removegroupscommand.cpp

   1 /*
   2  *  removegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "removegroupscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "sharedutilities.h"
  14 #include "inputdata.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> RemoveGroupsCommand::setParameters(){
  18         try {
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
  20                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
  21         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  22         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);         CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
  24                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
  25                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
  26                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  27                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  28                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  29                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  30
  31                 vector<string> myArray;
  32                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  33                 return myArray;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "RemoveGroupsCommand", "setParameters");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 string RemoveGroupsCommand::getHelpString(){
  42         try {
  43                 string helpString = "";
  44                 helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design or sharedfile.\n";
  45                 helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
  46                 helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group or count parameter is required, unless you have a current group or count file or are using a sharedfile.\n";
  47                 helpString += "You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n";
  48                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like removed.  You can separate group names with dashes.\n";
  49                 helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  50                 helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  51                 helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, amazon.groups).\n";
  52                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  53                 return helpString;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "RemoveGroupsCommand", "getHelpString");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 string RemoveGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
  62         try {
  63         string outputFileName = "";
  64                 map<string, vector<string> >::iterator it;
  65
  66         //is this a type this command creates
  67         it = outputTypes.find(type);
  68         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  69         else {
  70             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  71             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  72             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "count")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else if (type == "shared")      {   outputFileName =  "pick" + m->getExtension(inputName);   }
  77             else if (type == "design")      {   outputFileName =  "pick" + m->getExtension(inputName);   }
  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, "RemoveGroupsCommand", "getOutputFileNameTag");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 RemoveGroupsCommand::RemoveGroupsCommand(){
  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["list"] = tempOutNames;
  98                 outputTypes["shared"] = tempOutNames;
  99         outputTypes["design"] = tempOutNames;
 100         outputTypes["count"] = tempOutNames;
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 104                 exit(1);
 105         }
 106 }
 107 //**********************************************************************************************************************
 108 RemoveGroupsCommand::RemoveGroupsCommand(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["list"] = tempOutNames;
 137                         outputTypes["shared"] = tempOutNames;
 138             outputTypes["design"] = tempOutNames;
 139             outputTypes["count"] = tempOutNames;
 140
 141
 142                         //if the user changes the output directory command factory will send this info to us in the output parameter
 143                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 144
 145                         //if the user changes the input directory command factory will send this info to us in the output parameter
 146                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 147                         if (inputDir == "not found"){   inputDir = "";          }
 148                         else {
 149                                 string path;
 150                                 it = parameters.find("fasta");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 156                                 }
 157
 158                                 it = parameters.find("accnos");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 164                                 }
 165
 166                                 it = parameters.find("list");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 172                                 }
 173
 174                                 it = parameters.find("name");
 175                                 //user has given a template file
 176                                 if(it != parameters.end()){
 177                                         path = m->hasPath(it->second);
 178                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 180                                 }
 181
 182                                 it = parameters.find("group");
 183                                 //user has given a template file
 184                                 if(it != parameters.end()){
 185                                         path = m->hasPath(it->second);
 186                                         //if the user has not given a path then, add inputdir. else leave path alone.
 187                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 188                                 }
 189
 190                                 it = parameters.find("taxonomy");
 191                                 //user has given a template file
 192                                 if(it != parameters.end()){
 193                                         path = m->hasPath(it->second);
 194                                         //if the user has not given a path then, add inputdir. else leave path alone.
 195                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 196                                 }
 197
 198                                 it = parameters.find("shared");
 199                                 //user has given a template file
 200                                 if(it != parameters.end()){
 201                                         path = m->hasPath(it->second);
 202                                         //if the user has not given a path then, add inputdir. else leave path alone.
 203                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 204                                 }
 205
 206                 it = parameters.find("design");
 207                                 //user has given a template file
 208                                 if(it != parameters.end()){
 209                                         path = m->hasPath(it->second);
 210                                         //if the user has not given a path then, add inputdir. else leave path alone.
 211                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 212                                 }
 213
 214                 it = parameters.find("count");
 215                                 //user has given a template file
 216                                 if(it != parameters.end()){
 217                                         path = m->hasPath(it->second);
 218                                         //if the user has not given a path then, add inputdir. else leave path alone.
