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; calledHelp = true;
  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; calledHelp = false;
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; calledHelp = 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);
 184                         if (temp == "not found") {
 185                                 if (namefile != "") {  temp = "true";                                   }
 186                                 else                            {  temp = "false"; usedDups = "";       }
 187                         }
 188                         dups = m->isTrue(temp);
 189
 190                         taxons = validParameter.validFile(parameters, "taxon", false);
 191                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 192                         else {
 193                                 //rip off quotes
 194                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 195                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 196                         }
 197
 198
 199                         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; }
 200
 201                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 202
 203                 }
 204
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 208                 exit(1);
 209         }
 210 }
 211 //**********************************************************************************************************************
 212
 213 void RemoveLineageCommand::help(){
 214         try {
 215                 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");
 216                 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");
 217                 m->mothurOut("The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide taxonomy and taxon.\n");
 218                 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");
 219                 m->mothurOut("The taxon parameter allows you to select the taxons you would like to remove.\n");
 220                 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");
 221                 m->mothurOut("If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n");
 222                 m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 223                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 224                 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");
 225                 m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
 226                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "RemoveLineageCommand", "help");
 230                 exit(1);
 231         }
 232 }
 233
 234 //**********************************************************************************************************************
 235
 236 int RemoveLineageCommand::execute(){
 237         try {
 238
 239                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 240
 241                 if (m->control_pressed) { return 0; }
 242
 243                 //read through the correct file and output lines you want to keep
 244                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 245                 if (namefile != "")                     {               readName();             }
 246                 if (fastafile != "")            {               readFasta();    }
 247                 if (groupfile != "")            {               readGroup();    }
 248                 if (alignfile != "")            {               readAlign();    }
 249                 if (listfile != "")                     {               readList();             }
 250
 251
 252                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 253
 254                 if (outputNames.size() != 0) {
 255                         m->mothurOutEndLine();
 256                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 257                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 258                         m->mothurOutEndLine();
 259                 }
 260
 261                 return 0;
 262         }
 263
 264         catch(exception& e) {
 265                 m->errorOut(e, "RemoveLineageCommand", "execute");
 266                 exit(1);
 267         }
 268 }
 269
 270 //**********************************************************************************************************************
 271 int RemoveLineageCommand::readFasta(){
 272         try {
 273                 string thisOutputDir = outputDir;
 274                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 275                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 276
 277                 ofstream out;
 278                 m->openOutputFile(outputFileName, out);
 279
 280                 ifstream in;
 281                 m->openInputFile(fastafile, in);
 282                 string name;
 283
 284                 bool wroteSomething = false;
 285
 286                 while(!in.eof()){
 287                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 288
 289                         Sequence currSeq(in);
 290                         name = currSeq.getName();
 291
 292                         if (name != "") {
 293                                 //if this name is in the accnos file
 294                                 if (names.count(name) == 0) {
 295                                         wroteSomething = true;
 296
 297                                         currSeq.printSequence(out);
 298                                 }
 299                         }
 300                         m->gobble(in);
 301                 }
 302                 in.close();
 303                 out.close();
 304
 305                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 306                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 307
 308                 return 0;
 309
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 313                 exit(1);
 314         }
 315 }
 316 //**********************************************************************************************************************
 317 int RemoveLineageCommand::readList(){
 318         try {
 319                 string thisOutputDir = outputDir;
 320                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 321                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 322
 323                 ofstream out;
 324                 m->openOutputFile(outputFileName, out);
 325
 326                 ifstream in;
 327                 m->openInputFile(listfile, in);
 328
 329                 bool wroteSomething = false;
 330
 331                 while(!in.eof()){
 332                         //read in list vector
