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("You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n");
 222                 m->mothurOut("If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n");
 223                 m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 224                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 225                 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");
 226                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
 227                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "RemoveLineageCommand", "help");
 231                 exit(1);
 232         }
 233 }
 234
 235 //**********************************************************************************************************************
 236
 237 int RemoveLineageCommand::execute(){
 238         try {
 239
 240                 if (abort == true) { return 0; }
 241
 242                 if (m->control_pressed) { return 0; }
 243
 244                 //read through the correct file and output lines you want to keep
 245                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 246                 if (namefile != "")                     {               readName();             }
 247                 if (fastafile != "")            {               readFasta();    }
 248                 if (groupfile != "")            {               readGroup();    }
 249                 if (alignfile != "")            {               readAlign();    }
 250                 if (listfile != "")                     {               readList();             }
 251
 252
 253                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 254
 255                 if (outputNames.size() != 0) {
 256                         m->mothurOutEndLine();
 257                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 258                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 259                         m->mothurOutEndLine();
 260                 }
 261
 262                 return 0;
 263         }
 264
 265         catch(exception& e) {
 266                 m->errorOut(e, "RemoveLineageCommand", "execute");
 267                 exit(1);
 268         }
 269 }
 270
 271 //**********************************************************************************************************************
 272 int RemoveLineageCommand::readFasta(){
 273         try {
 274                 string thisOutputDir = outputDir;
 275                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 276                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 277
 278                 ofstream out;
 279                 m->openOutputFile(outputFileName, out);
 280
 281                 ifstream in;
 282                 m->openInputFile(fastafile, in);
 283                 string name;
 284
 285                 bool wroteSomething = false;
 286
 287                 while(!in.eof()){
 288                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 289
 290                         Sequence currSeq(in);
 291                         name = currSeq.getName();
 292
 293                         if (name != "") {
 294                                 //if this name is in the accnos file
 295                                 if (names.count(name) == 0) {
 296                                         wroteSomething = true;
 297
 298                                         currSeq.printSequence(out);
 299                                 }
 300                         }
 301                         m->gobble(in);
 302                 }
 303                 in.close();
 304                 out.close();
 305
 306                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 307                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 308
 309                 return 0;
 310
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************
 318 int RemoveLineageCommand::readList(){
 319         try {
 320                 string thisOutputDir = outputDir;
 321                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 322                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 323
 324                 ofstream out;
 325                 m->openOutputFile(outputFileName, out);
 326
 327                 ifstream in;
 328                 m->openInputFile(listfile, in);
 329
 330                 bool wroteSomething = false;
 331
 332                 while(!in.eof()){
 333                         //read in list vector
 334                         ListVector list(in);
 335
 336                         //make a new list vector
 337                         ListVector newList;
 338                         newList.setLabel(list.getLabel());
 339
 340                         //for each bin
 341                         for (int i = 0; i < list.getNumBins(); i++) {
 342                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 343
 344                                 //parse out names that are in accnos file
 345                                 string binnames = list.get(i);
 346
 347                                 string newNames = "";
 348                                 while (binnames.find_first_of(',') != -1) {
 349                                         string name = binnames.substr(0,binnames.find_first_of(','));
 350                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 351
 352                                         //if that name is in the .accnos file, add it
 353                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 354                                 }
 355
 356                                 //get last name
 357                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 358
 359                                 //if there are names in this bin add to new list
 360                                 if (newNames != "") {
 361                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 362                                         newList.push_back(newNames);
 363                                 }
 364                         }
 365
 366                         //print new listvector
 367                         if (newList.getNumBins() != 0) {
 368                                 wroteSomething = true;
 369                                 newList.print(out);
 370                         }
 371
 372                         m->gobble(in);
 373                 }
 374                 in.close();
 375                 out.close();
 376
 377                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 378                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 379
 380                 return 0;
 381
 382         }
 383         catch(exception& e) {
 384                 m->errorOut(e, "RemoveLineageCommand", "readList");
 385                 exit(1);
 386         }
 387 }
 388 //**********************************************************************************************************************
 389 int RemoveLineageCommand::readName(){
 390         try {
 391                 string thisOutputDir = outputDir;
 392                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 393                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 394
 395                 ofstream out;
 396                 m->openOutputFile(outputFileName, out);
 397
 398                 ifstream in;
 399                 m->openInputFile(namefile, in);
 400                 string name, firstCol, secondCol;
 401
 402                 bool wroteSomething = false;
 403
 404                 while(!in.eof()){
 405                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 406
 407                         in >> firstCol;
 408                         in >> secondCol;
 409
 410                         vector<string> parsedNames;
 411                         //parse second column saving each name
 412                         while (secondCol.find_first_of(',') != -1) {
 413                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 414                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 415                                 parsedNames.push_back(name);
 416                         }
 417
 418                         //get name after last ,
 419                         parsedNames.push_back(secondCol);
 420
 421                         vector<string> validSecond;  validSecond.clear();
 422                         for (int i = 0; i < parsedNames.size(); i++) {
 423                                 if (names.count(parsedNames[i]) == 0) {
 424                                         validSecond.push_back(parsedNames[i]);
 425                                 }
 426                         }
 427
 428                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 429                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 430                         }else {
