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);
 185                         if (temp == "not found") {
 186                                 if (namefile != "") {  temp = "true";                                   }
 187                                 else                            {  temp = "false"; usedDups = "";       }
 188                         }
 189                         dups = m->isTrue(temp);
 190
 191                         taxons = validParameter.validFile(parameters, "taxon", false);
 192                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 193                         else {
 194                                 //rip off quotes
 195                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 196                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 197                         }
 198
 199
 200                         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; }
 201
 202                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 203
 204                 }
 205
 206         }
 207         catch(exception& e) {
 208                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 209                 exit(1);
 210         }
 211 }
 212 //**********************************************************************************************************************
 213
 214 void RemoveLineageCommand::help(){
 215         try {
 216                 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");
 217                 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");
 218                 m->mothurOut("The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide taxonomy and taxon.\n");
 219                 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");
 220                 m->mothurOut("The taxon parameter allows you to select the taxons you would like to remove.\n");
 221                 m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 222                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 223                 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");
 224                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
 225                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "RemoveLineageCommand", "help");
 229                 exit(1);
 230         }
 231 }
 232
 233 //**********************************************************************************************************************
 234
 235 int RemoveLineageCommand::execute(){
 236         try {
 237
 238                 if (abort == true) { return 0; }
 239
 240                 if (m->control_pressed) { return 0; }
 241
 242                 //read through the correct file and output lines you want to keep
 243                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 244                 if (namefile != "")                     {               readName();             }
 245                 if (fastafile != "")            {               readFasta();    }
 246                 if (groupfile != "")            {               readGroup();    }
 247                 if (alignfile != "")            {               readAlign();    }
 248                 if (listfile != "")                     {               readList();             }
 249
 250
 251                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 252
 253                 if (outputNames.size() != 0) {
 254                         m->mothurOutEndLine();
 255                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 256                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 257                         m->mothurOutEndLine();
 258                 }
 259
 260                 return 0;
 261         }
 262
 263         catch(exception& e) {
 264                 m->errorOut(e, "RemoveLineageCommand", "execute");
 265                 exit(1);
 266         }
 267 }
 268
 269 //**********************************************************************************************************************
 270 int RemoveLineageCommand::readFasta(){
 271         try {
 272                 string thisOutputDir = outputDir;
 273                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 274                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 275
 276                 ofstream out;
 277                 m->openOutputFile(outputFileName, out);
 278
 279                 ifstream in;
 280                 m->openInputFile(fastafile, in);
 281                 string name;
 282
 283                 bool wroteSomething = false;
 284
 285                 while(!in.eof()){
 286                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 287
 288                         Sequence currSeq(in);
 289                         name = currSeq.getName();
 290
 291                         if (name != "") {
 292                                 //if this name is in the accnos file
 293                                 if (names.count(name) == 0) {
 294                                         wroteSomething = true;
 295
 296                                         currSeq.printSequence(out);
 297                                 }
 298                         }
 299                         m->gobble(in);
 300                 }
 301                 in.close();
 302                 out.close();
 303
 304                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 305                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 306
 307                 return 0;
 308
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 312                 exit(1);
 313         }
 314 }
 315 //**********************************************************************************************************************
 316 int RemoveLineageCommand::readList(){
 317         try {
 318                 string thisOutputDir = outputDir;
 319                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 320                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 321
 322                 ofstream out;
 323                 m->openOutputFile(outputFileName, out);
 324
 325                 ifstream in;
 326                 m->openInputFile(listfile, in);
 327
 328                 bool wroteSomething = false;
 329
 330                 while(!in.eof()){
 331                         //read in list vector
 332                         ListVector list(in);
 333
 334                         //make a new list vector
 335                         ListVector newList;
 336                         newList.setLabel(list.getLabel());
 337
 338                         //for each bin
 339                         for (int i = 0; i < list.getNumBins(); i++) {
 340                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 341
 342                                 //parse out names that are in accnos file
