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 #include "counttable.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> RemoveLineageCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  19         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  23                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
  24                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  25                 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
  26                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  27                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  28                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  29
  30                 vector<string> myArray;
  31                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "RemoveLineageCommand", "setParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 string RemoveLineageCommand::getHelpString(){
  41         try {
  42                 string helpString = "";
  43                 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";
  44                 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";
  45                 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";
  46                 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";
  47                 helpString += "The taxon parameter allows you to select the taxons you would like to remove, and is required.\n";
  48                 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";
  49                 helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
  50                 helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
  51                 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
  52                 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";
  53                 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
  54                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  55                 return helpString;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "RemoveLineageCommand", "getHelpString");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 string RemoveLineageCommand::getOutputFileNameTag(string type, string inputName=""){
  64         try {
  65         string outputFileName = "";
  66                 map<string, vector<string> >::iterator it;
  67
  68         //is this a type this command creates
  69         it = outputTypes.find(type);
  70         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  71         else {
  72             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  77             else if (type == "count")       {   outputFileName =  "pick.count_table";   }
  78             else if (type == "alignreport")      {   outputFileName =  "pick.align.report";   }
  79             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  80         }
  81         return outputFileName;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "RemoveLineageCommand", "getOutputFileNameTag");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 RemoveLineageCommand::RemoveLineageCommand(){
  90         try {
  91                 abort = true; calledHelp = true;
  92                 setParameters();
  93                 vector<string> tempOutNames;
  94                 outputTypes["fasta"] = tempOutNames;
  95                 outputTypes["taxonomy"] = tempOutNames;
  96                 outputTypes["name"] = tempOutNames;
  97                 outputTypes["group"] = tempOutNames;
  98                 outputTypes["alignreport"] = tempOutNames;
  99                 outputTypes["list"] = tempOutNames;
 100         outputTypes["count"] = tempOutNames;
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 104                 exit(1);
 105         }
 106 }
 107 //**********************************************************************************************************************
 108 RemoveLineageCommand::RemoveLineageCommand(string option)  {
 109         try {
 110                 abort = false; calledHelp = false;
 111
 112                 //allow user to run help
 113                 if(option == "help") { help(); abort = true; calledHelp = true; }
 114                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 115
 116                 else {
 117                         vector<string> myArray = setParameters();
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter;
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         //initialize outputTypes
 131                         vector<string> tempOutNames;
 132                         outputTypes["fasta"] = tempOutNames;
 133                         outputTypes["taxonomy"] = tempOutNames;
 134                         outputTypes["name"] = tempOutNames;
 135                         outputTypes["group"] = tempOutNames;
 136                         outputTypes["alignreport"] = tempOutNames;
 137                         outputTypes["list"] = tempOutNames;
 138             outputTypes["count"] = tempOutNames;
 139
 140                         //if the user changes the output directory command factory will send this info to us in the output parameter
 141                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 142
 143                         //if the user changes the input directory command factory will send this info to us in the output parameter
 144                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 145                         if (inputDir == "not found"){   inputDir = "";          }
 146                         else {
 147                                 string path;
 148                                 it = parameters.find("alignreport");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 154                                 }
 155
 156                                 it = parameters.find("fasta");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 162                                 }
 163
 164                                 it = parameters.find("list");
 165                                 //user has given a template file
 166                                 if(it != parameters.end()){
 167                                         path = m->hasPath(it->second);
 168                                         //if the user has not given a path then, add inputdir. else leave path alone.
 169                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 170                                 }
 171
 172                                 it = parameters.find("name");
 173                                 //user has given a template file
 174                                 if(it != parameters.end()){
 175                                         path = m->hasPath(it->second);
 176                                         //if the user has not given a path then, add inputdir. else leave path alone.
 177                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 178                                 }
 179
 180                                 it = parameters.find("group");
 181                                 //user has given a template file
 182                                 if(it != parameters.end()){
 183                                         path = m->hasPath(it->second);
 184                                         //if the user has not given a path then, add inputdir. else leave path alone.
