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