 333                         ListVector list(in);
 334
 335                         //make a new list vector
 336                         ListVector newList;
 337                         newList.setLabel(list.getLabel());
 338
 339                         //for each bin
 340                         for (int i = 0; i < list.getNumBins(); i++) {
 341                                 if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 342
 343                                 //parse out names that are in accnos file
 344                                 string binnames = list.get(i);
 345
 346                                 string newNames = "";
 347                                 while (binnames.find_first_of(',') != -1) {
 348                                         string name = binnames.substr(0,binnames.find_first_of(','));
 349                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 350
 351                                         //if that name is in the .accnos file, add it
 352                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 353                                 }
 354
 355                                 //get last name
 356                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 357
 358                                 //if there are names in this bin add to new list
 359                                 if (newNames != "") {
 360                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 361                                         newList.push_back(newNames);
 362                                 }
 363                         }
 364
 365                         //print new listvector
 366                         if (newList.getNumBins() != 0) {
 367                                 wroteSomething = true;
 368                                 newList.print(out);
 369                         }
 370
 371                         m->gobble(in);
 372                 }
 373                 in.close();
 374                 out.close();
 375
 376                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 377                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 378
 379                 return 0;
 380
 381         }
 382         catch(exception& e) {
 383                 m->errorOut(e, "RemoveLineageCommand", "readList");
 384                 exit(1);
 385         }
 386 }
 387 //**********************************************************************************************************************
 388 int RemoveLineageCommand::readName(){
 389         try {
 390                 string thisOutputDir = outputDir;
 391                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 392                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 393
 394                 ofstream out;
 395                 m->openOutputFile(outputFileName, out);
 396
 397                 ifstream in;
 398                 m->openInputFile(namefile, in);
 399                 string name, firstCol, secondCol;
 400
 401                 bool wroteSomething = false;
 402
 403                 while(!in.eof()){
 404                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 405
 406                         in >> firstCol;
 407                         in >> secondCol;
 408
 409                         vector<string> parsedNames;
 410                         //parse second column saving each name
 411                         while (secondCol.find_first_of(',') != -1) {
 412                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 413                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 414                                 parsedNames.push_back(name);
 415                         }
 416
 417                         //get name after last ,
 418                         parsedNames.push_back(secondCol);
 419
 420                         vector<string> validSecond;  validSecond.clear();
 421                         for (int i = 0; i < parsedNames.size(); i++) {
 422                                 if (names.count(parsedNames[i]) == 0) {
 423                                         validSecond.push_back(parsedNames[i]);
 424                                 }
 425                         }
 426
 427                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 428                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 429                         }else {
 430                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 431                                 if (names.count(firstCol) == 0) {
 432
 433                                         wroteSomething = true;
 434
 435                                         out << firstCol << '\t';
 436
 437                                         //you know you have at least one valid second since first column is valid
 438                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 439                                         out << validSecond[validSecond.size()-1] << endl;
 440
 441                                         //make first name in set you come to first column and then add the remaining names to second column
 442                                 }else {
 443
 444                                         //you want part of this row
 445                                         if (validSecond.size() != 0) {
 446
 447                                                 wroteSomething = true;
 448
 449                                                 out << validSecond[0] << '\t';
 450
 451                                                 //you know you have at least one valid second since first column is valid
 452                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 453                                                 out << validSecond[validSecond.size()-1] << endl;
 454                                         }
 455                                 }
 456                         }
 457                         m->gobble(in);
 458                 }
 459                 in.close();
 460                 out.close();
 461
 462                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 463                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 464
 465                 return 0;
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "RemoveLineageCommand", "readName");
 469                 exit(1);
 470         }
 471 }
 472
 473 //**********************************************************************************************************************
 474 int RemoveLineageCommand::readGroup(){
 475         try {
 476                 string thisOutputDir = outputDir;