 185                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 186                                 }
 187
 188                                 it = parameters.find("taxonomy");
 189                                 //user has given a template file
 190                                 if(it != parameters.end()){
 191                                         path = m->hasPath(it->second);
 192                                         //if the user has not given a path then, add inputdir. else leave path alone.
 193                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 194                                 }
 195
 196                 it = parameters.find("count");
 197                                 //user has given a template file
 198                                 if(it != parameters.end()){
 199                                         path = m->hasPath(it->second);
 200                                         //if the user has not given a path then, add inputdir. else leave path alone.
 201                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 202                                 }
 203                         }
 204
 205
 206                         //check for required parameters
 207                         fastafile = validParameter.validFile(parameters, "fasta", true);
 208                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 209                         else if (fastafile == "not found") {  fastafile = "";  }
 210                         else { m->setFastaFile(fastafile); }
 211
 212                         namefile = validParameter.validFile(parameters, "name", true);
 213                         if (namefile == "not open") { namefile = ""; abort = true; }
 214                         else if (namefile == "not found") {  namefile = "";  }
 215                         else { m->setNameFile(namefile); }
 216
 217                         groupfile = validParameter.validFile(parameters, "group", true);
 218                         if (groupfile == "not open") { abort = true; }
 219                         else if (groupfile == "not found") {  groupfile = "";  }
 220                         else { m->setGroupFile(groupfile); }
 221
 222                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 223                         if (alignfile == "not open") { abort = true; }
 224                         else if (alignfile == "not found") {  alignfile = "";  }
 225
 226                         listfile = validParameter.validFile(parameters, "list", true);
 227                         if (listfile == "not open") { abort = true; }
 228                         else if (listfile == "not found") {  listfile = "";  }
 229                         else { m->setListFile(listfile); }
 230
 231                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 232                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 233                         else if (taxfile == "not found") {
 234                                 taxfile = m->getTaxonomyFile();
 235                                 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 236                                 else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
 237                         }else { m->setTaxonomyFile(taxfile); }
 238
 239             countfile = validParameter.validFile(parameters, "count", true);
 240             if (countfile == "not open") { countfile = ""; abort = true; }
 241             else if (countfile == "not found") { countfile = "";  }
 242             else { m->setCountTableFile(countfile); }
 243
 244             if ((namefile != "") && (countfile != "")) {
 245                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 246             }
 247
 248             if ((groupfile != "") && (countfile != "")) {
 249                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 250             }
 251
 252                         string usedDups = "true";
 253                         string temp = validParameter.validFile(parameters, "dups", false);
 254                         if (temp == "not found") {
 255                                 if (namefile != "") {  temp = "true";                                   }
 256                                 else                            {  temp = "false"; usedDups = "";       }
 257                         }
 258                         dups = m->isTrue(temp);
 259
 260                         taxons = validParameter.validFile(parameters, "taxon", false);
 261                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 262                         else {
 263                                 //rip off quotes
 264                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 265                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 266                         }
 267                         m->splitAtChar(taxons, listOfTaxons, '-');
 268
 269                         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; }
 270
 271                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 272
 273                         if (countfile == "") {
 274                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 275                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 276                     parser.getNameFile(files);
 277                 }
 278             }
 279
 280                 }
 281
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 285                 exit(1);
 286         }
 287 }
 288 //**********************************************************************************************************************
 289
 290 int RemoveLineageCommand::execute(){
 291         try {
 292
 293                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 294
 295                 if (m->control_pressed) { return 0; }
 296
 297         if (countfile != "") {
 298             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 299                 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");
 300             }
 301         }
 302
 303                 //read through the correct file and output lines you want to keep
 304                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 305                 if (namefile != "")                     {               readName();             }
 306                 if (fastafile != "")            {               readFasta();    }
 307                 if (groupfile != "")            {               readGroup();    }
 308                 if (alignfile != "")            {               readAlign();    }
 309                 if (listfile != "")                     {               readList();             }
 310         if (countfile != "")            {               readCount();    }
 311
 312
 313                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 314
 315                 if (outputNames.size() != 0) {
 316                         m->mothurOutEndLine();
