getlineagecommand.cpp

   1 /*
   2  *  getlineagecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/24/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlineagecommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetLineageCommand::getValidParameters(){
  17         try {
  18                 string Array[] =  {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
  19                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  20                 return myArray;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "GetLineageCommand", "getValidParameters");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 GetLineageCommand::GetLineageCommand(){
  29         try {
  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, "GetLineageCommand", "GetLineageCommand");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 vector<string> GetLineageCommand::getRequiredParameters(){
  46         try {
  47                 string Array[] =  {"taxonomy","taxon"};
  48                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "GetLineageCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> GetLineageCommand::getRequiredFiles(){
  58         try {
  59                 vector<string> myArray;
  60                 return myArray;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "GetLineageCommand", "getRequiredFiles");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 GetLineageCommand::GetLineageCommand(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", "taxon", "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("list");
 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["list"] = inputDir + it->second;             }
 130                                 }
 131
 132                                 it = parameters.find("name");
 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["name"] = inputDir + it->second;             }
 138                                 }
 139
 140                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 146                                 }
 147
 148                                 it = parameters.find("taxonomy");
 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["taxonomy"] = inputDir + it->second;         }
 154                                 }
 155                         }
 156
 157
 158                         //check for required parameters
 159                         fastafile = validParameter.validFile(parameters, "fasta", true);
 160                         if (fastafile == "not open") { abort = true; }
 161                         else if (fastafile == "not found") {  fastafile = "";  }
 162
 163                         namefile = validParameter.validFile(parameters, "name", true);
 164                         if (namefile == "not open") { abort = true; }
 165                         else if (namefile == "not found") {  namefile = "";  }
 166
 167                         groupfile = validParameter.validFile(parameters, "group", true);
 168                         if (groupfile == "not open") { abort = true; }
 169                         else if (groupfile == "not found") {  groupfile = "";  }
 170
 171                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 172                         if (alignfile == "not open") { abort = true; }
 173                         else if (alignfile == "not found") {  alignfile = "";  }
 174
 175                         listfile = validParameter.validFile(parameters, "list", true);
 176                         if (listfile == "not open") { abort = true; }
 177                         else if (listfile == "not found") {  listfile = "";  }
 178
 179                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 180                         if (taxfile == "not open") { abort = true; }
 181                         else if (taxfile == "not found") {  taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine();  abort = true; }
 182
 183                         string usedDups = "true";
 184                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
 185                         dups = m->isTrue(temp);
 186
 187                         taxons = validParameter.validFile(parameters, "taxon", false);
 188                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 189                         else {
 190                                 //rip off quotes
 191                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 192                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 193                         }
 194
 195
 196                         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; }
 197
 198                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 199
 200                 }
 201
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 void GetLineageCommand::help(){
 211         try {
 212                 m->mothurOut("The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
 213                 m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n");
 214                 m->mothurOut("The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide taxonomy and taxon.\n");
 215                 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");
 216                 m->mothurOut("The taxon parameter allows you to select the taxons you would like to get.\n");
 217                 m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 218                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 219                 m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n");
 220                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\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, "GetLineageCommand", "help");
 225                 exit(1);
 226         }
 227 }
 228
 229 //**********************************************************************************************************************
 230
 231 int GetLineageCommand::execute(){
 232         try {
 233
 234                 if (abort == true) { return 0; }
 235
 236                 if (m->control_pressed) { return 0; }
 237
 238                 //read through the correct file and output lines you want to keep
 239                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 240                 if (namefile != "")                     {               readName();             }
 241                 if (fastafile != "")            {               readFasta();    }
 242                 if (groupfile != "")            {               readGroup();    }
 243                 if (alignfile != "")            {               readAlign();    }
 244                 if (listfile != "")                     {               readList();             }
 245
 246
 247                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 248
 249                 if (outputNames.size() != 0) {
 250                         m->mothurOutEndLine();
 251                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 252                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 253                         m->mothurOutEndLine();
 254                 }
 255
 256                 return 0;
 257         }
 258
 259         catch(exception& e) {
 260                 m->errorOut(e, "GetLineageCommand", "execute");
 261                 exit(1);
 262         }
 263 }
 264
 265 //**********************************************************************************************************************
 266 int GetLineageCommand::readFasta(){
 267         try {
 268                 string thisOutputDir = outputDir;
 269                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 270                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 271                 ofstream out;
 272                 m->openOutputFile(outputFileName, out);
 273
 274
 275                 ifstream in;
 276                 m->openInputFile(fastafile, in);
 277                 string name;
 278
 279                 bool wroteSomething = false;
 280
 281                 while(!in.eof()){
 282
 283                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 284