 477                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 478                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 479
 480                 ofstream out;
 481                 m->openOutputFile(outputFileName, out);
 482
 483                 ifstream in;
 484                 m->openInputFile(groupfile, in);
 485                 string name, group;
 486
 487                 bool wroteSomething = false;
 488
 489                 while(!in.eof()){
 490                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 491
 492                         in >> name;                             //read from first column
 493                         in >> group;                    //read from second column
 494
 495                         //if this name is in the accnos file
 496                         if (names.count(name) == 0) {
 497                                 wroteSomething = true;
 498                                 out << name << '\t' << group << endl;
 499                         }
 500
 501                         m->gobble(in);
 502                 }
 503                 in.close();
 504                 out.close();
 505
 506                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 507                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 508
 509                 return 0;
 510         }
 511         catch(exception& e) {
 512                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 513                 exit(1);
 514         }
 515 }
 516 //**********************************************************************************************************************
 517 int RemoveLineageCommand::readTax(){
 518         try {
 519                 string thisOutputDir = outputDir;
 520                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 521                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 522                 ofstream out;
 523                 m->openOutputFile(outputFileName, out);
 524
 525                 ifstream in;
 526                 m->openInputFile(taxfile, in);
 527                 string name, tax;
 528
 529                 bool wroteSomething = false;
 530
 531                 bool taxonsHasConfidence = false;
 532                 vector< map<string, int> > searchTaxons;
 533                 string noConfidenceTaxons = taxons;
 534                 int hasConPos = taxons.find_first_of('(');
 535                 if (hasConPos != string::npos) {
 536                         taxonsHasConfidence = true;
 537                         searchTaxons = getTaxons(taxons);
 538                         noConfidenceTaxons = removeConfidences(taxons);
 539                 }
 540
 541
 542                 while(!in.eof()){
 543
 544                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 545
 546                         in >> name;                             //read from first column
 547                         in >> tax;                      //read from second column
 548
 549                         string newtax = tax;
 550
 551                         //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 552                         if (!taxonsHasConfidence) {
 553
 554                                 int hasConfidences = tax.find_first_of('(');
 555                                 if (hasConfidences != string::npos) {
 556                                         newtax = removeConfidences(tax);
 557                                 }
 558
 559                                 int pos = newtax.find(taxons);
 560
 561                                 if (pos == string::npos) {
 562                                         wroteSomething = true;
 563                                         out << name << '\t' << tax << endl;
 564                                 }else{ //this sequence contains the taxon the user wants to remove
 565                                         names.insert(name);
 566                                 }
 567
 568                         }else{//if taxons has them and you don't them remove taxons
 569                                 int hasConfidences = tax.find_first_of('(');
 570                                 if (hasConfidences == string::npos) {
 571
 572                                         int pos = newtax.find(noConfidenceTaxons);
 573
 574                                         if (pos == string::npos) {
 575                                                 wroteSomething = true;
 576                                                 out << name << '\t' << tax << endl;
 577                                         }else{ //this sequence contains the taxon the user wants to remove
 578                                                 names.insert(name);
 579                                         }
 580                                 }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 581                                         //first remove confidences from both and see if the taxonomy exists
 582
 583                                         string noNewTax = tax;
 584                                         int hasConfidences = tax.find_first_of('(');
 585                                         if (hasConfidences != string::npos) {
 586                                                 noNewTax = removeConfidences(tax);
 587                                         }
 588
 589                                         int pos = noNewTax.find(noConfidenceTaxons);
 590
 591                                         if (pos != string::npos) { //if yes, then are the confidences okay
 592
 593                                                 bool remove = false;
 594                                                 vector< map<string, int> > usersTaxon = getTaxons(newtax);
 595
 596                                                 //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 597                                                 //we want to "line them up", so we will find the the index where the searchstring starts
 598                                                 int index = 0;
 599                                                 for (int i = 0; i < usersTaxon.size(); i++) {
 600
 601                                                         if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
 602                                                                 index = i;
 603                                                                 int spot = 0;
 604                                                                 bool goodspot = true;
 605                                                                 //is this really the start, or are we dealing with a taxon of the same name?