 219                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 220                                 }
 221                         }
 222
 223
 224                         //check for required parameters
 225                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 226                         if (accnosfile == "not open") { accnosfile = ""; abort = true; }
 227                         else if (accnosfile == "not found") {  accnosfile = ""; }
 228                         else { m->setAccnosFile(accnosfile); }
 229
 230                         fastafile = validParameter.validFile(parameters, "fasta", true);
 231                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 232                         else if (fastafile == "not found") {  fastafile = "";  }
 233                         else { m->setFastaFile(fastafile); }
 234
 235                         namefile = validParameter.validFile(parameters, "name", true);
 236                         if (namefile == "not open") { namefile = ""; abort = true; }
 237                         else if (namefile == "not found") {  namefile = "";  }
 238                         else { m->setNameFile(namefile); }
 239
 240                         groupfile = validParameter.validFile(parameters, "group", true);
 241                         if (groupfile == "not open") { groupfile = "";  abort = true; }
 242                         else if (groupfile == "not found") {    groupfile = "";         }
 243                         else { m->setGroupFile(groupfile); }
 244
 245                         listfile = validParameter.validFile(parameters, "list", true);
 246                         if (listfile == "not open") { listfile = ""; abort = true; }
 247                         else if (listfile == "not found") {  listfile = "";  }
 248                         else { m->setListFile(listfile); }
 249
 250                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 251                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 252                         else if (taxfile == "not found") {  taxfile = "";  }
 253                         else { m->setTaxonomyFile(taxfile); }
 254
 255             designfile = validParameter.validFile(parameters, "design", true);
 256                         if (designfile == "not open") { designfile = ""; abort = true; }
 257                         else if (designfile == "not found") {  designfile = "";  }
 258                         else { m->setDesignFile(designfile); }
 259
 260                         groups = validParameter.validFile(parameters, "groups", false);
 261                         if (groups == "not found") { groups = ""; }
 262                         else {
 263                                 m->splitAtDash(groups, Groups);
 264                                 m->setGroups(Groups);
 265                         }
 266
 267                         sharedfile = validParameter.validFile(parameters, "shared", true);
 268                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 269                         else if (sharedfile == "not found") {  sharedfile = "";  }
 270                         else { m->setSharedFile(sharedfile); }
 271
 272
 273                         countfile = validParameter.validFile(parameters, "count", true);
 274             if (countfile == "not open") { countfile = ""; abort = true; }
 275             else if (countfile == "not found") { countfile = "";  }
 276             else { m->setCountTableFile(countfile); }
 277
 278             if ((namefile != "") && (countfile != "")) {
 279                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 280             }
 281
 282             if ((groupfile != "") && (countfile != "")) {
 283                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 284             }
 285
 286
 287                         if ((sharedfile == "") && (groupfile == "") && (designfile == "") && (countfile == "")) {
 288                                 //is there are current file available for any of these?
 289                                 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
 290                                         //give priority to group, then shared
 291                                         groupfile = m->getGroupFile();
 292                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 293                                         else {
 294                                                 sharedfile = m->getSharedFile();
 295                                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 296                                                 else {
 297                                                         countfile = m->getCountTableFile();
 298                             if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 299                             else {
 300                                 m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 301                             }
 302                                                 }
 303                                         }
 304                                 }else {
 305                                         //give priority to shared, then group
 306                                         sharedfile = m->getSharedFile();
 307                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 308                                         else {
 309                                                 groupfile = m->getGroupFile();
 310                                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 311                                                 else {
 312                                                         designfile = m->getDesignFile();
 313                             if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 314                             else {
 315                                 countfile = m->getCountTableFile();
 316                                 if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 317                                 else {
 318                                     m->mothurOut("You have no current groupfile, designfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 319                                 }
 320
 321                             }
 322                                                 }
 323                                         }
 324                                 }
 325                         }
 326
 327                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file containing group names or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 328