 285                         Sequence currSeq(in);
 286                         name = currSeq.getName();
 287
 288                         if (name != "") {
 289                                 //if this name is in the accnos file
 290                                 if (names.count(name) != 0) {
 291                                         wroteSomething = true;
 292
 293                                         currSeq.printSequence(out);
 294                                 }
 295                         }
 296                         m->gobble(in);
 297                 }
 298                 in.close();
 299                 out.close();
 300
 301                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 302                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 303
 304                 return 0;
 305
 306         }
 307         catch(exception& e) {
 308                 m->errorOut(e, "GetLineageCommand", "readFasta");
 309                 exit(1);
 310         }
 311 }
 312 //**********************************************************************************************************************
 313 int GetLineageCommand::readList(){
 314         try {
 315                 string thisOutputDir = outputDir;
 316                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 317                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 318                 ofstream out;
 319                 m->openOutputFile(outputFileName, out);
 320
 321                 ifstream in;
 322                 m->openInputFile(listfile, in);
 323
 324                 bool wroteSomething = false;
 325
 326                 while(!in.eof()){
 327
 328                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 329
 330                         //read in list vector
 331                         ListVector list(in);
 332
 333                         //make a new list vector
 334                         ListVector newList;
 335                         newList.setLabel(list.getLabel());
 336
 337                         //for each bin
 338                         for (int i = 0; i < list.getNumBins(); i++) {
 339
 340                                 //parse out names that are in accnos file
 341                                 string binnames = list.get(i);
 342
 343                                 string newNames = "";
 344                                 while (binnames.find_first_of(',') != -1) {
 345                                         string name = binnames.substr(0,binnames.find_first_of(','));
 346                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 347
 348                                         //if that name is in the .accnos file, add it
 349                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 350                                 }
 351
 352                                 //get last name
 353                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 354
 355                                 //if there are names in this bin add to new list
 356                                 if (newNames != "") {
 357                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 358                                         newList.push_back(newNames);
 359                                 }
 360                         }
 361
 362                         //print new listvector
 363                         if (newList.getNumBins() != 0) {
 364                                 wroteSomething = true;
 365                                 newList.print(out);
 366                         }
 367
 368                         m->gobble(in);
 369                 }
 370                 in.close();
 371                 out.close();
 372
 373                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 374                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 375
 376                 return 0;
 377
 378         }
 379         catch(exception& e) {
 380                 m->errorOut(e, "GetLineageCommand", "readList");
 381                 exit(1);
 382         }
 383 }
 384 //**********************************************************************************************************************
 385 int GetLineageCommand::readName(){
 386         try {
 387                 string thisOutputDir = outputDir;
 388                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 389                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 390                 ofstream out;
 391                 m->openOutputFile(outputFileName, out);
 392
 393
 394                 ifstream in;
 395                 m->openInputFile(namefile, in);
 396                 string name, firstCol, secondCol;
 397
 398                 bool wroteSomething = false;
 399
 400
 401                 while(!in.eof()){
 402
 403                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 404
 405                         in >> firstCol;
 406                         in >> secondCol;
 407
 408                         string hold = "";
 409                         if (dups) { hold = secondCol; }
 410
 411                         vector<string> parsedNames;
 412                         //parse second column saving each name
 413                         while (secondCol.find_first_of(',') != -1) {
 414                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 415                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 416                                 parsedNames.push_back(name);
 417                         }
 418
 419                         //get name after last ,
 420                         parsedNames.push_back(secondCol);
 421
 422                         vector<string> validSecond;
 423                         for (int i = 0; i < parsedNames.size(); i++) {
 424                                 if (names.count(parsedNames[i]) != 0) {
 425                                         validSecond.push_back(parsedNames[i]);
 426                                 }
 427                         }
 428
 429                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 430                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 431                                 out << firstCol << '\t' << hold << endl;
 432                                 wroteSomething = true;
 433                         }else {
 434                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 435                                 if (names.count(firstCol) != 0) {
 436
 437                                         wroteSomething = true;
 438
 439                                         out << firstCol << '\t';
 440
 441                                         //you know you have at least one valid second since first column is valid
 442                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 443                                         out << validSecond[validSecond.size()-1] << endl;
 444
 445
 446                                 //make first name in set you come to first column and then add the remaining names to second column
 447                                 }else {
 448                                         //you want part of this row
 449                                         if (validSecond.size() != 0) {
 450
 451                                                 wroteSomething = true;
 452
 453                                                 out << validSecond[0] << '\t';
 454
 455                                                 //you know you have at least one valid second since first column is valid
 456                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 457                                                 out << validSecond[validSecond.size()-1] << endl;
 458                                         }
 459                                 }
 460                         }
 461                         m->gobble(in);
 462                 }
 463                 in.close();
 464                 out.close();
 465
 466                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 467                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 468