 317                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 318                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 319                         m->mothurOutEndLine();
 320
 321                         //set fasta file as new current fastafile
 322                         string current = "";
 323                         itTypes = outputTypes.find("fasta");
 324                         if (itTypes != outputTypes.end()) {
 325                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 326                         }
 327
 328                         itTypes = outputTypes.find("name");
 329                         if (itTypes != outputTypes.end()) {
 330                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 331                         }
 332
 333                         itTypes = outputTypes.find("group");
 334                         if (itTypes != outputTypes.end()) {
 335                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 336                         }
 337
 338                         itTypes = outputTypes.find("list");
 339                         if (itTypes != outputTypes.end()) {
 340                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 341                         }
 342
 343                         itTypes = outputTypes.find("taxonomy");
 344                         if (itTypes != outputTypes.end()) {
 345                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 346                         }
 347
 348             itTypes = outputTypes.find("count");
 349                         if (itTypes != outputTypes.end()) {
 350                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 351                         }
 352                 }
 353
 354                 return 0;
 355         }
 356
 357         catch(exception& e) {
 358                 m->errorOut(e, "RemoveLineageCommand", "execute");
 359                 exit(1);
 360         }
 361 }
 362
 363 //**********************************************************************************************************************
 364 int RemoveLineageCommand::readFasta(){
 365         try {
 366                 string thisOutputDir = outputDir;
 367                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 368                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 369                 ofstream out;
 370                 m->openOutputFile(outputFileName, out);
 371
 372                 ifstream in;
 373                 m->openInputFile(fastafile, in);
 374                 string name;
 375
 376                 bool wroteSomething = false;
 377
 378                 while(!in.eof()){
 379                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 380
 381                         Sequence currSeq(in);
 382                         name = currSeq.getName();
 383
 384                         if (name != "") {
 385                                 //if this name is in the accnos file
 386                                 if (names.count(name) == 0) {
 387                                         wroteSomething = true;
 388
 389                                         currSeq.printSequence(out);
 390                                 }
 391                         }
 392                         m->gobble(in);
 393                 }
 394                 in.close();
 395                 out.close();
 396
 397                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 398                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 399
 400                 return 0;
 401
 402         }
 403         catch(exception& e) {
 404                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 405                 exit(1);
 406         }
 407 }
 408 //**********************************************************************************************************************
 409 int RemoveLineageCommand::readList(){
 410         try {
 411                 string thisOutputDir = outputDir;
 412                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 413                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 414                 ofstream out;
 415                 m->openOutputFile(outputFileName, out);
 416
 417                 ifstream in;
 418                 m->openInputFile(listfile, in);
 419
 420                 bool wroteSomething = false;
 421
 422                 while(!in.eof()){
 423                         //read in list vector
 424                         ListVector list(in);
 425
 426                         //make a new list vector
 427                         ListVector newList;
 428                         newList.setLabel(list.getLabel());
 429
 430                         //for each bin
 431                         for (int i = 0; i < list.getNumBins(); i++) {
 432                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 433
 434                                 //parse out names that are in accnos file
 435                                 string binnames = list.get(i);
 436
 437                                 string newNames = "";
 438                                 while (binnames.find_first_of(',') != -1) {
 439                                         string name = binnames.substr(0,binnames.find_first_of(','));
 440                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 441
 442                                         //if that name is in the .accnos file, add it
 443                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 444                                 }
 445
 446                                 //get last name
 447                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 448
 449                                 //if there are names in this bin add to new list
 450                                 if (newNames != "") {
 451                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 452                                         newList.push_back(newNames);
 453                                 }
 454                         }
 455
 456                         //print new listvector
 457                         if (newList.getNumBins() != 0) {
 458                                 wroteSomething = true;
 459                                 newList.print(out);
 460                         }
 461
 462                         m->gobble(in);
 463                 }
 464                 in.close();
 465                 out.close();
 466
 467                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 468                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 469
 470                 return 0;
 471
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "RemoveLineageCommand", "readList");
 475                 exit(1);
 476         }
 477 }
 478 //**********************************************************************************************************************
 479 int RemoveLineageCommand::readName(){
