removeseqscommand.cpp

   1 /*
   2  *  removeseqscommand.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 "removeseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14 //**********************************************************************************************************************
  15 vector<string> RemoveSeqsCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "qfile","list","taxonomy","outputdir","inputdir", "dups" };
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "RemoveSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 RemoveSeqsCommand::RemoveSeqsCommand(){
  28         try {
  29                 abort = true; calledHelp = true;
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32                 outputTypes["taxonomy"] = tempOutNames;
  33                 outputTypes["name"] = tempOutNames;
  34                 outputTypes["group"] = tempOutNames;
  35                 outputTypes["alignreport"] = tempOutNames;
  36                 outputTypes["list"] = tempOutNames;
  37                 outputTypes["qfile"] = tempOutNames;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 vector<string> RemoveSeqsCommand::getRequiredParameters(){
  46         try {
  47                 string Array[] =  {"accnos"};
  48                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> RemoveSeqsCommand::getRequiredFiles(){
  58         try {
  59                 vector<string> myArray;
  60                 return myArray;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
  69         try {
  70                 abort = false; calledHelp = false;
  71
  72                 //allow user to run help
  73                 if(option == "help") { help(); abort = true; calledHelp = true; }
  74
  75                 else {
  76                         //valid paramters for this command
  77                         string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "qfile", "list","taxonomy","outputdir","inputdir", "dups" };
  78                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  79
  80                         OptionParser parser(option);
  81                         map<string,string> parameters = parser.getParameters();
  82
  83                         ValidParameters validParameter;
  84                         map<string,string>::iterator it;
  85
  86                         //check to make sure all parameters are valid for command
  87                         for (it = parameters.begin(); it != parameters.end(); it++) {
  88                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  89                         }
  90
  91                         //initialize outputTypes
  92                         vector<string> tempOutNames;
  93                         outputTypes["fasta"] = tempOutNames;
  94                         outputTypes["taxonomy"] = tempOutNames;
  95                         outputTypes["name"] = tempOutNames;
  96                         outputTypes["group"] = tempOutNames;
  97                         outputTypes["alignreport"] = tempOutNames;
  98                         outputTypes["list"] = tempOutNames;
  99                         outputTypes["qfile"] = tempOutNames;
 100
 101                         //if the user changes the output directory command factory will send this info to us in the output parameter
 102                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 103
 104                         //if the user changes the input directory command factory will send this info to us in the output parameter
 105                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 106                         if (inputDir == "not found"){   inputDir = "";          }
 107                         else {
 108                                 string path;
 109                                 it = parameters.find("alignreport");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 115                                 }
 116
 117                                 it = parameters.find("fasta");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 123                                 }
 124
 125                                 it = parameters.find("accnos");
 126                                 //user has given a template file
 127                                 if(it != parameters.end()){
 128                                         path = m->hasPath(it->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 131                                 }
 132
 133                                 it = parameters.find("list");
 134                                 //user has given a template file
 135                                 if(it != parameters.end()){
 136                                         path = m->hasPath(it->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 139                                 }
 140
 141                                 it = parameters.find("name");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 147                                 }
 148
 149                                 it = parameters.find("group");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 155                                 }
 156
 157                                 it = parameters.find("taxonomy");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 163                                 }
 164
 165                                 it = parameters.find("qfile");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 171                                 }
 172                         }
 173
 174
 175                         //check for required parameters
 176                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 177                         if (accnosfile == "not open") { abort = true; }
 178                         else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
 179
 180                         fastafile = validParameter.validFile(parameters, "fasta", true);
 181                         if (fastafile == "not open") { abort = true; }
 182                         else if (fastafile == "not found") {  fastafile = "";  }
 183
 184                         namefile = validParameter.validFile(parameters, "name", true);
 185                         if (namefile == "not open") { abort = true; }
 186                         else if (namefile == "not found") {  namefile = "";  }
 187
 188                         groupfile = validParameter.validFile(parameters, "group", true);
 189                         if (groupfile == "not open") { abort = true; }
 190                         else if (groupfile == "not found") {  groupfile = "";  }
 191
 192                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 193                         if (alignfile == "not open") { abort = true; }
 194                         else if (alignfile == "not found") {  alignfile = "";  }
 195
 196                         listfile = validParameter.validFile(parameters, "list", true);
 197                         if (listfile == "not open") { abort = true; }
 198                         else if (listfile == "not found") {  listfile = "";  }
 199
 200                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 201                         if (taxfile == "not open") { abort = true; }
 202                         else if (taxfile == "not found") {  taxfile = "";  }
 203
 204                         qualfile = validParameter.validFile(parameters, "qfile", true);
 205                         if (qualfile == "not open") { abort = true; }
 206                         else if (qualfile == "not found") {  qualfile = "";  }
 207
 208
 209                         string usedDups = "true";
 210                         string temp = validParameter.validFile(parameters, "dups", false);