 343                                 string binnames = list.get(i);
 344
 345                                 string newNames = "";
 346                                 while (binnames.find_first_of(',') != -1) {
 347                                         string name = binnames.substr(0,binnames.find_first_of(','));
 348                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 349
 350                                         //if that name is in the .accnos file, add it
 351                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 352                                 }
 353
 354                                 //get last name
 355                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 356
 357                                 //if there are names in this bin add to new list
 358                                 if (newNames != "") {
 359                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 360                                         newList.push_back(newNames);
 361                                 }
 362                         }
 363
 364                         //print new listvector
 365                         if (newList.getNumBins() != 0) {
 366                                 wroteSomething = true;
 367                                 newList.print(out);
 368                         }
 369
 370                         m->gobble(in);
 371                 }
 372                 in.close();
 373                 out.close();
 374
 375                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 376                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 377
 378                 return 0;
 379
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "RemoveLineageCommand", "readList");
 383                 exit(1);
 384         }
 385 }
 386 //**********************************************************************************************************************
 387 int RemoveLineageCommand::readName(){
 388         try {
 389                 string thisOutputDir = outputDir;
 390                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 391                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 392
 393                 ofstream out;
 394                 m->openOutputFile(outputFileName, out);
 395
 396                 ifstream in;
 397                 m->openInputFile(namefile, in);
 398                 string name, firstCol, secondCol;
 399
 400                 bool wroteSomething = false;
 401
 402                 while(!in.eof()){
 403                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 404
 405                         in >> firstCol;
 406                         in >> secondCol;
 407
 408                         vector<string> parsedNames;
 409                         //parse second column saving each name
 410                         while (secondCol.find_first_of(',') != -1) {
 411                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 412                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 413                                 parsedNames.push_back(name);
 414                         }
 415
 416                         //get name after last ,
 417                         parsedNames.push_back(secondCol);
 418
 419                         vector<string> validSecond;  validSecond.clear();
 420                         for (int i = 0; i < parsedNames.size(); i++) {
 421                                 if (names.count(parsedNames[i]) == 0) {
 422                                         validSecond.push_back(parsedNames[i]);
 423                                 }
 424                         }
 425
 426                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 427                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 428                         }else {
 429                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 430                                 if (names.count(firstCol) == 0) {
 431
 432                                         wroteSomething = true;
 433
 434                                         out << firstCol << '\t';
 435
 436                                         //you know you have at least one valid second since first column is valid
 437                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 438                                         out << validSecond[validSecond.size()-1] << endl;
 439
 440                                         //make first name in set you come to first column and then add the remaining names to second column
 441                                 }else {
 442
 443                                         //you want part of this row
 444                                         if (validSecond.size() != 0) {
 445
 446                                                 wroteSomething = true;
 447
 448                                                 out << validSecond[0] << '\t';
 449
 450                                                 //you know you have at least one valid second since first column is valid
 451                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 452                                                 out << validSecond[validSecond.size()-1] << endl;
 453                                         }
 454                                 }
 455                         }
 456                         m->gobble(in);
 457                 }
 458                 in.close();
 459                 out.close();
 460
 461                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 462                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 463
 464                 return 0;
 465         }
 466         catch(exception& e) {
 467                 m->errorOut(e, "RemoveLineageCommand", "readName");
 468                 exit(1);
 469         }
 470 }
 471
 472 //**********************************************************************************************************************
 473 int RemoveLineageCommand::readGroup(){
 474         try {
 475                 string thisOutputDir = outputDir;
 476                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 477                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 478
 479                 ofstream out;
 480                 m->openOutputFile(outputFileName, out);
 481
 482                 ifstream in;
 483                 m->openInputFile(groupfile, in);
 484                 string name, group;
 485
 486                 bool wroteSomething = false;
 487
 488                 while(!in.eof()){
 489                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 490
 491                         in >> name;                             //read from first column
 492                         in >> group;                    //read from second column
 493