 469                 return 0;
 470
 471         }
 472         catch(exception& e) {
 473                 m->errorOut(e, "GetLineageCommand", "readName");
 474                 exit(1);
 475         }
 476 }
 477
 478 //**********************************************************************************************************************
 479 int GetLineageCommand::readGroup(){
 480         try {
 481                 string thisOutputDir = outputDir;
 482                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 483                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 484                 ofstream out;
 485                 m->openOutputFile(outputFileName, out);
 486
 487
 488                 ifstream in;
 489                 m->openInputFile(groupfile, in);
 490                 string name, group;
 491
 492                 bool wroteSomething = false;
 493
 494                 while(!in.eof()){
 495
 496                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 497
 498
 499                         in >> name;                             //read from first column
 500                         in >> group;                    //read from second column
 501
 502                         //if this name is in the accnos file
 503                         if (names.count(name) != 0) {
 504                                 wroteSomething = true;
 505
 506                                 out << name << '\t' << group << endl;
 507                         }
 508
 509                         m->gobble(in);
 510                 }
 511                 in.close();
 512                 out.close();
 513
 514                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 515                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 516
 517                 return 0;
 518
 519         }
 520         catch(exception& e) {
 521                 m->errorOut(e, "GetLineageCommand", "readGroup");
 522                 exit(1);
 523         }
 524 }
 525 //**********************************************************************************************************************
 526 int GetLineageCommand::readTax(){
 527         try {
 528                 string thisOutputDir = outputDir;
 529                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 530                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 531                 ofstream out;
 532                 m->openOutputFile(outputFileName, out);
 533
 534                 ifstream in;
 535                 m->openInputFile(taxfile, in);
 536                 string name, tax;
 537
 538                 bool wroteSomething = false;
 539
 540                 while(!in.eof()){
 541
 542                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 543
 544                         in >> name;                             //read from first column
 545                         in >> tax;                      //read from second column
 546
 547                         string newtax = tax;
 548
 549                         //if the users file contains confidence scores we want to ignore them when searching for the taxons
 550                         int hasConfidences = tax.find_first_of('(');
 551                         if (hasConfidences != string::npos) {
 552                                 newtax = removeConfidences(tax);
 553                         }
 554
 555                         int pos = newtax.find(taxons);
 556
 557                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 558                                 names.insert(name);
 559                                 out << name << '\t' << tax << endl;
 560                         }
 561
 562                         m->gobble(in);
 563                 }
 564                 in.close();
 565                 out.close();
 566
 567                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 568                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 569
 570                 return 0;
 571
 572         }
 573         catch(exception& e) {
 574                 m->errorOut(e, "GetLineageCommand", "readTax");
 575                 exit(1);
 576         }
 577 }
 578 /**************************************************************************************************/
 579 string GetLineageCommand::removeConfidences(string tax) {
 580         try {
 581
 582                 string taxon = "";
 583                 int taxLength = tax.length();
 584                 for(int i=0;i<taxLength;i++){
 585                         if(tax[i] == ';'){
 586                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 587                                 taxon += ";";
 588                         }
 589                         else{
 590                                 taxon += tax[i];
 591                         }
 592                 }
 593
 594                 return taxon;
 595         }
 596         catch(exception& e) {
 597                 m->errorOut(e, "GetLineageCommand", "removeConfidences");
 598                 exit(1);
 599         }
 600 }
 601 //**********************************************************************************************************************
 602 //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
 603 int GetLineageCommand::readAlign(){
 604         try {
 605                 string thisOutputDir = outputDir;
 606                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 607                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 608                 ofstream out;
 609                 m->openOutputFile(outputFileName, out);
 610
 611
 612                 ifstream in;
 613                 m->openInputFile(alignfile, in);
 614                 string name, junk;
 615
 616                 bool wroteSomething = false;
 617
 618                 //read column headers
 619                 for (int i = 0; i < 16; i++) {
 620                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 621                         else                    {       break;                  }
 622                 }
 623                 out << endl;
 624
 625                 while(!in.eof()){
 626
 627                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 628
 629
 630                         in >> name;                             //read from first column
 631
 632                         //if this name is in the accnos file
 633                         if (names.count(name) != 0) {
 634                                 wroteSomething = true;
 635
 636                                 out << name << '\t';
 637
 638                                 //read rest
 639                                 for (int i = 0; i < 15; i++) {
 640                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 641                                         else                    {       break;                  }
 642                                 }
 643                                 out << endl;
 644
 645                         }else {//still read just don't do anything with it
 646                                 //read rest
 647                                 for (int i = 0; i < 15; i++) {
 648                                         if (!in.eof())  {       in >> junk;             }
 649                                         else                    {       break;                  }
 650                                 }
 651                         }
 652
 653                         m->gobble(in);
 654                 }
 655                 in.close();
 656                 out.close();
 657
 658                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 659                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 660
 661                 return 0;
 662
 663         }
 664         catch(exception& e) {
 665                 m->errorOut(e, "GetLineageCommand", "readAlign");
 666                 exit(1);
 667         }
 668 }
 669 //**********************************************************************************************************************
 670
 671
 672
 673