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::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  18         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  19         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  22                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
  23                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  24                 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
  25                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "RemoveLineageCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string RemoveLineageCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 helpString += "The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, count, list or alignreport file.\n";
  43                 helpString += "It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n";
  44                 helpString += "The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, count, alignreport and dups.  You must provide taxonomy unless you have a valid current taxonomy file.\n";
  45                 helpString += "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";
  46                 helpString += "The taxon parameter allows you to select the taxons you would like to remove, and is required.\n";
  47                 helpString += "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";
  48                 helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
  49                 helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
  50                 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
  51                 helpString += "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";
  52                 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "RemoveLineageCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string RemoveLineageCommand::getOutputFileNameTag(string type, string inputName=""){
  63         try {
  64         string outputFileName = "";
  65                 map<string, vector<string> >::iterator it;
  66
  67         //is this a type this command creates
  68         it = outputTypes.find(type);
  69         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  70         else {
  71             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  72             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else if (type == "count")       {   outputFileName =  "pick.count.table";   }
  77             else if (type == "alignreport")      {   outputFileName =  "pick.align.report";   }
  78             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  79         }
  80         return outputFileName;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "RemoveLineageCommand", "getOutputFileNameTag");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 RemoveLineageCommand::RemoveLineageCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  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         outputTypes["count"] = tempOutNames;
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107 RemoveLineageCommand::RemoveLineageCommand(string option)  {
 108         try {
 109                 abort = false; calledHelp = false;
 110
 111                 //allow user to run help
 112                 if(option == "help") { help(); abort = true; calledHelp = true; }
 113                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 114
 115                 else {
 116                         vector<string> myArray = setParameters();
 117
 118                         OptionParser parser(option);
 119                         map<string,string> parameters = parser.getParameters();
 120
 121                         ValidParameters validParameter;
 122                         map<string,string>::iterator it;
 123
 124                         //check to make sure all parameters are valid for command
 125                         for (it = parameters.begin(); it != parameters.end(); it++) {
 126                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 127                         }
 128
 129                         //initialize outputTypes
 130                         vector<string> tempOutNames;
 131                         outputTypes["fasta"] = tempOutNames;
 132                         outputTypes["taxonomy"] = tempOutNames;
 133                         outputTypes["name"] = tempOutNames;
 134                         outputTypes["group"] = tempOutNames;
 135                         outputTypes["alignreport"] = tempOutNames;
 136                         outputTypes["list"] = tempOutNames;
 137             outputTypes["count"] = tempOutNames;
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 141
 142                         //if the user changes the input directory command factory will send this info to us in the output parameter
 143                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 144                         if (inputDir == "not found"){   inputDir = "";          }
 145                         else {
 146                                 string path;
 147                                 it = parameters.find("alignreport");
 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["alignreport"] = inputDir + it->second;              }
 153                                 }
 154
 155                                 it = parameters.find("fasta");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 161                                 }
 162
 163                                 it = parameters.find("list");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 169                                 }
 170
 171                                 it = parameters.find("name");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 177                                 }
 178
 179                                 it = parameters.find("group");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 185                                 }
 186
 187                                 it = parameters.find("taxonomy");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 193                                 }
 194
 195                 it = parameters.find("count");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 201                                 }
 202                         }
 203
 204
 205                         //check for required parameters
 206                         fastafile = validParameter.validFile(parameters, "fasta", true);
 207                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 208                         else if (fastafile == "not found") {  fastafile = "";  }
 209                         else { m->setFastaFile(fastafile); }
 210
 211                         namefile = validParameter.validFile(parameters, "name", true);
 212                         if (namefile == "not open") { namefile = ""; abort = true; }
 213                         else if (namefile == "not found") {  namefile = "";  }
 214                         else { m->setNameFile(namefile); }
 215
 216                         groupfile = validParameter.validFile(parameters, "group", true);
 217                         if (groupfile == "not open") { abort = true; }
 218                         else if (groupfile == "not found") {  groupfile = "";  }
 219                         else { m->setGroupFile(groupfile); }
 220
 221                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 222                         if (alignfile == "not open") { abort = true; }
 223                         else if (alignfile == "not found") {  alignfile = "";  }
 224
 225                         listfile = validParameter.validFile(parameters, "list", true);
 226                         if (listfile == "not open") { abort = true; }
 227                         else if (listfile == "not found") {  listfile = "";  }
 228                         else { m->setListFile(listfile); }
 229