 480         try {
 481                 string thisOutputDir = outputDir;
 482                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 483                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 484                 ofstream out;
 485                 m->openOutputFile(outputFileName, out);
 486
 487                 ifstream in;
 488                 m->openInputFile(namefile, in);
 489                 string name, firstCol, secondCol;
 490
 491                 bool wroteSomething = false;
 492
 493                 while(!in.eof()){
 494                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 495
 496                         in >> firstCol;
 497                         in >> secondCol;
 498
 499                         vector<string> parsedNames;
 500                         m->splitAtComma(secondCol, parsedNames);
 501
 502                         vector<string> validSecond;  validSecond.clear();
 503                         for (int i = 0; i < parsedNames.size(); i++) {
 504                                 if (names.count(parsedNames[i]) == 0) {
 505                                         validSecond.push_back(parsedNames[i]);
 506                                 }
 507                         }
 508
 509                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 510                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 511                         }else {
 512                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 513                                 if (names.count(firstCol) == 0) {
 514
 515                                         wroteSomething = true;
 516
 517                                         out << firstCol << '\t';
 518
 519                                         //you know you have at least one valid second since first column is valid
 520                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 521                                         out << validSecond[validSecond.size()-1] << endl;
 522
 523                                         //make first name in set you come to first column and then add the remaining names to second column
 524                                 }else {
 525
 526                                         //you want part of this row
 527                                         if (validSecond.size() != 0) {
 528
 529                                                 wroteSomething = true;
 530
 531                                                 out << validSecond[0] << '\t';
 532
 533                                                 //you know you have at least one valid second since first column is valid
 534                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 535                                                 out << validSecond[validSecond.size()-1] << endl;
 536                                         }
 537                                 }
 538                         }
 539                         m->gobble(in);
 540                 }
 541                 in.close();
 542                 out.close();
 543
 544                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 545                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 546
 547                 return 0;
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "RemoveLineageCommand", "readName");
 551                 exit(1);
 552         }
 553 }
 554 //**********************************************************************************************************************
 555 int RemoveLineageCommand::readCount(){
 556         try {
 557                 string thisOutputDir = outputDir;
 558                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 559                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 560
 561                 ofstream out;
 562                 m->openOutputFile(outputFileName, out);
 563
 564                 ifstream in;
 565                 m->openInputFile(countfile, in);
 566
 567                 bool wroteSomething = false;
 568
 569         string headers = m->getline(in); m->gobble(in);
 570         out << headers << endl;
 571
 572         string name, rest; int thisTotal;
 573         while (!in.eof()) {
 574
 575             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 576
 577             in >> name; m->gobble(in);
 578             in >> thisTotal; m->gobble(in);
 579             rest = m->getline(in); m->gobble(in);
 580             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 581
 582             if (names.count(name) == 0) {
 583                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 584                 wroteSomething = true;
 585             }
 586         }
 587         in.close();
 588                 out.close();
 589
 590         //check for groups that have been eliminated
 591         CountTable ct;
 592         if (ct.testGroups(outputFileName)) {
 593             ct.readTable(outputFileName);
 594             ct.printTable(outputFileName);
 595         }
 596
 597                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 598                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 599
 600                 return 0;
 601         }
 602         catch(exception& e) {
 603                 m->errorOut(e, "RemoveLineageCommand", "readCount");
 604                 exit(1);
 605         }
 606 }
 607 //**********************************************************************************************************************
 608 int RemoveLineageCommand::readGroup(){
 609         try {
 610                 string thisOutputDir = outputDir;
 611                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 612                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 613                 ofstream out;
 614                 m->openOutputFile(outputFileName, out);
 615
 616                 ifstream in;
 617                 m->openInputFile(groupfile, in);
 618                 string name, group;
 619
 620                 bool wroteSomething = false;
 621
 622                 while(!in.eof()){
 623                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 624
 625                         in >> name;                             //read from first column
 626                         in >> group;                    //read from second column
 627
 628                         //if this name is in the accnos file
 629                         if (names.count(name) == 0) {
 630                                 wroteSomething = true;
 631                                 out << name << '\t' << group << endl;
 632                         }
 633
 634                         m->gobble(in);
 635                 }
 636                 in.close();
 637                 out.close();
 638
 639                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 640                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 641
 642                 return 0;
