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
 278                 return 0;
 279         }
 280
 281         catch(exception& e) {
 282                 m->errorOut(e, "RemoveSeqsCommand", "execute");
 283                 exit(1);
 284         }
 285 }
 286
 287 //**********************************************************************************************************************
 288 int RemoveSeqsCommand::readFasta(){
 289         try {
 290                 string thisOutputDir = outputDir;
 291                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 292                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 293
 294                 ofstream out;
 295                 m->openOutputFile(outputFileName, out);
 296
 297                 ifstream in;
 298                 m->openInputFile(fastafile, in);
 299                 string name;
 300
 301                 bool wroteSomething = false;
 302
 303                 while(!in.eof()){
 304                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 305
 306                         Sequence currSeq(in);
 307                         name = currSeq.getName();
 308
 309                         if (name != "") {
 310                                 //if this name is in the accnos file
 311                                 if (names.count(name) == 0) {
 312                                         wroteSomething = true;
 313
 314                                         currSeq.printSequence(out);
 315                                 }
 316                         }
 317                         m->gobble(in);
 318                 }
 319                 in.close();
 320                 out.close();
 321
 322                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 323                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 324
 325                 return 0;
 326
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "RemoveSeqsCommand", "readFasta");
 330                 exit(1);
 331         }
 332 }
 333 //**********************************************************************************************************************
 334 int RemoveSeqsCommand::readQual(){
 335         try {
 336                 string thisOutputDir = outputDir;
 337                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 338                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 339                 ofstream out;
 340                 m->openOutputFile(outputFileName, out);
 341
 342
 343                 ifstream in;
 344                 m->openInputFile(qualfile, in);
 345                 string name;
 346
 347                 bool wroteSomething = false;
 348
 349
 350                 while(!in.eof()){
 351                         string saveName = "";
 352                         string name = "";
 353                         string scores = "";
 354
 355                         in >> name;
 356
 357                         if (name.length() != 0) {
 358                                 saveName = name.substr(1);
 359                                 while (!in.eof())       {
 360                                         char c = in.get();
 361                                         if (c == 10 || c == 13){        break;  }
 362                                         else { name += c; }
 363                                 }
 364                                 m->gobble(in);
 365                         }
 366
 367                         while(in){
 368                                 char letter= in.get();
 369                                 if(letter == '>'){      in.putback(letter);     break;  }
 370                                 else{ scores += letter; }
 371                         }
 372
 373                         m->gobble(in);
 374
 375                         if (names.count(saveName) == 0) {
 376                                 wroteSomething = true;
 377
 378                                 out << name << endl << scores;
 379                         }
 380
 381                         m->gobble(in);
 382                 }
 383                 in.close();
 384                 out.close();
 385
 386
 387                 if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 388                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 389
 390                 return 0;
 391
 392         }
 393         catch(exception& e) {
 394                 m->errorOut(e, "RemoveSeqsCommand", "readQual");
 395                 exit(1);
 396         }
 397 }
 398 //**********************************************************************************************************************
 399 int RemoveSeqsCommand::readList(){
 400         try {
 401                 string thisOutputDir = outputDir;
 402                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 403                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 404
 405                 ofstream out;
 406                 m->openOutputFile(outputFileName, out);
 407
 408                 ifstream in;
 409                 m->openInputFile(listfile, in);
 410
 411                 bool wroteSomething = false;
 412
 413                 while(!in.eof()){
 414                         //read in list vector
 415                         ListVector list(in);
 416
 417                         //make a new list vector
 418                         ListVector newList;
 419                         newList.setLabel(list.getLabel());
 420
 421                         //for each bin
 422                         for (int i = 0; i < list.getNumBins(); i++) {
 423                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 424
 425                                 //parse out names that are in accnos file
 426                                 string binnames = list.get(i);
 427
 428                                 string newNames = "";
 429                                 while (binnames.find_first_of(',') != -1) {
 430                                         string name = binnames.substr(0,binnames.find_first_of(','));
 431                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 432
 433                                         //if that name is in the .accnos file, add it
 434                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 435                                 }
 436
 437                                 //get last name
 438                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 439
 440                                 //if there are names in this bin add to new list
 441                                 if (newNames != "") {
 442                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 443                                         newList.push_back(newNames);
 444                                 }
 445                         }
 446
 447                         //print new listvector
 448                         if (newList.getNumBins() != 0) {
 449                                 wroteSomething = true;
 450                                 newList.print(out);
 451                         }
 452
 453                         m->gobble(in);
 454                 }
 455                 in.close();
 456                 out.close();
 457
 458                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 459                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 460
 461                 return 0;
 462
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "RemoveSeqsCommand", "readList");
 466                 exit(1);
 467         }
 468 }
 469 //**********************************************************************************************************************
 470 int RemoveSeqsCommand::readName(){
 471         try {
 472                 string thisOutputDir = outputDir;
 473                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 474                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 475
 476                 ofstream out;
 477                 m->openOutputFile(outputFileName, out);
 478
 479                 ifstream in;
 480                 m->openInputFile(namefile, in);
 481                 string name, firstCol, secondCol;
 482
 483                 bool wroteSomething = false;
 484
 485                 while(!in.eof()){
 486                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 487
 488                         in >> firstCol;         m->gobble(in);
 489                         in >> secondCol;
 490
 491                         vector<string> parsedNames;
 492                         //parse second column saving each name
 493                         while (secondCol.find_first_of(',') != -1) {
 494                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 495                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 496                                 parsedNames.push_back(name);
 497                         }
 498
 499                         //get name after last ,
 500                         parsedNames.push_back(secondCol);
 501
 502                         vector<string> validSecond;  validSecond.clear();
 503                         for (int i = 0; i < parsedNames.size(); i++) {
 504                                 if (names.count(parsedNames[i]) == 0) {
 505                                         validSecond.push_back(parsedNames[i]);
 506                                 }
 507                         }