 230                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 231                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 232                         else if (taxfile == "not found") {
 233                                 taxfile = m->getTaxonomyFile();
 234                                 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 235                                 else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
 236                         }else { m->setTaxonomyFile(taxfile); }
 237
 238             countfile = validParameter.validFile(parameters, "count", true);
 239             if (countfile == "not open") { countfile = ""; abort = true; }
 240             else if (countfile == "not found") { countfile = "";  }
 241             else { m->setCountTableFile(countfile); }
 242
 243             if ((namefile != "") && (countfile != "")) {
 244                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 245             }
 246
 247             if ((groupfile != "") && (countfile != "")) {
 248                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 249             }
 250
 251                         string usedDups = "true";
 252                         string temp = validParameter.validFile(parameters, "dups", false);
 253                         if (temp == "not found") {
 254                                 if (namefile != "") {  temp = "true";                                   }
 255                                 else                            {  temp = "false"; usedDups = "";       }
 256                         }
 257                         dups = m->isTrue(temp);
 258
 259                         taxons = validParameter.validFile(parameters, "taxon", false);
 260                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 261                         else {
 262                                 //rip off quotes
 263                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 264                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 265                         }
 266                         m->splitAtChar(taxons, listOfTaxons, '-');
 267
 268                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
 269
 270                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 271
 272                         if (countfile == "") {
 273                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 274                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 275                     parser.getNameFile(files);
 276                 }
 277             }
 278
 279                 }
 280
 281         }
 282         catch(exception& e) {
 283                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 284                 exit(1);
 285         }
 286 }
 287 //**********************************************************************************************************************
 288
 289 int RemoveLineageCommand::execute(){
 290         try {
 291
 292                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 293
 294                 if (m->control_pressed) { return 0; }
 295
 296         if (countfile != "") {
 297             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 298                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
 299             }
 300         }
 301
 302                 //read through the correct file and output lines you want to keep
 303                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 304                 if (namefile != "")                     {               readName();             }
 305                 if (fastafile != "")            {               readFasta();    }
 306                 if (groupfile != "")            {               readGroup();    }
 307                 if (alignfile != "")            {               readAlign();    }
 308                 if (listfile != "")                     {               readList();             }
 309         if (countfile != "")            {               readCount();    }
 310
 311
 312                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 313
 314                 if (outputNames.size() != 0) {
 315                         m->mothurOutEndLine();
 316                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 317                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 318                         m->mothurOutEndLine();
 319
 320                         //set fasta file as new current fastafile
 321                         string current = "";
 322                         itTypes = outputTypes.find("fasta");
 323                         if (itTypes != outputTypes.end()) {
 324                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 325                         }
 326
 327                         itTypes = outputTypes.find("name");
 328                         if (itTypes != outputTypes.end()) {
 329                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 330                         }
 331
 332                         itTypes = outputTypes.find("group");
 333                         if (itTypes != outputTypes.end()) {
 334                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 335                         }
 336
 337                         itTypes = outputTypes.find("list");
 338                         if (itTypes != outputTypes.end()) {
 339                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 340                         }
 341
 342                         itTypes = outputTypes.find("taxonomy");
 343                         if (itTypes != outputTypes.end()) {
 344                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 345                         }
 346
 347             itTypes = outputTypes.find("count");
 348                         if (itTypes != outputTypes.end()) {
 349                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 350                         }
 351                 }
 352
 353                 return 0;
 354         }
 355
 356         catch(exception& e) {
 357                 m->errorOut(e, "RemoveLineageCommand", "execute");
 358                 exit(1);
 359         }
 360 }
 361
 362 //**********************************************************************************************************************
 363 int RemoveLineageCommand::readFasta(){
 364         try {
 365                 string thisOutputDir = outputDir;
 366                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 367                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 368                 ofstream out;
 369                 m->openOutputFile(outputFileName, out);
 370
 371                 ifstream in;
 372                 m->openInputFile(fastafile, in);
 373                 string name;
 374
 375                 bool wroteSomething = false;
 376
 377                 while(!in.eof()){
 378                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 379
 380                         Sequence currSeq(in);
 381                         name = currSeq.getName();
 382
 383                         if (name != "") {
 384                                 //if this name is in the accnos file
 385                                 if (names.count(name) == 0) {
 386                                         wroteSomething = true;
 387
 388                                         currSeq.printSequence(out);
 389                                 }
 390                         }
 391                         m->gobble(in);
 392                 }
 393                 in.close();
 394                 out.close();
 395
 396                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 397                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 398
 399                 return 0;
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 404                 exit(1);
 405         }
 406 }