 211                         if (temp == "not found") {
 212                                 if (namefile != "") {  temp = "true";                                   }
 213                                 else                            {  temp = "false"; usedDups = "";       }
 214                         }
 215                         dups = m->isTrue(temp);
 216
 217                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
 218
 219                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
 225                 exit(1);
 226         }
 227 }
 228 //**********************************************************************************************************************
 229
 230 void RemoveSeqsCommand::help(){
 231         try {
 232                 m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n");
 233                 m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
 234                 m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos and at least one of the file parameters.\n");
 235                 m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n");
 236                 m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
 237                 m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
 238                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 239         }
 240         catch(exception& e) {
 241                 m->errorOut(e, "RemoveSeqsCommand", "help");
 242                 exit(1);
 243         }
 244 }
 245
 246 //**********************************************************************************************************************
 247
 248 int RemoveSeqsCommand::execute(){
 249         try {
 250
 251                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 252
 253                 //get names you want to keep
 254                 readAccnos();
 255
 256                 if (m->control_pressed) { return 0; }
 257
 258                 //read through the correct file and output lines you want to keep
 259                 if (namefile != "")                     {               readName();             }
 260                 if (fastafile != "")            {               readFasta();    }
 261                 if (groupfile != "")            {               readGroup();    }
 262                 if (alignfile != "")            {               readAlign();    }
 263                 if (listfile != "")                     {               readList();             }
 264                 if (taxfile != "")                      {               readTax();              }
 265                 if (qualfile != "")                     {               readQual();             }
 266
 267                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 268
 269                 m->mothurOut("Removed " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
 270
 271                 if (outputNames.size() != 0) {
 272                         m->mothurOutEndLine();
 273                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 274                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 275                         m->mothurOutEndLine();
 276
 277                         //set fasta file as new current fastafile
 278                         string current = "";
 279                         itTypes = outputTypes.find("fasta");
 280                         if (itTypes != outputTypes.end()) {
 281                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 282                         }
 283
 284                         itTypes = outputTypes.find("name");
 285                         if (itTypes != outputTypes.end()) {
 286                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 287                         }
 288
 289                         itTypes = outputTypes.find("group");
 290                         if (itTypes != outputTypes.end()) {
 291                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 292                         }
 293
 294                         itTypes = outputTypes.find("list");
 295                         if (itTypes != outputTypes.end()) {
 296                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 297                         }
 298
 299                         itTypes = outputTypes.find("taxonomy");
 300                         if (itTypes != outputTypes.end()) {
 301                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 302                         }
 303
 304                         itTypes = outputTypes.find("qfile");
 305                         if (itTypes != outputTypes.end()) {
 306                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 307                         }
 308                 }
 309
 310                 return 0;
 311         }
 312
 313         catch(exception& e) {
 314                 m->errorOut(e, "RemoveSeqsCommand", "execute");
 315                 exit(1);
 316         }
 317 }
 318
 319 //**********************************************************************************************************************
 320 int RemoveSeqsCommand::readFasta(){
 321         try {
 322                 string thisOutputDir = outputDir;
 323                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 324                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 325
 326                 ofstream out;
 327                 m->openOutputFile(outputFileName, out);
 328
 329                 ifstream in;
 330                 m->openInputFile(fastafile, in);
 331                 string name;
 332
 333                 bool wroteSomething = false;
 334
 335                 while(!in.eof()){
 336                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 337
 338                         Sequence currSeq(in);
 339                         name = currSeq.getName();
 340
 341                         if (name != "") {
 342                                 //if this name is in the accnos file
 343                                 if (names.count(name) == 0) {
 344                                         wroteSomething = true;
 345
 346                                         currSeq.printSequence(out);
 347                                 }
 348                         }
 349                         m->gobble(in);
 350                 }
 351                 in.close();
 352                 out.close();
 353
 354                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 355                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 356
 357                 return 0;
 358
 359         }
 360         catch(exception& e) {
 361                 m->errorOut(e, "RemoveSeqsCommand", "readFasta");
 362                 exit(1);
 363         }
 364 }
 365 //**********************************************************************************************************************
 366 int RemoveSeqsCommand::readQual(){
 367         try {
 368                 string thisOutputDir = outputDir;
 369                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 370                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 371                 ofstream out;
 372                 m->openOutputFile(outputFileName, out);
 373
 374
 375                 ifstream in;
 376                 m->openInputFile(qualfile, in);
 377                 string name;
 378
 379                 bool wroteSomething = false;
 380
 381
 382                 while(!in.eof()){
 383                         string saveName = "";
 384                         string name = "";
 385                         string scores = "";
 386
 387                         in >> name;
 388
 389                         if (name.length() != 0) {