 329                         if ((fastafile == "") && (namefile == "") && (countfile == "") && (groupfile == "")  && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design, count or list."); m->mothurOutEndLine(); abort = true; }
 330                         if (((groupfile == "") && (countfile == "")) && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group or count file."); m->mothurOutEndLine(); abort = true; }
 331
 332             if (countfile == "") {
 333                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 334                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 335                     parser.getNameFile(files);
 336                 }
 337             }
 338                 }
 339
 340         }
 341         catch(exception& e) {
 342                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 343                 exit(1);
 344         }
 345 }
 346 //**********************************************************************************************************************
 347
 348 int RemoveGroupsCommand::execute(){
 349         try {
 350
 351                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 352
 353                 //get groups you want to remove
 354                 if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
 355
 356                 if (groupfile != "") {
 357                         groupMap = new GroupMap(groupfile);
 358                         groupMap->readMap();
 359
 360                         //make sure groups are valid
 361                         //takes care of user setting groupNames that are invalid or setting groups=all
 362                         SharedUtil* util = new SharedUtil();
 363                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 364                         util->setGroups(Groups, namesGroups);
 365                         delete util;
 366
 367                         //fill names with names of sequences that are from the groups we want to remove
 368                         fillNames();
 369
 370                         delete groupMap;
 371                 }else if (countfile != ""){
 372             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 373                 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");
 374             }
 375             CountTable ct;
 376             ct.readTable(countfile);
 377             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
 378
 379             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
 380             SharedUtil util;
 381             util.setGroups(Groups, gNamesOfGroups);
 382             vector<string> namesOfSeqs = ct.getNamesOfSeqs();
 383             sort(Groups.begin(), Groups.end());
 384
 385             for (int i = 0; i < namesOfSeqs.size(); i++) {
 386                 vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
 387                 if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
 388                     names.insert(namesOfSeqs[i]);
 389                 }
 390             }
 391         }
 392
 393
 394                 if (m->control_pressed) { return 0; }
 395
 396                 //read through the correct file and output lines you want to keep
 397                 if (namefile != "")                     {               readName();             }
 398                 if (fastafile != "")            {               readFasta();    }
 399                 if (groupfile != "")            {               readGroup();    }
 400         if (countfile != "")            {               readCount();    }
 401                 if (listfile != "")                     {               readList();             }
 402                 if (taxfile != "")                      {               readTax();              }
 403                 if (sharedfile != "")           {               readShared();   }
 404         if (designfile != "")           {               readDesign();   }
 405
 406                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 407
 408                 if (outputNames.size() != 0) {
 409                         m->mothurOutEndLine();
 410                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 411                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 412                         m->mothurOutEndLine();
 413
 414                         //set fasta file as new current fastafile
 415                         string current = "";
 416                         itTypes = outputTypes.find("fasta");
 417                         if (itTypes != outputTypes.end()) {
 418                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 419                         }
 420
 421                         itTypes = outputTypes.find("name");
 422                         if (itTypes != outputTypes.end()) {
 423                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 424                         }
 425
 426                         itTypes = outputTypes.find("group");
 427                         if (itTypes != outputTypes.end()) {
 428                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 429                         }
 430
 431                         itTypes = outputTypes.find("list");
 432                         if (itTypes != outputTypes.end()) {
 433                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 434                         }
 435
 436                         itTypes = outputTypes.find("taxonomy");
 437                         if (itTypes != outputTypes.end()) {
 438                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 439                         }
 440
 441                         itTypes = outputTypes.find("shared");
 442                         if (itTypes != outputTypes.end()) {
 443                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 444                         }
 445
 446             itTypes = outputTypes.find("design");
 447                         if (itTypes != outputTypes.end()) {
 448                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
 449                         }
 450
 451             itTypes = outputTypes.find("count");
 452                         if (itTypes != outputTypes.end()) {
 453                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 454                         }
 455                 }
 456
 457                 return 0;
 458         }
 459
 460         catch(exception& e) {
 461                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 462                 exit(1);
 463         }
 464 }
 465