 606                                                                 while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
 607                                                                         if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
 608                                                                         else { spot++; }
 609                                                                 }
 610
 611                                                                 if (goodspot) { break; }
 612                                                         }
 613                                                 }
 614
 615                                                 for (int i = 0; i < searchTaxons.size(); i++) {
 616
 617                                                         if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 618                                                                 if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
 619                                                                         remove = true;
 620                                                                         break;
 621                                                                 }
 622                                                         }else {
 623                                                                 remove = true;
 624                                                                 break;
 625                                                         }
 626                                                 }
 627
 628                                                 //passed the test so remove you
 629                                                 if (remove) {
 630                                                         names.insert(name);
 631                                                 }else {
 632                                                         wroteSomething = true;
 633                                                         out << name << '\t' << tax << endl;
 634                                                 }
 635                                         }else {
 636                                                 wroteSomething = true;
 637                                                 out << name << '\t' << tax << endl;
 638                                         }
 639                                 }
 640                         }
 641
 642
 643
 644
 645                         m->gobble(in);
 646                 }
 647                 in.close();
 648                 out.close();
 649
 650                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 651                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 652
 653                 return 0;
 654
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 658                 exit(1);
 659         }
 660 }
 661 /**************************************************************************************************/
 662 vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
 663         try {
 664
 665                 vector< map<string, int> > t;
 666                 string taxon = "";
 667                 int taxLength = tax.length();
 668                 for(int i=0;i<taxLength;i++){
 669                         if(tax[i] == ';'){
 670
 671                                 int openParen = taxon.find_first_of('(');
 672                                 int closeParen = taxon.find_last_of(')');
 673
 674                                 string newtaxon, confidence;
 675                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 676                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 677                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 678                                 }else{
 679                                         newtaxon = taxon;
 680                                         confidence = "0";
 681                                 }
 682                                 int con = 0;
 683                                 convert(confidence, con);
 684
 685                                 map<string, int> temp;
 686                                 temp[newtaxon] = con;
 687                                 t.push_back(temp);
 688
 689                                 taxon = "";
 690                         }
 691                         else{
 692                                 taxon += tax[i];
 693                         }
 694                 }
 695
 696                 return t;
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
 700                 exit(1);
 701         }
 702 }
 703 /**************************************************************************************************/
 704 string RemoveLineageCommand::removeConfidences(string tax) {
 705         try {
 706
 707                 string taxon = "";
 708                 int taxLength = tax.length();
 709                 for(int i=0;i<taxLength;i++){
 710                         if(tax[i] == ';'){
 711                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 712                                 taxon += ";";
 713                         }
 714                         else{
 715                                 taxon += tax[i];
 716                         }
 717                 }
 718
 719                 return taxon;
 720         }
 721         catch(exception& e) {
 722                 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
 723                 exit(1);
 724         }
 725 }
 726 //**********************************************************************************************************************
 727 //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
 728 int RemoveLineageCommand::readAlign(){
 729         try {
 730                 string thisOutputDir = outputDir;
 731                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 732                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 733
 734                 ofstream out;
 735                 m->openOutputFile(outputFileName, out);
 736
 737                 ifstream in;
 738                 m->openInputFile(alignfile, in);
 739                 string name, junk;
 740
 741                 bool wroteSomething = false;
 742
 743                 //read column headers
 744                 for (int i = 0; i < 16; i++) {
 745                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 746                         else                    {       break;                  }
 747                 }
 748                 out << endl;
 749
 750                 while(!in.eof()){
 751                         if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 752
 753                         in >> name;                             //read from first column
 754
 755                         //if this name is in the accnos file
 756                         if (names.count(name) == 0) {
 757                                 wroteSomething = true;
 758
 759                                 out << name << '\t';
 760
 761                                 //read rest
 762                                 for (int i = 0; i < 15; i++) {
 763                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 764                                         else                    {       break;                  }
 765                                 }
 766                                 out << endl;
 767
 768                         }else {//still read just don't do anything with it
 769
 770                                 //read rest
 771                                 for (int i = 0; i < 15; i++) {
 772                                         if (!in.eof())  {       in >> junk;             }
 773                                         else                    {       break;                  }
 774                                 }
 775                         }
 776
 777                         m->gobble(in);
 778                 }
 779                 in.close();
 780                 out.close();
 781
 782                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 783                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 784
 785                 return 0;
 786
 787         }
 788         catch(exception& e) {
 789                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 790                 exit(1);
 791         }
 792 }
 793 //**********************************************************************************************************************
 794