 390                                 saveName = name.substr(1);
 391                                 while (!in.eof())       {
 392                                         char c = in.get();
 393                                         if (c == 10 || c == 13){        break;  }
 394                                         else { name += c; }
 395                                 }
 396                                 m->gobble(in);
 397                         }
 398
 399                         while(in){
 400                                 char letter= in.get();
 401                                 if(letter == '>'){      in.putback(letter);     break;  }
 402                                 else{ scores += letter; }
 403                         }
 404
 405                         m->gobble(in);
 406
 407                         if (names.count(saveName) == 0) {
 408                                 wroteSomething = true;
 409
 410                                 out << name << endl << scores;
 411                         }
 412
 413                         m->gobble(in);
 414                 }
 415                 in.close();
 416                 out.close();
 417
 418
 419                 if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 420                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 421
 422                 return 0;
 423
 424         }
 425         catch(exception& e) {
 426                 m->errorOut(e, "RemoveSeqsCommand", "readQual");
 427                 exit(1);
 428         }
 429 }
 430 //**********************************************************************************************************************
 431 int RemoveSeqsCommand::readList(){
 432         try {
 433                 string thisOutputDir = outputDir;
 434                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 435                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 436
 437                 ofstream out;
 438                 m->openOutputFile(outputFileName, out);
 439
 440                 ifstream in;
 441                 m->openInputFile(listfile, in);
 442
 443                 bool wroteSomething = false;
 444
 445                 while(!in.eof()){
 446                         //read in list vector
 447                         ListVector list(in);
 448
 449                         //make a new list vector
 450                         ListVector newList;
 451                         newList.setLabel(list.getLabel());
 452
 453                         //for each bin
 454                         for (int i = 0; i < list.getNumBins(); i++) {
 455                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 456
 457                                 //parse out names that are in accnos file
 458                                 string binnames = list.get(i);
 459
 460                                 string newNames = "";
 461                                 while (binnames.find_first_of(',') != -1) {
 462                                         string name = binnames.substr(0,binnames.find_first_of(','));
 463                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 464
 465                                         //if that name is in the .accnos file, add it
 466                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 467                                 }
 468
 469                                 //get last name
 470                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 471
 472                                 //if there are names in this bin add to new list
 473                                 if (newNames != "") {
 474                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 475                                         newList.push_back(newNames);
 476                                 }
 477                         }
 478
 479                         //print new listvector
 480                         if (newList.getNumBins() != 0) {
 481                                 wroteSomething = true;
 482                                 newList.print(out);
 483                         }
 484
 485                         m->gobble(in);
 486                 }
 487                 in.close();
 488                 out.close();
 489
 490                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 491                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 492
 493                 return 0;
 494
 495         }
 496         catch(exception& e) {
 497                 m->errorOut(e, "RemoveSeqsCommand", "readList");
 498                 exit(1);
 499         }
 500 }
 501 //**********************************************************************************************************************
 502 int RemoveSeqsCommand::readName(){
 503         try {
 504                 string thisOutputDir = outputDir;
 505                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 506                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 507
 508                 ofstream out;
 509                 m->openOutputFile(outputFileName, out);
 510
 511                 ifstream in;
 512                 m->openInputFile(namefile, in);
 513                 string name, firstCol, secondCol;
 514
 515                 bool wroteSomething = false;
 516
 517
 518                 while(!in.eof()){
 519                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 520
 521                         in >> firstCol;         m->gobble(in);
 522                         in >> secondCol;
 523
 524                         vector<string> parsedNames;
 525                         m->splitAtComma(secondCol, parsedNames);
 526
 527                         vector<string> validSecond;  validSecond.clear();
 528                         for (int i = 0; i < parsedNames.size(); i++) {
 529                                 if (names.count(parsedNames[i]) == 0) {
 530                                         validSecond.push_back(parsedNames[i]);
 531                                 }
 532                         }
 533
 534                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 535                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 536                         }else {
 537                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 538                                 if (names.count(firstCol) == 0) {
 539
 540                                         wroteSomething = true;
 541
 542                                         out << firstCol << '\t';
 543
 544                                         //you know you have at least one valid second since first column is valid
 545                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 546                                         out << validSecond[validSecond.size()-1] << endl;
 547
 548                                         //make first name in set you come to first column and then add the remaining names to second column
 549                                 }else {
 550
 551                                         //you want part of this row
 552                                         if (validSecond.size() != 0) {
 553
 554                                                 wroteSomething = true;
 555
 556                                                 out << validSecond[0] << '\t';
 557
 558                                                 //you know you have at least one valid second since first column is valid
 559                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 560                                                 out << validSecond[validSecond.size()-1] << endl;
 561                                         }
 562                                 }
 563                         }