 466 //**********************************************************************************************************************
 467 int RemoveGroupsCommand::readFasta(){
 468         try {
 469                 string thisOutputDir = outputDir;
 470                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 471                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 472
 473                 ofstream out;
 474                 m->openOutputFile(outputFileName, out);
 475
 476                 ifstream in;
 477                 m->openInputFile(fastafile, in);
 478                 string name;
 479
 480                 bool wroteSomething = false;
 481                 int removedCount = 0;
 482
 483                 while(!in.eof()){
 484                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 485
 486                         Sequence currSeq(in);
 487                         name = currSeq.getName();
 488
 489                         if (name != "") {
 490                                 //if this name is in the accnos file
 491                                 if (names.count(name) == 0) {
 492                                         wroteSomething = true;
 493                                         currSeq.printSequence(out);
 494                                 }else {
 495                                         //if you are not in the accnos file check if you are a name that needs to be changed
 496                                         map<string, string>::iterator it = uniqueToRedundant.find(name);
 497                                         if (it != uniqueToRedundant.end()) {
 498                                                 wroteSomething = true;
 499                                                 currSeq.setName(it->second);
 500                                                 currSeq.printSequence(out);
 501                                         }else { removedCount++; }
 502                                 }
 503                         }
 504                         m->gobble(in);
 505                 }
 506                 in.close();
 507                 out.close();
 508
 509                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 510                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 511
 512                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 513
 514                 return 0;
 515
 516         }
 517         catch(exception& e) {
 518                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 519                 exit(1);
 520         }
 521 }
 522 //**********************************************************************************************************************
 523 int RemoveGroupsCommand::readShared(){
 524         try {
 525                 string thisOutputDir = outputDir;
 526                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 527
 528                 //get group names from sharedfile so we can set Groups to the groupNames we want to keep
 529                 //that way we can take advantage of the reads in inputdata and sharedRabundVector
 530                 InputData* tempInput = new InputData(sharedfile, "sharedfile");
 531                 vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
 532
 533                 //save m->Groups
 534                 vector<string> allGroupsNames = m->getAllGroups();
 535                 vector<string> mothurOutGroups = m->getGroups();
 536
 537                 vector<string> groupsToKeep;
 538                 for (int i = 0; i < allGroupsNames.size(); i++) {
 539                         if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
 540                                 groupsToKeep.push_back(allGroupsNames[i]);
 541                         }
 542                 }
 543
 544                 if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 545
 546                 //reset read
 547                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 548                 delete tempInput;
 549                 m->setGroups(groupsToKeep);
 550                 m->clearAllGroups();
 551                 m->saveNextLabel = "";
 552                 m->printedHeaders = false;
 553                 m->currentBinLabels.clear();
 554                 m->binLabelsInFile.clear();
 555
 556                 InputData input(sharedfile, "sharedfile");
 557                 lookup = input.getSharedRAbundVectors();
 558
 559                 bool wroteSomething = false;
 560
 561                 while(lookup[0] != NULL) {
 562
 563                         string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
 564                         ofstream out;
 565                         m->openOutputFile(outputFileName, out);
 566                         outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 567
 568                         if (m->control_pressed) { out.close();  m->mothurRemove(outputFileName);  for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
 569
 570                         lookup[0]->printHeaders(out);
 571
 572                         for (int i = 0; i < lookup.size(); i++) {
 573                                 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
 574                                 lookup[i]->print(out);
 575                                 wroteSomething = true;
 576
 577                         }
 578
 579                         //get next line to process
 580                         //prevent memory leak
 581                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 582                         lookup = input.getSharedRAbundVectors();
 583
 584                         out.close();
 585                 }
 586
 587
 588                 m->setGroups(mothurOutGroups);
 589
 590                 if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 591
 592                 string groupsString = "";
 593                 for (int i = 0; i < Groups.size()-1; i++) {     groupsString += Groups[i] + ", "; }
 594                 groupsString += Groups[Groups.size()-1];
 595
 596                 m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
 597
 598                 return 0;
 599
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "RemoveGroupsCommand", "readShared");
 603                 exit(1);
 604         }
 605 }
 606 //**********************************************************************************************************************
 607 int RemoveGroupsCommand::readList(){
 608         try {
 609                 string thisOutputDir = outputDir;
 610                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 611                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 612