 494                         //if this name is in the accnos file
 495                         if (names.count(name) == 0) {
 496                                 wroteSomething = true;
 497                                 out << name << '\t' << group << endl;
 498                         }
 499
 500                         m->gobble(in);
 501                 }
 502                 in.close();
 503                 out.close();
 504
 505                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 506                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 507
 508                 return 0;
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 512                 exit(1);
 513         }
 514 }
 515 //**********************************************************************************************************************
 516 int RemoveLineageCommand::readTax(){
 517         try {
 518                 string thisOutputDir = outputDir;
 519                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 520                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 521                 ofstream out;
 522                 m->openOutputFile(outputFileName, out);
 523
 524                 ifstream in;
 525                 m->openInputFile(taxfile, in);
 526                 string name, tax;
 527
 528                 bool wroteSomething = false;
 529
 530                 while(!in.eof()){
 531
 532                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 533
 534                         in >> name;                             //read from first column
 535                         in >> tax;                      //read from second column
 536
 537                         string newtax = tax;
 538
 539                         //if the users file contains confidence scores we want to ignore them when searching for the taxons
 540                         int hasConfidences = tax.find_first_of('(');
 541                         if (hasConfidences != string::npos) {
 542                                 newtax = removeConfidences(tax);
 543                         }
 544
 545                         int pos = newtax.find(taxons);
 546
 547                         if (pos == string::npos) {
 548                                 wroteSomething = true;
 549                                 out << name << '\t' << tax << endl;
 550                         }else{ //this sequence contains the taxon the user wants to remove
 551                                 names.insert(name);
 552                         }
 553
 554                         m->gobble(in);
 555                 }
 556                 in.close();
 557                 out.close();
 558
 559                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 560                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 561
 562                 return 0;
 563
 564         }
 565         catch(exception& e) {
 566                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 567                 exit(1);
 568         }
 569 }
 570 /**************************************************************************************************/
 571 string RemoveLineageCommand::removeConfidences(string tax) {
 572         try {
 573
 574                 string taxon = "";
 575                 int taxLength = tax.length();
 576                 for(int i=0;i<taxLength;i++){
 577                         if(tax[i] == ';'){
 578                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 579                                 taxon += ";";
 580                         }
 581                         else{
 582                                 taxon += tax[i];
 583                         }
 584                 }
 585
 586                 return taxon;
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
 590                 exit(1);
 591         }
 592 }
 593 //**********************************************************************************************************************
 594 //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
 595 int RemoveLineageCommand::readAlign(){
 596         try {
 597                 string thisOutputDir = outputDir;
 598                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 599                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 600
 601                 ofstream out;
 602                 m->openOutputFile(outputFileName, out);
 603
 604                 ifstream in;
 605                 m->openInputFile(alignfile, in);
 606                 string name, junk;
 607
 608                 bool wroteSomething = false;
 609
 610                 //read column headers
 611                 for (int i = 0; i < 16; i++) {
 612                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 613                         else                    {       break;                  }
 614                 }
 615                 out << endl;
 616
 617                 while(!in.eof()){
 618                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 619
 620                         in >> name;                             //read from first column
 621
 622                         //if this name is in the accnos file
 623                         if (names.count(name) == 0) {
 624                                 wroteSomething = true;
 625
 626                                 out << name << '\t';
 627
 628                                 //read rest
 629                                 for (int i = 0; i < 15; i++) {
 630                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 631                                         else                    {       break;                  }
 632                                 }
 633                                 out << endl;
 634
 635                         }else {//still read just don't do anything with it
 636
 637                                 //read rest
 638                                 for (int i = 0; i < 15; i++) {
 639                                         if (!in.eof())  {       in >> junk;             }
 640                                         else                    {       break;                  }
 641                                 }
 642                         }
 643
 644                         m->gobble(in);
 645                 }
 646                 in.close();
 647                 out.close();
 648
 649                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 650                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 651
 652                 return 0;
 653
 654         }
 655         catch(exception& e) {
 656                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 657                 exit(1);
 658         }
 659 }
 660 //**********************************************************************************************************************
 661