 564                         m->gobble(in);
 565                 }
 566                 in.close();
 567                 out.close();
 568
 569                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 570                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 571
 572                 return 0;
 573         }
 574         catch(exception& e) {
 575                 m->errorOut(e, "RemoveSeqsCommand", "readName");
 576                 exit(1);
 577         }
 578 }
 579
 580 //**********************************************************************************************************************
 581 int RemoveSeqsCommand::readGroup(){
 582         try {
 583                 string thisOutputDir = outputDir;
 584                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 585                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 586
 587                 ofstream out;
 588                 m->openOutputFile(outputFileName, out);
 589
 590                 ifstream in;
 591                 m->openInputFile(groupfile, in);
 592                 string name, group;
 593
 594                 bool wroteSomething = false;
 595
 596                 while(!in.eof()){
 597                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 598
 599                         in >> name;                             //read from first column
 600                         in >> group;                    //read from second column
 601
 602                         //if this name is in the accnos file
 603                         if (names.count(name) == 0) {
 604                                 wroteSomething = true;
 605                                 out << name << '\t' << group << endl;
 606                         }
 607
 608                         m->gobble(in);
 609                 }
 610                 in.close();
 611                 out.close();
 612
 613                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 614                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 615
 616                 return 0;
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "RemoveSeqsCommand", "readGroup");
 620                 exit(1);
 621         }
 622 }
 623 //**********************************************************************************************************************
 624 int RemoveSeqsCommand::readTax(){
 625         try {
 626                 string thisOutputDir = outputDir;
 627                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 628                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 629                 ofstream out;
 630                 m->openOutputFile(outputFileName, out);
 631
 632                 ifstream in;
 633                 m->openInputFile(taxfile, in);
 634                 string name, tax;
 635
 636                 bool wroteSomething = false;
 637
 638                 while(!in.eof()){
 639                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 640
 641                         in >> name;                             //read from first column
 642                         in >> tax;                      //read from second column
 643
 644                         //if this name is in the accnos file
 645                         if (names.count(name) == 0) {
 646                                 wroteSomething = true;
 647                                 out << name << '\t' << tax << endl;
 648                         }
 649
 650                         m->gobble(in);
 651                 }
 652                 in.close();
 653                 out.close();
 654
 655                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 656                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 657
 658                 return 0;
 659         }
 660         catch(exception& e) {
 661                 m->errorOut(e, "RemoveSeqsCommand", "readTax");
 662                 exit(1);
 663         }
 664 }
 665 //**********************************************************************************************************************
 666 //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
 667 int RemoveSeqsCommand::readAlign(){
 668         try {
 669                 string thisOutputDir = outputDir;
 670                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 671                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 672
 673                 ofstream out;
 674                 m->openOutputFile(outputFileName, out);
 675
 676                 ifstream in;
 677                 m->openInputFile(alignfile, in);
 678                 string name, junk;
 679
 680                 bool wroteSomething = false;
 681
 682                 //read column headers
 683                 for (int i = 0; i < 16; i++) {
 684                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 685                         else                    {       break;                  }
 686                 }
 687                 out << endl;
 688
 689                 while(!in.eof()){
 690                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 691
 692                         in >> name;                             //read from first column
 693
 694                         //if this name is in the accnos file
 695                         if (names.count(name) == 0) {
 696                                 wroteSomething = true;
 697
 698                                 out << name << '\t';
 699
 700                                 //read rest
 701                                 for (int i = 0; i < 15; i++) {
 702                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 703                                         else                    {       break;                  }
 704                                 }
 705                                 out << endl;
 706
 707                         }else {//still read just don't do anything with it
 708
 709                                 //read rest
 710                                 for (int i = 0; i < 15; i++) {
 711                                         if (!in.eof())  {       in >> junk;             }
 712                                         else                    {       break;                  }
 713                                 }
 714                         }
 715
 716                         m->gobble(in);
 717                 }
 718                 in.close();
 719                 out.close();
 720
 721                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 722                 outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName);
 723
 724                 return 0;
 725
 726         }
 727         catch(exception& e) {
 728                 m->errorOut(e, "RemoveSeqsCommand", "readAlign");
 729                 exit(1);
 730         }
 731 }
 732 //**********************************************************************************************************************
 733 void RemoveSeqsCommand::readAccnos(){
 734         try {
 735
 736                 ifstream in;
 737                 m->openInputFile(accnosfile, in);
 738                 string name;
 739
 740                 while(!in.eof()){
 741                         in >> name;
 742
 743                         names.insert(name);
 744
 745                         m->gobble(in);
 746                 }
 747                 in.close();
 748
 749         }
 750         catch(exception& e) {
 751                 m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
 752                 exit(1);
 753         }
 754 }
 755
 756 //**********************************************************************************************************************
 757
 758