 613                 ofstream out;
 614                 m->openOutputFile(outputFileName, out);
 615
 616                 ifstream in;
 617                 m->openInputFile(listfile, in);
 618
 619                 bool wroteSomething = false;
 620                 int removedCount = 0;
 621
 622                 while(!in.eof()){
 623
 624                         removedCount = 0;
 625
 626                         //read in list vector
 627                         ListVector list(in);
 628
 629                         //make a new list vector
 630                         ListVector newList;
 631                         newList.setLabel(list.getLabel());
 632
 633                         //for each bin
 634                         for (int i = 0; i < list.getNumBins(); i++) {
 635                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 636
 637                                 //parse out names that are in accnos file
 638                                 string binnames = list.get(i);
 639
 640                                 string newNames = "";
 641                                 while (binnames.find_first_of(',') != -1) {
 642                                         string name = binnames.substr(0,binnames.find_first_of(','));
 643                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 644
 645                                         //if that name is in the .accnos file, add it
 646                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 647                                         else {
 648                                                 //if you are not in the accnos file check if you are a name that needs to be changed
 649                                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 650                                                 if (it != uniqueToRedundant.end()) {
 651                                                         newNames += it->second + ",";
 652                                                 }else { removedCount++; }
 653                                         }
 654                                 }
 655
 656                                 //get last name
 657                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 658                                 else { //if you are not in the accnos file check if you are a name that needs to be changed
 659                                         map<string, string>::iterator it = uniqueToRedundant.find(binnames);
 660                                         if (it != uniqueToRedundant.end()) {
 661                                                 newNames += it->second + ",";
 662                                         }else { removedCount++; }
 663                                 }
 664
 665                                 //if there are names in this bin add to new list
 666                                 if (newNames != "") {
 667                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 668                                         newList.push_back(newNames);
 669                                 }
 670                         }
 671
 672                         //print new listvector
 673                         if (newList.getNumBins() != 0) {
 674                                 wroteSomething = true;
 675                                 newList.print(out);
 676                         }
 677
 678                         m->gobble(in);
 679                 }
 680                 in.close();
 681                 out.close();
 682
 683                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 684                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 685
 686                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
 687
 688                 return 0;
 689
 690         }
 691         catch(exception& e) {
 692                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 693                 exit(1);
 694         }
 695 }
 696 //**********************************************************************************************************************
 697 int RemoveGroupsCommand::readName(){
 698         try {
 699                 string thisOutputDir = outputDir;
 700                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 701                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 702                 ofstream out;
 703                 m->openOutputFile(outputFileName, out);
 704
 705                 ifstream in;
 706                 m->openInputFile(namefile, in);
 707                 string name, firstCol, secondCol;
 708
 709                 bool wroteSomething = false;
 710                 int removedCount = 0;
 711
 712                 while(!in.eof()){
 713                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 714
 715                         in >> firstCol;         m->gobble(in);
 716                         in >> secondCol;
 717
 718                         vector<string> parsedNames;
 719                         m->splitAtComma(secondCol, parsedNames);
 720
 721                         vector<string> validSecond;  validSecond.clear();
 722                         for (int i = 0; i < parsedNames.size(); i++) {
 723                                 if (names.count(parsedNames[i]) == 0) {
 724                                         validSecond.push_back(parsedNames[i]);
 725                                 }
 726                         }
 727
 728                         removedCount += parsedNames.size()-validSecond.size();
 729
 730                         //if the name in the first column is in the set then print it and any other names in second column also in set
 731                         if (names.count(firstCol) == 0) {
 732
 733                                 wroteSomething = true;
 734
 735                                 out << firstCol << '\t';
 736
 737                                 //you know you have at least one valid second since first column is valid
 738                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 739                                 out << validSecond[validSecond.size()-1] << endl;
 740
 741                                 //make first name in set you come to first column and then add the remaining names to second column
 742                         }else {
 743
 744                                 //you want part of this row
 745                                 if (validSecond.size() != 0) {
 746
 747                                         wroteSomething = true;
 748
 749                                         out << validSecond[0] << '\t';