 431                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 432                                 if (names.count(firstCol) == 0) {
 433
 434                                         wroteSomething = true;
 435
 436                                         out << firstCol << '\t';
 437
 438                                         //you know you have at least one valid second since first column is valid
 439                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 440                                         out << validSecond[validSecond.size()-1] << endl;
 441
 442                                         //make first name in set you come to first column and then add the remaining names to second column
 443                                 }else {
 444
 445                                         //you want part of this row
 446                                         if (validSecond.size() != 0) {
 447
 448                                                 wroteSomething = true;
 449
 450                                                 out << validSecond[0] << '\t';
 451
 452                                                 //you know you have at least one valid second since first column is valid
 453                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 454                                                 out << validSecond[validSecond.size()-1] << endl;
 455                                         }
 456                                 }
 457                         }
 458                         m->gobble(in);
 459                 }
 460                 in.close();
 461                 out.close();
 462
 463                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 464                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 465
 466                 return 0;
 467         }
 468         catch(exception& e) {
 469                 m->errorOut(e, "RemoveLineageCommand", "readName");
 470                 exit(1);
 471         }
 472 }
 473
 474 //**********************************************************************************************************************
 475 int RemoveLineageCommand::readGroup(){
 476         try {
 477                 string thisOutputDir = outputDir;
 478                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 479                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 480
 481                 ofstream out;
 482                 m->openOutputFile(outputFileName, out);
 483
 484                 ifstream in;
 485                 m->openInputFile(groupfile, in);
 486                 string name, group;
 487
 488                 bool wroteSomething = false;
 489
 490                 while(!in.eof()){
 491                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 492
 493                         in >> name;                             //read from first column
 494                         in >> group;                    //read from second column
 495
 496                         //if this name is in the accnos file
 497                         if (names.count(name) == 0) {
 498                                 wroteSomething = true;
 499                                 out << name << '\t' << group << endl;
 500                         }
 501
 502                         m->gobble(in);
 503                 }
 504                 in.close();
 505                 out.close();
 506
 507                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 508                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 509
 510                 return 0;
 511         }
 512         catch(exception& e) {
 513                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 514                 exit(1);
 515         }
 516 }
 517 //**********************************************************************************************************************
 518 int RemoveLineageCommand::readTax(){
 519         try {
 520                 string thisOutputDir = outputDir;
 521                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 522                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 523                 ofstream out;
 524                 m->openOutputFile(outputFileName, out);
 525
 526                 ifstream in;
 527                 m->openInputFile(taxfile, in);
 528                 string name, tax;
 529
 530                 bool wroteSomething = false;
 531
 532                 bool taxonsHasConfidence = false;
 533                 vector< map<string, int> > searchTaxons;
 534                 string noConfidenceTaxons = taxons;
 535                 int hasConPos = taxons.find_first_of('(');
 536                 if (hasConPos != string::npos) {
 537                         taxonsHasConfidence = true;
 538                         searchTaxons = getTaxons(taxons);
 539                         noConfidenceTaxons = removeConfidences(taxons);
 540                 }
 541
 542
 543                 while(!in.eof()){
 544
 545                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 546
 547                         in >> name;                             //read from first column
 548                         in >> tax;                      //read from second column
 549
 550                         string newtax = tax;
 551
 552                         //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 553                         if (!taxonsHasConfidence) {
 554
 555                                 int hasConfidences = tax.find_first_of('(');
 556                                 if (hasConfidences != string::npos) {
 557                                         newtax = removeConfidences(tax);
 558                                 }
 559
 560                                 int pos = newtax.find(taxons);
 561
 562                                 if (pos == string::npos) {
 563                                         wroteSomething = true;
 564                                         out << name << '\t' << tax << endl;
 565                                 }else{ //this sequence contains the taxon the user wants to remove
 566                                         names.insert(name);
 567                                 }
 568
 569                         }else{//if taxons has them and you don't them remove taxons
 570                                 int hasConfidences = tax.find_first_of('(');
 571                                 if (hasConfidences == string::npos) {
 572
 573                                         int pos = newtax.find(noConfidenceTaxons);
 574
 575                                         if (pos == string::npos) {
 576                                                 wroteSomething = true;
 577                                                 out << name << '\t' << tax << endl;
 578                                         }else{ //this sequence contains the taxon the user wants to remove
 579                                                 names.insert(name);
 580                                         }
 581                                 }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 582                                         //first remove confidences from both and see if the taxonomy exists
 583
 584                                         string noNewTax = tax;
 585                                         int hasConfidences = tax.find_first_of('(');
 586                                         if (hasConfidences != string::npos) {
 587                                                 noNewTax = removeConfidences(tax);
 588                                         }
 589
 590                                         int pos = noNewTax.find(noConfidenceTaxons);
 591
 592                                         if (pos != string::npos) { //if yes, then are the confidences okay
 593
 594                                                 bool remove = false;
 595                                                 vector< map<string, int> > usersTaxon = getTaxons(newtax);
 596
 597                                                 //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 598                                                 //we want to "line them up", so we will find the the index where the searchstring starts
 599                                                 int index = 0;
 600                                                 for (int i = 0; i < usersTaxon.size(); i++) {
 601
 602                                                         if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
 603                                                                 index = i;
 604                                                                 int spot = 0;
 605                                                                 bool goodspot = true;
 606                                                                 //is this really the start, or are we dealing with a taxon of the same name?