 407 //**********************************************************************************************************************
 408 int RemoveLineageCommand::readList(){
 409         try {
 410                 string thisOutputDir = outputDir;
 411                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 412                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 413                 ofstream out;
 414                 m->openOutputFile(outputFileName, out);
 415
 416                 ifstream in;
 417                 m->openInputFile(listfile, in);
 418
 419                 bool wroteSomething = false;
 420
 421                 while(!in.eof()){
 422                         //read in list vector
 423                         ListVector list(in);
 424
 425                         //make a new list vector
 426                         ListVector newList;
 427                         newList.setLabel(list.getLabel());
 428
 429                         //for each bin
 430                         for (int i = 0; i < list.getNumBins(); i++) {
 431                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 432
 433                                 //parse out names that are in accnos file
 434                                 string binnames = list.get(i);
 435
 436                                 string newNames = "";
 437                                 while (binnames.find_first_of(',') != -1) {
 438                                         string name = binnames.substr(0,binnames.find_first_of(','));
 439                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 440
 441                                         //if that name is in the .accnos file, add it
 442                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 443                                 }
 444
 445                                 //get last name
 446                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 447
 448                                 //if there are names in this bin add to new list
 449                                 if (newNames != "") {
 450                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 451                                         newList.push_back(newNames);
 452                                 }
 453                         }
 454
 455                         //print new listvector
 456                         if (newList.getNumBins() != 0) {
 457                                 wroteSomething = true;
 458                                 newList.print(out);
 459                         }
 460
 461                         m->gobble(in);
 462                 }
 463                 in.close();
 464                 out.close();
 465
 466                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 467                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 468
 469                 return 0;
 470
 471         }
 472         catch(exception& e) {
 473                 m->errorOut(e, "RemoveLineageCommand", "readList");
 474                 exit(1);
 475         }
 476 }
 477 //**********************************************************************************************************************
 478 int RemoveLineageCommand::readName(){
 479         try {
 480                 string thisOutputDir = outputDir;
 481                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 482                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 483                 ofstream out;
 484                 m->openOutputFile(outputFileName, out);
 485
 486                 ifstream in;
 487                 m->openInputFile(namefile, in);
 488                 string name, firstCol, secondCol;
 489
 490                 bool wroteSomething = false;
 491
 492                 while(!in.eof()){
 493                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 494
 495                         in >> firstCol;
 496                         in >> secondCol;
 497
 498                         vector<string> parsedNames;
 499                         m->splitAtComma(secondCol, parsedNames);
 500
 501                         vector<string> validSecond;  validSecond.clear();
 502                         for (int i = 0; i < parsedNames.size(); i++) {
 503                                 if (names.count(parsedNames[i]) == 0) {
 504                                         validSecond.push_back(parsedNames[i]);
 505                                 }
 506                         }
 507
 508                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 509                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 510                         }else {
 511                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 512                                 if (names.count(firstCol) == 0) {
 513
 514                                         wroteSomething = true;
 515
 516                                         out << firstCol << '\t';
 517
 518                                         //you know you have at least one valid second since first column is valid
 519                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 520                                         out << validSecond[validSecond.size()-1] << endl;
 521
 522                                         //make first name in set you come to first column and then add the remaining names to second column
 523                                 }else {
 524
 525                                         //you want part of this row
 526                                         if (validSecond.size() != 0) {
 527
 528                                                 wroteSomething = true;
 529
 530                                                 out << validSecond[0] << '\t';
 531
 532                                                 //you know you have at least one valid second since first column is valid
 533                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 534                                                 out << validSecond[validSecond.size()-1] << endl;
 535                                         }
 536                                 }
 537                         }
 538                         m->gobble(in);
 539                 }
 540                 in.close();
 541                 out.close();
 542
 543                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 544                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 545
 546                 return 0;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "RemoveLineageCommand", "readName");
 550                 exit(1);
 551         }
 552 }
 553 //**********************************************************************************************************************
 554 int RemoveLineageCommand::readCount(){
 555         try {
 556                 string thisOutputDir = outputDir;
 557                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 558                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 559
 560                 ofstream out;
 561                 m->openOutputFile(outputFileName, out);
 562
 563                 ifstream in;
 564                 m->openInputFile(countfile, in);
 565
 566                 bool wroteSomething = false;
 567
 568         string headers = m->getline(in); m->gobble(in);
 569         out << headers << endl;
 570
 571         string name, rest; int thisTotal;
 572         while (!in.eof()) {
 573
 574             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 575
 576             in >> name; m->gobble(in);
 577             in >> thisTotal; m->gobble(in);
 578             rest = m->getline(in); m->gobble(in);
 579             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 580
 581             if (names.count(name) == 0) {
 582                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 583                 wroteSomething = true;
 584             }
 585         }
