removelineagecommand.cpp

   1 /*
   2  *  removelineagecommand.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 "removelineagecommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14 //**********************************************************************************************************************
  15 vector<string> RemoveLineageCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta","name", "group", "alignreport", "taxon", "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, "RemoveLineageCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 RemoveLineageCommand::RemoveLineageCommand(){
  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, "RemoveLineageCommand", "RemoveLineageCommand");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 vector<string> RemoveLineageCommand::getRequiredParameters(){
  46         try {
  47                 string Array[] =  {"taxonomy"};
  48                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "RemoveLineageCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> RemoveLineageCommand::getRequiredFiles(){
  58         try {
  59                 vector<string> myArray;
  60                 return myArray;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "RemoveLineageCommand", "getRequiredFiles");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 RemoveLineageCommand::RemoveLineageCommand(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, "RemoveLineageCommand", "RemoveLineageCommand");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 void RemoveLineageCommand::help(){
 211         try {
 212                 m->mothurOut("The remove.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 not from the taxon you requested to be removed.\n");
 214                 m->mothurOut("The remove.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 remove.\n");
 217                 m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 218                 m->mothurOut("Example remove.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 remove.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, "RemoveLineageCommand", "help");
 225                 exit(1);
 226         }
 227 }
 228
 229 //**********************************************************************************************************************
 230
 231 int RemoveLineageCommand::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 remove
 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) { 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, "RemoveLineageCommand", "execute");
 261                 exit(1);
 262         }
 263 }
 264
 265 //**********************************************************************************************************************
 266 int RemoveLineageCommand::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
 272                 ofstream out;
 273                 m->openOutputFile(outputFileName, out);
 274
 275                 ifstream in;
 276                 m->openInputFile(fastafile, in);
 277                 string name;
 278
 279                 bool wroteSomething = false;
 280
 281                 while(!in.eof()){
 282                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 283
 284                         Sequence currSeq(in);
 285                         name = currSeq.getName();
 286
 287                         if (name != "") {
 288                                 //if this name is in the accnos file
 289                                 if (names.count(name) == 0) {
 290                                         wroteSomething = true;
 291
 292                                         currSeq.printSequence(out);
 293                                 }
 294                         }
 295                         m->gobble(in);
 296                 }
 297                 in.close();
 298                 out.close();
 299
 300                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 301                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 302
 303                 return 0;
 304
 305         }
 306         catch(exception& e) {
 307                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 308                 exit(1);
 309         }
 310 }
 311 //**********************************************************************************************************************
 312 int RemoveLineageCommand::readList(){
 313         try {
 314                 string thisOutputDir = outputDir;
 315                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 316                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 317
 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                         //read in list vector
 328                         ListVector list(in);
 329
 330                         //make a new list vector
 331                         ListVector newList;
 332                         newList.setLabel(list.getLabel());
 333
 334                         //for each bin
 335                         for (int i = 0; i < list.getNumBins(); i++) {
 336                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 337
 338                                 //parse out names that are in accnos file
 339                                 string binnames = list.get(i);
 340
 341                                 string newNames = "";
 342                                 while (binnames.find_first_of(',') != -1) {
 343                                         string name = binnames.substr(0,binnames.find_first_of(','));
 344                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 345
 346                                         //if that name is in the .accnos file, add it
 347                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 348                                 }
 349
 350                                 //get last name
 351                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 352
 353                                 //if there are names in this bin add to new list
 354                                 if (newNames != "") {
 355                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 356                                         newList.push_back(newNames);
 357                                 }
 358                         }
 359
 360                         //print new listvector
 361                         if (newList.getNumBins() != 0) {
 362                                 wroteSomething = true;
 363                                 newList.print(out);
 364                         }
 365
 366                         m->gobble(in);
 367                 }
 368                 in.close();
 369                 out.close();
 370
 371                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 372                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 373
 374                 return 0;
 375
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "RemoveLineageCommand", "readList");
 379                 exit(1);
 380         }
 381 }
 382 //**********************************************************************************************************************
 383 int RemoveLineageCommand::readName(){
 384         try {
 385                 string thisOutputDir = outputDir;
 386                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 387                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 388
 389                 ofstream out;
 390                 m->openOutputFile(outputFileName, out);
 391
 392                 ifstream in;
 393                 m->openInputFile(namefile, in);
 394                 string name, firstCol, secondCol;
 395
 396                 bool wroteSomething = false;
 397
 398                 while(!in.eof()){
 399                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 400
 401                         in >> firstCol;
 402                         in >> secondCol;
 403
 404                         vector<string> parsedNames;
 405                         //parse second column saving each name
 406                         while (secondCol.find_first_of(',') != -1) {
 407                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 408                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 409                                 parsedNames.push_back(name);
 410                         }
 411
 412                         //get name after last ,
 413                         parsedNames.push_back(secondCol);
 414
 415                         vector<string> validSecond;  validSecond.clear();
 416                         for (int i = 0; i < parsedNames.size(); i++) {
 417                                 if (names.count(parsedNames[i]) == 0) {
 418                                         validSecond.push_back(parsedNames[i]);
 419                                 }
 420                         }
 421
 422                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 423                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 424                         }else {
 425                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 426                                 if (names.count(firstCol) == 0) {
 427
 428                                         wroteSomething = true;
 429
 430                                         out << firstCol << '\t';
 431
 432                                         //you know you have at least one valid second since first column is valid