 607                                                                 while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
 608                                                                         if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
 609                                                                         else { spot++; }
 610                                                                 }
 611
 612                                                                 if (goodspot) { break; }
 613                                                         }
 614                                                 }
 615
 616                                                 for (int i = 0; i < searchTaxons.size(); i++) {
 617
 618                                                         if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 619                                                                 if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
 620                                                                         remove = true;
 621                                                                         break;
 622                                                                 }
 623                                                         }else {
 624                                                                 remove = true;
 625                                                                 break;
 626                                                         }
 627                                                 }
 628
 629                                                 //passed the test so remove you
 630                                                 if (remove) {
 631                                                         names.insert(name);
 632                                                 }else {
 633                                                         wroteSomething = true;
 634                                                         out << name << '\t' << tax << endl;
 635                                                 }
 636                                         }else {
 637                                                 wroteSomething = true;
 638                                                 out << name << '\t' << tax << endl;
 639                                         }
 640                                 }
 641                         }
 642
 643
 644
 645
 646                         m->gobble(in);
 647                 }
 648                 in.close();
 649                 out.close();
 650
 651                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 652                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 653
 654                 return 0;
 655
 656         }
 657         catch(exception& e) {
 658                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 659                 exit(1);
 660         }
 661 }
 662 /**************************************************************************************************/
 663 vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
 664         try {
 665
 666                 vector< map<string, int> > t;
 667                 string taxon = "";
 668                 int taxLength = tax.length();
 669                 for(int i=0;i<taxLength;i++){
 670                         if(tax[i] == ';'){
 671
 672                                 int openParen = taxon.find_first_of('(');
 673                                 int closeParen = taxon.find_last_of(')');
 674
 675                                 string newtaxon, confidence;
 676                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 677                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 678                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 679                                 }else{
 680                                         newtaxon = taxon;
 681                                         confidence = "0";
 682                                 }
 683                                 int con = 0;
 684                                 convert(confidence, con);
 685
 686                                 map<string, int> temp;
 687                                 temp[newtaxon] = con;
 688                                 t.push_back(temp);
 689
 690                                 taxon = "";
 691                         }
 692                         else{
 693                                 taxon += tax[i];
 694                         }
 695                 }
 696
 697                 return t;
 698         }
 699         catch(exception& e) {
 700                 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
 701                 exit(1);
 702         }
 703 }
 704 /**************************************************************************************************/
 705 string RemoveLineageCommand::removeConfidences(string tax) {
 706         try {
 707
 708                 string taxon = "";
 709                 int taxLength = tax.length();
 710                 for(int i=0;i<taxLength;i++){
 711                         if(tax[i] == ';'){
 712                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 713                                 taxon += ";";
 714                         }
 715                         else{
 716                                 taxon += tax[i];
 717                         }
 718                 }
 719
 720                 return taxon;
 721         }
 722         catch(exception& e) {
 723                 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
 724                 exit(1);
 725         }
 726 }
 727 //**********************************************************************************************************************
 728 //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
 729 int RemoveLineageCommand::readAlign(){
 730         try {
 731                 string thisOutputDir = outputDir;
 732                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 733                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 734
 735                 ofstream out;
 736                 m->openOutputFile(outputFileName, out);
 737
 738                 ifstream in;
 739                 m->openInputFile(alignfile, in);
 740                 string name, junk;
 741
 742                 bool wroteSomething = false;
 743
 744                 //read column headers
 745                 for (int i = 0; i < 16; i++) {
 746                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 747                         else                    {       break;                  }
 748                 }
 749                 out << endl;
 750
 751                 while(!in.eof()){
 752                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 753
 754                         in >> name;                             //read from first column
 755
 756                         //if this name is in the accnos file
 757                         if (names.count(name) == 0) {
 758                                 wroteSomething = true;
 759
 760                                 out << name << '\t';
 761
 762                                 //read rest
 763                                 for (int i = 0; i < 15; i++) {
 764                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 765                                         else                    {       break;                  }
 766                                 }
 767                                 out << endl;
 768
 769                         }else {//still read just don't do anything with it
 770
 771                                 //read rest
 772                                 for (int i = 0; i < 15; i++) {
 773                                         if (!in.eof())  {       in >> junk;             }
 774                                         else                    {       break;                  }
 775                                 }
 776                         }
 777
 778                         m->gobble(in);
 779                 }
 780                 in.close();
 781                 out.close();
 782
 783                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 784                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 785
 786                 return 0;
 787
 788         }
 789         catch(exception& e) {
 790                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 791                 exit(1);
 792         }
 793 }
 794 //**********************************************************************************************************************
 795