 586         in.close();
 587                 out.close();
 588
 589                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 590                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 591
 592                 return 0;
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "RemoveLineageCommand", "readCount");
 596                 exit(1);
 597         }
 598 }
 599 //**********************************************************************************************************************
 600 int RemoveLineageCommand::readGroup(){
 601         try {
 602                 string thisOutputDir = outputDir;
 603                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 604                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 605                 ofstream out;
 606                 m->openOutputFile(outputFileName, out);
 607
 608                 ifstream in;
 609                 m->openInputFile(groupfile, in);
 610                 string name, group;
 611
 612                 bool wroteSomething = false;
 613
 614                 while(!in.eof()){
 615                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 616
 617                         in >> name;                             //read from first column
 618                         in >> group;                    //read from second column
 619
 620                         //if this name is in the accnos file
 621                         if (names.count(name) == 0) {
 622                                 wroteSomething = true;
 623                                 out << name << '\t' << group << endl;
 624                         }
 625
 626                         m->gobble(in);
 627                 }
 628                 in.close();
 629                 out.close();
 630
 631                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 632                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 633
 634                 return 0;
 635         }
 636         catch(exception& e) {
 637                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 638                 exit(1);
 639         }
 640 }
 641 //**********************************************************************************************************************
 642 int RemoveLineageCommand::readTax(){
 643         try {
 644                 string thisOutputDir = outputDir;
 645                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 646                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 647                 ofstream out;
 648                 m->openOutputFile(outputFileName, out);
 649
 650                 ifstream in;
 651                 m->openInputFile(taxfile, in);
 652                 string name, tax;
 653
 654                 bool wroteSomething = false;
 655
 656                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 657                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 658                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 659
 660                 for (int i = 0; i < listOfTaxons.size(); i++) {
 661                         noConfidenceTaxons[i] = listOfTaxons[i];
 662                         int hasConPos = listOfTaxons[i].find_first_of('(');
 663                         if (hasConPos != string::npos) {
 664                                 taxonsHasConfidence[i] = true;
 665                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 666                                 noConfidenceTaxons[i] = listOfTaxons[i];
 667                                 m->removeConfidences(noConfidenceTaxons[i]);
 668                         }
 669                 }
 670
 671
 672                 while(!in.eof()){
 673
 674                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 675
 676                         in >> name;                             //read from first column
 677                         in >> tax;                      //read from second column
 678
 679                         bool remove = false;
 680
 681                         for (int j = 0; j < listOfTaxons.size(); j++) {
 682                                 string newtax = tax;
 683
 684                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 685                                 if (!taxonsHasConfidence[j]) {
 686
 687                                         int hasConfidences = tax.find_first_of('(');
 688                                         if (hasConfidences != string::npos) {
 689                                                 newtax = tax;
 690                                                 m->removeConfidences(newtax);
 691                                         }
 692
 693                                         int pos = newtax.find(noConfidenceTaxons[j]);
 694
 695                                         if (pos == string::npos) {
 696                                                 //wroteSomething = true;
 697                                                 //out << name << '\t' << tax << endl;
 698                                         }else{ //this sequence contains the taxon the user wants to remove
 699                                                 names.insert(name);
 700                                                 remove=true; break;
 701                                         }
 702
 703                                 }else{//if taxons has them and you don't them remove taxons
 704                                         int hasConfidences = tax.find_first_of('(');
 705                                         if (hasConfidences == string::npos) {
 706
 707                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 708
 709                                                 if (pos == string::npos) {
 710                                                         //wroteSomething = true;
 711                                                         //out << name << '\t' << tax << endl;
 712                                                 }else{ //this sequence contains the taxon the user wants to remove
 713                                                         names.insert(name);
 714                                                         remove=true; break;
 715                                                 }
 716                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 717                                                 //first remove confidences from both and see if the taxonomy exists
 718
 719                                                 string noNewTax = tax;
 720                                                 int hasConfidences = tax.find_first_of('(');
 721                                                 if (hasConfidences != string::npos) {
 722                                                         noNewTax = tax;
 723                                                         m->removeConfidences(noNewTax);
 724                                                 }
 725
 726                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 727
 728                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 729
 730                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 731
 732                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 733                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 734                                                         int index = 0;
 735                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 736
 737                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 738                                                                         index = i;
 739                                                                         int spot = 0;
 740                                                                         bool goodspot = true;
