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