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