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 646                 exit(1);
 647         }
 648 }
 649 //**********************************************************************************************************************
 650 int RemoveLineageCommand::readTax(){
 651         try {
 652                 string thisOutputDir = outputDir;
 653                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 654                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 655                 ofstream out;
 656                 m->openOutputFile(outputFileName, out);
 657
 658                 ifstream in;
 659                 m->openInputFile(taxfile, in);
 660                 string name, tax;
 661
 662                 bool wroteSomething = false;
 663
 664                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 665                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 666                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 667
 668                 for (int i = 0; i < listOfTaxons.size(); i++) {
 669                         noConfidenceTaxons[i] = listOfTaxons[i];
 670                         int hasConPos = listOfTaxons[i].find_first_of('(');
 671                         if (hasConPos != string::npos) {
 672                                 taxonsHasConfidence[i] = true;
 673                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 674                                 noConfidenceTaxons[i] = listOfTaxons[i];
 675                                 m->removeConfidences(noConfidenceTaxons[i]);
 676                         }
 677                 }
 678
 679
 680                 while(!in.eof()){
 681
 682                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 683
 684                         in >> name;                             //read from first column
 685                         in >> tax;                      //read from second column
 686
 687                         bool remove = false;
 688
 689             string noQuotesTax = m->removeQuotes(tax);
 690
 691                         for (int j = 0; j < listOfTaxons.size(); j++) {
 692                                 string newtax = noQuotesTax;
 693
 694                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 695                                 if (!taxonsHasConfidence[j]) {
 696
 697                                         int hasConfidences = noQuotesTax.find_first_of('(');
 698                                         if (hasConfidences != string::npos) {
 699                                                 newtax = noQuotesTax;
 700                                                 m->removeConfidences(newtax);
 701                                         }
 702
 703                                         int pos = newtax.find(noConfidenceTaxons[j]);
 704
 705                                         if (pos == string::npos) {
 706                                                 //wroteSomething = true;
 707                                                 //out << name << '\t' << tax << endl;
 708                                         }else{ //this sequence contains the taxon the user wants to remove
 709                                                 names.insert(name);
 710                                                 remove=true; break;
 711                                         }
 712
 713                                 }else{//if taxons has them and you don't them remove taxons
 714                                         int hasConfidences = noQuotesTax.find_first_of('(');
 715                                         if (hasConfidences == string::npos) {
 716
 717                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 718
 719                                                 if (pos == string::npos) {
 720                                                         //wroteSomething = true;
 721                                                         //out << name << '\t' << tax << endl;
 722                                                 }else{ //this sequence contains the taxon the user wants to remove
 723                                                         names.insert(name);
 724                                                         remove=true; break;
 725                                                 }
 726                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 727                                                 //first remove confidences from both and see if the taxonomy exists
 728
 729                                                 string noNewTax = noQuotesTax;
 730                                                 int hasConfidences = noQuotesTax.find_first_of('(');
 731                                                 if (hasConfidences != string::npos) {
 732                                                         noNewTax = noQuotesTax;
 733                                                         m->removeConfidences(noNewTax);
 734                                                 }
 735
 736                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 737
 738                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 739
 740                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 741
 742                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 743                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 744                                                         int index = 0;
 745                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 746
 747                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 748                                                                         index = i;
 749                                                                         int spot = 0;
 750                                                                         bool goodspot = true;
 751                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 752                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 753                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 754                                                                                 else { spot++; }
 755                                                                         }
 756
 757                                                                         if (goodspot) { break; }
 758                                                                 }
 759                                                         }
 760
 761                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 762
 763                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 764                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 765                                                                                 remove = true;
 766                                                                                 break;
