out << "Names unique to " << filename1 << ":\n";
1147
1148         //remove names in set1 that are also in set2
1149         for (set<string>::iterator it = set1.begin(); it != set1.end();) {
1150             string name = *it;
1151
1152             if (set2.count(name) == 0)  { out << name << endl;  } //name unique to set1
1153             else                        { set2.erase(name);     } //you are in both so erase
1154             set1.erase(it++);
1155         }
1156
1157         out << "\nNames unique to " << filename2 << ":\n";
1158         //output results
1159         for (set<string>::iterator it = set2.begin(); it != set2.end(); it++) {  out << *it << endl;  }
1160
1161         out << "****************************************" << endl << endl;
1162
1163         return 0;
1164     }
1165         catch(exception& e) {
1166                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1167                 exit(1);
1168         }
1169 }
1170 //**********************************************************************************************************************
1171
1172 int GetSeqsCommand::compareAccnos(){
1173         try {
1174
1175                 string thisOutputDir = outputDir;
1176                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
1177         map<string, string> variables;
1178                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile));
1179                 string outputFileName = getOutputFileName("accnosreport", variables);
1180
1181                 ofstream out;
1182                 m->openOutputFile(outputFileName, out);
1183
1184                 ifstream in;
1185                 m->openInputFile(accnosfile2, in);
1186                 string name;
1187
1188                 set<string> namesAccnos2;
1189                 set<string> namesDups;
1190                 set<string> namesAccnos = names;
1191
1192                 map<string, int> nameCount;
1193
1194                 if (namefile != "") {
1195                         ifstream inName;
1196                         m->openInputFile(namefile, inName);
1197
1198
1199                         while(!inName.eof()){
1200
1201                                 if (m->control_pressed) { inName.close(); return 0; }
1202
1203                                 string thisname, repnames;
1204
1205                                 inName >> thisname;             m->gobble(inName);              //read from first column
1206                                 inName >> repnames;                     //read from second column
1207
1208                                 int num = m->getNumNames(repnames);
1209                                 nameCount[thisname] = num;
1210
1211                                 m->gobble(inName);
1212                         }
1213                         inName.close();
1214                 }
1215
1216                 while(!in.eof()){
1217                         in >> name;
1218
1219                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
1220                                 int pos = name.find_last_of('_');
1221                                 string tempName = name;
1222                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
1223                                 if (namesAccnos.count(tempName) == 0){
1224                                         namesAccnos2.insert(name);
1225                                 }else { //you are in both so erase
1226                                         namesAccnos.erase(name);
1227                                         namesDups.insert(name);
1228                                 }
1229                         }else { //you are in both so erase
1230                                 namesAccnos.erase(name);
1231                                 namesDups.insert(name);
1232                         }
1233
1234                         m->gobble(in);
1235                 }
1236                 in.close();
1237
1238                 out << "Names in both files : " + toString(namesDups.size()) << endl;
1239                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
1240
1241                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
1242                         out << (*it);
1243                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1244                         out << endl;
1245                 }
1246
1247                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
1248                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
1249
1250                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
1251                         out << (*it);
1252                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1253                         out << endl;
1254                 }
1255
1256                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
1257                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
1258
1259                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
1260                         out << (*it);
1261                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1262                         out << endl;
1263                 }
1264
1265                 out.close();
1266
1267                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
1268
1269                 return 0;
1270
1271         }
1272         catch(exception& e) {
1273                 m->errorOut(e, "GetSeqsCommand", "compareAccnos");
1274                 exit(1);
1275         }
1276 }
1277
1278
1279 //**********************************************************************************************************************
1280