 433                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 434                                         out << validSecond[validSecond.size()-1] << endl;
 435
 436                                         //make first name in set you come to first column and then add the remaining names to second column
 437                                 }else {
 438
 439                                         //you want part of this row
 440                                         if (validSecond.size() != 0) {
 441
 442                                                 wroteSomething = true;
 443
 444                                                 out << validSecond[0] << '\t';
 445
 446                                                 //you know you have at least one valid second since first column is valid
 447                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 448                                                 out << validSecond[validSecond.size()-1] << endl;
 449                                         }
 450                                 }
 451                         }
 452                         m->gobble(in);
 453                 }
 454                 in.close();
 455                 out.close();
 456
 457                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 458                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 459
 460                 return 0;
 461         }
 462         catch(exception& e) {
 463                 m->errorOut(e, "RemoveLineageCommand", "readName");
 464                 exit(1);
 465         }
 466 }
 467
 468 //**********************************************************************************************************************
 469 int RemoveLineageCommand::readGroup(){
 470         try {
 471                 string thisOutputDir = outputDir;
 472                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 473                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 474
 475                 ofstream out;
 476                 m->openOutputFile(outputFileName, out);
 477
 478                 ifstream in;
 479                 m->openInputFile(groupfile, in);
 480                 string name, group;
 481
 482                 bool wroteSomething = false;
 483
 484                 while(!in.eof()){
 485                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 486
 487                         in >> name;                             //read from first column
 488                         in >> group;                    //read from second column
 489
 490                         //if this name is in the accnos file
 491                         if (names.count(name) == 0) {
 492                                 wroteSomething = true;
 493                                 out << name << '\t' << group << endl;
 494                         }
 495
 496                         m->gobble(in);
 497                 }
 498                 in.close();
 499                 out.close();
 500
 501                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 502                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 503
 504                 return 0;
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 508                 exit(1);
 509         }
 510 }
 511 //**********************************************************************************************************************
 512 int RemoveLineageCommand::readTax(){
 513         try {
 514                 string thisOutputDir = outputDir;
 515                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 516                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 517                 ofstream out;
 518                 m->openOutputFile(outputFileName, out);
 519
 520                 ifstream in;
 521                 m->openInputFile(taxfile, in);
 522                 string name, tax;
 523
 524                 bool wroteSomething = false;
 525
 526                 while(!in.eof()){
 527
 528                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 529
 530                         in >> name;                             //read from first column
 531                         in >> tax;                      //read from second column
 532
 533                         string newtax = tax;
 534
 535                         //if the users file contains confidence scores we want to ignore them when searching for the taxons
 536                         int hasConfidences = tax.find_first_of('(');
 537                         if (hasConfidences != string::npos) {
 538                                 newtax = removeConfidences(tax);
 539                         }
 540
 541                         int pos = newtax.find(taxons);
 542
 543                         if (pos == string::npos) {
 544                                 wroteSomething = true;
 545                                 out << name << '\t' << tax << endl;
 546                         }else{ //this sequence contains the taxon the user wants to remove
 547                                 names.insert(name);
 548                         }
 549
 550                         m->gobble(in);
 551                 }
 552                 in.close();
 553                 out.close();
 554
 555                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 556                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 557
 558                 return 0;
 559
 560         }
 561         catch(exception& e) {
 562                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 563                 exit(1);
 564         }
 565 }
 566 /**************************************************************************************************/
 567 string RemoveLineageCommand::removeConfidences(string tax) {
 568         try {
 569
 570                 string taxon = "";
 571                 int taxLength = tax.length();
 572                 for(int i=0;i<taxLength;i++){
 573                         if(tax[i] == ';'){
 574                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 575                                 taxon += ";";
 576                         }
 577                         else{
 578                                 taxon += tax[i];
 579                         }
 580                 }
 581
 582                 return taxon;
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
 586                 exit(1);
 587         }
 588 }
 589 //**********************************************************************************************************************
 590 //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
 591 int RemoveLineageCommand::readAlign(){
 592         try {
 593                 string thisOutputDir = outputDir;
 594                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 595                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 596
 597                 ofstream out;
 598                 m->openOutputFile(outputFileName, out);
 599
 600                 ifstream in;
 601                 m->openInputFile(alignfile, in);
 602                 string name, junk;
 603
 604                 bool wroteSomething = false;
 605
 606                 //read column headers
 607                 for (int i = 0; i < 16; i++) {
 608                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 609                         else                    {       break;                  }
 610                 }
 611                 out << endl;
 612
 613                 while(!in.eof()){
 614                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 615
 616                         in >> name;                             //read from first column
 617
 618                         //if this name is in the accnos file
 619                         if (names.count(name) == 0) {
 620                                 wroteSomething = true;
 621
 622                                 out << name << '\t';
 623
 624                                 //read rest
 625                                 for (int i = 0; i < 15; i++) {
 626                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 627                                         else                    {       break;                  }
 628                                 }
 629                                 out << endl;
 630
 631                         }else {//still read just don't do anything with it
 632
 633                                 //read rest
 634                                 for (int i = 0; i < 15; i++) {
 635                                         if (!in.eof())  {       in >> junk;             }
 636                                         else                    {       break;                  }
 637                                 }
 638                         }
 639
 640                         m->gobble(in);
 641                 }
 642                 in.close();
 643                 out.close();
 644
 645                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 646                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 647
 648                 return 0;
 649
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 653                 exit(1);
 654         }
 655 }
 656 //**********************************************************************************************************************
 657