 767                                                                         }
 768                                                                 }else {
 769                                                                         remove = true;
 770                                                                         break;
 771                                                                 }
 772                                                         }
 773
 774                                                         //passed the test so remove you
 775                                                         if (remove) {
 776                                                                 names.insert(name);
 777                                                                 remove=true; break;
 778                                                         }else {
 779                                                                 //wroteSomething = true;
 780                                                                 //out << name << '\t' << tax << endl;
 781                                                         }
 782                                                 }else {
 783                                                         //wroteSomething = true;
 784                                                         //out << name << '\t' << tax << endl;
 785                                                 }
 786                                         }
 787                                 }
 788
 789                         }
 790
 791                         if (!remove) {  wroteSomething = true; out << name << '\t' << tax << endl; }
 792                         m->gobble(in);
 793                 }
 794                 in.close();
 795                 out.close();
 796
 797                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 798                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 799
 800                 return 0;
 801
 802         }
 803         catch(exception& e) {
 804                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 805                 exit(1);
 806         }
 807 }
 808 /**************************************************************************************************/
 809 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 810         try {
 811
 812                 vector< map<string, float> > t;
 813                 string taxon = "";
 814                 int taxLength = tax.length();
 815                 for(int i=0;i<taxLength;i++){
 816                         if(tax[i] == ';'){
 817
 818                                 int openParen = taxon.find_first_of('(');
 819                                 int closeParen = taxon.find_last_of(')');
 820
 821                                 string newtaxon, confidence;
 822                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 823                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 824                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 825                                 }else{
 826                                         newtaxon = taxon;
 827                                         confidence = "0";
 828                                 }
 829                                 float con = 0;
 830                                 convert(confidence, con);
 831
 832                                 map<string, float> temp;
 833                                 temp[newtaxon] = con;
 834                                 t.push_back(temp);
 835
 836                                 taxon = "";
 837                         }
 838                         else{
 839                                 taxon += tax[i];
 840                         }
 841                 }
 842
 843                 return t;
 844         }
 845         catch(exception& e) {
 846                 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
 847                 exit(1);
 848         }
 849 }
 850 //**********************************************************************************************************************
 851 //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
 852 int RemoveLineageCommand::readAlign(){
 853         try {
 854                 string thisOutputDir = outputDir;
 855                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 856                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 857
 858                 ofstream out;
 859                 m->openOutputFile(outputFileName, out);
 860
 861                 ifstream in;
 862                 m->openInputFile(alignfile, in);
 863                 string name, junk;
 864
 865                 bool wroteSomething = false;
 866
 867                 //read column headers
 868                 for (int i = 0; i < 16; i++) {
 869                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 870                         else                    {       break;                  }
 871                 }
 872                 out << endl;
 873
 874                 while(!in.eof()){
 875                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 876
 877                         in >> name;                             //read from first column
 878
 879                         //if this name is in the accnos file
 880                         if (names.count(name) == 0) {
 881                                 wroteSomething = true;
 882
 883                                 out << name << '\t';
 884
 885                                 //read rest
 886                                 for (int i = 0; i < 15; i++) {
 887                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 888                                         else                    {       break;                  }
 889                                 }
 890                                 out << endl;
 891
 892                         }else {//still read just don't do anything with it
 893
 894                                 //read rest
 895                                 for (int i = 0; i < 15; i++) {
 896                                         if (!in.eof())  {       in >> junk;             }
 897                                         else                    {       break;                  }
 898                                 }
 899                         }
 900
 901                         m->gobble(in);
 902                 }
 903                 in.close();
 904                 out.close();
 905
 906                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 907                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 908
 909                 return 0;
 910
 911         }
 912         catch(exception& e) {
 913                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 914                 exit(1);
 915         }
 916 }
 917 //**********************************************************************************************************************
 918