 508
 509                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 510                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 511                         }else {
 512                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 513                                 if (names.count(firstCol) == 0) {
 514
 515                                         wroteSomething = true;
 516
 517                                         out << firstCol << '\t';
 518
 519                                         //you know you have at least one valid second since first column is valid
 520                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 521                                         out << validSecond[validSecond.size()-1] << endl;
 522
 523                                         //make first name in set you come to first column and then add the remaining names to second column
 524                                 }else {
 525
 526                                         //you want part of this row
 527                                         if (validSecond.size() != 0) {
 528
 529                                                 wroteSomething = true;
 530
 531                                                 out << validSecond[0] << '\t';
 532
 533                                                 //you know you have at least one valid second since first column is valid
 534                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 535                                                 out << validSecond[validSecond.size()-1] << endl;
 536                                         }
 537                                 }
 538                         }
 539                         m->gobble(in);
 540                 }
 541                 in.close();
 542                 out.close();
 543
 544                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 545                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 546
 547                 return 0;
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "RemoveSeqsCommand", "readName");
 551                 exit(1);
 552         }
 553 }
 554
 555 //**********************************************************************************************************************
 556 int RemoveSeqsCommand::readGroup(){
 557         try {
 558                 string thisOutputDir = outputDir;
 559                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 560                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 561
 562                 ofstream out;
 563                 m->openOutputFile(outputFileName, out);
 564
 565                 ifstream in;
 566                 m->openInputFile(groupfile, in);
 567                 string name, group;
 568
 569                 bool wroteSomething = false;
 570
 571                 while(!in.eof()){
 572                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 573
 574                         in >> name;                             //read from first column
 575                         in >> group;                    //read from second column
 576
 577                         //if this name is in the accnos file
 578                         if (names.count(name) == 0) {
 579                                 wroteSomething = true;
 580                                 out << name << '\t' << group << endl;
 581                         }
 582
 583                         m->gobble(in);
 584                 }
 585                 in.close();
 586                 out.close();
 587
 588                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 589                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 590
 591                 return 0;
 592         }
 593         catch(exception& e) {
 594                 m->errorOut(e, "RemoveSeqsCommand", "readGroup");
 595                 exit(1);
 596         }
 597 }
 598 //**********************************************************************************************************************
 599 int RemoveSeqsCommand::readTax(){
 600         try {
 601                 string thisOutputDir = outputDir;
 602                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 603                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 604                 ofstream out;
 605                 m->openOutputFile(outputFileName, out);
 606
 607                 ifstream in;
 608                 m->openInputFile(taxfile, in);
 609                 string name, tax;
 610
 611                 bool wroteSomething = false;
 612
 613                 while(!in.eof()){
 614                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 615
 616                         in >> name;                             //read from first column
 617                         in >> tax;                      //read from second column
 618
 619                         //if this name is in the accnos file
 620                         if (names.count(name) == 0) {
 621                                 wroteSomething = true;
 622                                 out << name << '\t' << tax << endl;
 623                         }
 624
 625                         m->gobble(in);
 626                 }
 627                 in.close();
 628                 out.close();
 629
 630                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 631                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 632
 633                 return 0;
 634         }
 635         catch(exception& e) {
 636                 m->errorOut(e, "RemoveSeqsCommand", "readTax");
 637                 exit(1);
 638         }
 639 }
 640 //**********************************************************************************************************************
 641 //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
 642 int RemoveSeqsCommand::readAlign(){
 643         try {
 644                 string thisOutputDir = outputDir;
 645                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 646                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 647
 648                 ofstream out;
 649                 m->openOutputFile(outputFileName, out);
 650
 651                 ifstream in;
 652                 m->openInputFile(alignfile, in);
 653                 string name, junk;
 654
 655                 bool wroteSomething = false;
 656
 657                 //read column headers
 658                 for (int i = 0; i < 16; i++) {
 659                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 660                         else                    {       break;                  }
 661                 }
 662                 out << endl;
 663
 664                 while(!in.eof()){
 665                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 666
 667                         in >> name;                             //read from first column
 668
 669                         //if this name is in the accnos file
 670                         if (names.count(name) == 0) {
 671                                 wroteSomething = true;
 672
 673                                 out << name << '\t';
 674
 675                                 //read rest
 676                                 for (int i = 0; i < 15; i++) {
 677                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 678                                         else                    {       break;                  }
 679                                 }
 680                                 out << endl;
 681
 682                         }else {//still read just don't do anything with it
 683
 684                                 //read rest
 685                                 for (int i = 0; i < 15; i++) {
 686                                         if (!in.eof())  {       in >> junk;             }
 687                                         else                    {       break;                  }
 688                                 }
 689                         }
 690
 691                         m->gobble(in);
 692                 }
 693                 in.close();
 694                 out.close();
 695
 696                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
 697                 outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName);
 698
 699                 return 0;
 700
 701         }
 702         catch(exception& e) {
 703                 m->errorOut(e, "RemoveSeqsCommand", "readAlign");
 704                 exit(1);
 705         }
 706 }
 707 //**********************************************************************************************************************
 708 void RemoveSeqsCommand::readAccnos(){
 709         try {
 710
 711                 ifstream in;
 712                 m->openInputFile(accnosfile, in);
 713                 string name;
 714
 715                 while(!in.eof()){
 716                         in >> name;
 717
 718                         names.insert(name);
 719
 720                         m->gobble(in);
 721                 }
 722                 in.close();
 723
 724         }
 725         catch(exception& e) {
 726                 m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
 727                 exit(1);
 728         }
 729 }
 730
 731 //**********************************************************************************************************************
 732
 733