 741                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 742                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 743                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 744                                                                                 else { spot++; }
 745                                                                         }
 746
 747                                                                         if (goodspot) { break; }
 748                                                                 }
 749                                                         }
 750
 751                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 752
 753                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 754                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 755                                                                                 remove = true;
 756                                                                                 break;
 757                                                                         }
 758                                                                 }else {
 759                                                                         remove = true;
 760                                                                         break;
 761                                                                 }
 762                                                         }
 763
 764                                                         //passed the test so remove you
 765                                                         if (remove) {
 766                                                                 names.insert(name);
 767                                                                 remove=true; break;
 768                                                         }else {
 769                                                                 //wroteSomething = true;
 770                                                                 //out << name << '\t' << tax << endl;
 771                                                         }
 772                                                 }else {
 773                                                         //wroteSomething = true;
 774                                                         //out << name << '\t' << tax << endl;
 775                                                 }
 776                                         }
 777                                 }
 778
 779                         }
 780
 781                         if (!remove) {  wroteSomething = true; out << name << '\t' << tax << endl; }
 782                         m->gobble(in);
 783                 }
 784                 in.close();
 785                 out.close();
 786
 787                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 788                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 789
 790                 return 0;
 791
 792         }
 793         catch(exception& e) {
 794                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 795                 exit(1);
 796         }
 797 }
 798 /**************************************************************************************************/
 799 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 800         try {
 801
 802                 vector< map<string, float> > t;
 803                 string taxon = "";
 804                 int taxLength = tax.length();
 805                 for(int i=0;i<taxLength;i++){
 806                         if(tax[i] == ';'){
 807
 808                                 int openParen = taxon.find_first_of('(');
 809                                 int closeParen = taxon.find_last_of(')');
 810
 811                                 string newtaxon, confidence;
 812                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 813                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 814                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 815                                 }else{
 816                                         newtaxon = taxon;
 817                                         confidence = "0";
 818                                 }
 819                                 float con = 0;
 820                                 convert(confidence, con);
 821
 822                                 map<string, float> temp;
 823                                 temp[newtaxon] = con;
 824                                 t.push_back(temp);
 825
 826                                 taxon = "";
 827                         }
 828                         else{
 829                                 taxon += tax[i];
 830                         }
 831                 }
 832
 833                 return t;
 834         }
 835         catch(exception& e) {
 836                 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
 837                 exit(1);
 838         }
 839 }
 840 //**********************************************************************************************************************
 841 //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
 842 int RemoveLineageCommand::readAlign(){
 843         try {
 844                 string thisOutputDir = outputDir;
 845                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 846                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 847
 848                 ofstream out;
 849                 m->openOutputFile(outputFileName, out);
 850
 851                 ifstream in;
 852                 m->openInputFile(alignfile, in);
 853                 string name, junk;
 854
 855                 bool wroteSomething = false;
 856
 857                 //read column headers
 858                 for (int i = 0; i < 16; i++) {
 859                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 860                         else                    {       break;                  }
 861                 }
 862                 out << endl;
 863
 864                 while(!in.eof()){
 865                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 866
 867                         in >> name;                             //read from first column
 868
 869                         //if this name is in the accnos file
 870                         if (names.count(name) == 0) {
 871                                 wroteSomething = true;
 872
 873                                 out << name << '\t';
 874
 875                                 //read rest
 876                                 for (int i = 0; i < 15; i++) {
 877                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 878                                         else                    {       break;                  }
 879                                 }
 880                                 out << endl;
 881
 882                         }else {//still read just don't do anything with it
 883
 884                                 //read rest
 885                                 for (int i = 0; i < 15; i++) {
 886                                         if (!in.eof())  {       in >> junk;             }
 887                                         else                    {       break;                  }
 888                                 }
 889                         }
 890
 891                         m->gobble(in);
 892                 }
 893                 in.close();
 894                 out.close();
 895
 896                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 897                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 898
 899                 return 0;
 900
 901         }
 902         catch(exception& e) {
 903                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 904                 exit(1);
 905         }
 906 }
 907 //**********************************************************************************************************************
 908