 750
 751                                         //you know you have at least one valid second since first column is valid
 752                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 753                                         out << validSecond[validSecond.size()-1] << endl;
 754                                         uniqueToRedundant[firstCol] = validSecond[0];
 755                                 }
 756                         }
 757
 758                         m->gobble(in);
 759                 }
 760                 in.close();
 761                 out.close();
 762
 763                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 764                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 765
 766                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
 767
 768                 return 0;
 769         }
 770         catch(exception& e) {
 771                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 772                 exit(1);
 773         }
 774 }
 775
 776 //**********************************************************************************************************************
 777 int RemoveGroupsCommand::readGroup(){
 778         try {
 779                 string thisOutputDir = outputDir;
 780                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 781                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 782                 ofstream out;
 783                 m->openOutputFile(outputFileName, out);
 784
 785                 ifstream in;
 786                 m->openInputFile(groupfile, in);
 787                 string name, group;
 788
 789                 bool wroteSomething = false;
 790                 int removedCount = 0;
 791
 792                 while(!in.eof()){
 793                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 794
 795                         in >> name;                             //read from first column
 796                         in >> group;                    //read from second column
 797
 798                         //if this name is in the accnos file
 799                         if (names.count(name) == 0) {
 800                                 wroteSomething = true;
 801                                 out << name << '\t' << group << endl;
 802                         }else {  removedCount++;  }
 803
 804                         m->gobble(in);
 805                 }
 806                 in.close();
 807                 out.close();
 808
 809                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 810                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 811
 812                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
 813
 814
 815                 return 0;
 816         }
 817         catch(exception& e) {
 818                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 819                 exit(1);
 820         }
 821 }
 822 //**********************************************************************************************************************
 823 int RemoveGroupsCommand::readCount(){
 824         try {
 825                 string thisOutputDir = outputDir;
 826                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 827                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 828
 829                 ofstream out;
 830                 m->openOutputFile(outputFileName, out);
 831
 832                 ifstream in;
 833                 m->openInputFile(countfile, in);
 834
 835                 bool wroteSomething = false;
 836                 int removedCount = 0;
 837
 838         string headers = m->getline(in); m->gobble(in);
 839         vector<string> columnHeaders = m->splitWhiteSpace(headers);
 840
 841         vector<string> groups;
 842         map<int, string> originalGroupIndexes;
 843         map<string, int> GroupIndexes;
 844         set<int> indexOfGroupsChosen;
 845         for (int i = 2; i < columnHeaders.size(); i++) {  groups.push_back(columnHeaders[i]);  originalGroupIndexes[i-2] = columnHeaders[i]; }
 846         //sort groups to keep consistent with how we store the groups in groupmap
 847         sort(groups.begin(), groups.end());
 848         for (int i = 0; i < groups.size(); i++) {  GroupIndexes[groups[i]] = i; }
 849
 850                 vector<string> groupsToKeep;
 851                 for (int i = 0; i < groups.size(); i++) {
 852                         if (!m->inUsersGroups(groups[i], Groups)) { groupsToKeep.push_back(groups[i]); }
 853                 }
 854         sort(groupsToKeep.begin(), groupsToKeep.end());
 855         out << "Representative_Sequence\ttotal\t";
 856         for (int i = 0; i < groupsToKeep.size(); i++) { out << groupsToKeep[i] << '\t'; indexOfGroupsChosen.insert(GroupIndexes[groupsToKeep[i]]); }
 857         out << endl;
 858
 859         string name; int oldTotal;
 860         while (!in.eof()) {
 861
 862             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 863
 864             in >> name; m->gobble(in); in >> oldTotal; m->gobble(in);
 865             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(oldTotal) + "\n"); }
 866
 867             if (names.count(name) == 0) {
 868                 //if group info, then read it
 869                 vector<int> selectedCounts; int thisTotal = 0; int temp;
 870                 for (int i = 0; i < groups.size(); i++) {
 871                     int thisIndex = GroupIndexes[originalGroupIndexes[i]];
 872                     in >> temp;  m->gobble(in);
 873                     if (indexOfGroupsChosen.count(thisIndex) != 0) { //we want this group
 874                         selectedCounts.push_back(temp); thisTotal += temp;
 875                     }
 876                 }
 877
 878                 out << name << '\t' << thisTotal << '\t';
 879                 for (int i = 0; i < selectedCounts.size(); i++) {  out << selectedCounts[i] << '\t'; }
 880                 out << endl;
 881
 882                 wroteSomething = true;
 883                 removedCount+= (oldTotal - thisTotal);
 884             }else {  m->getline(in); removedCount += oldTotal; }
 885
 886             m->gobble(in);
 887         }
 888         in.close();
 889                 out.close();
 890
 891                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 892                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 893
 894                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your count file."); m->mothurOutEndLine();
 895
 896                 return 0;
 897         }
 898         catch(exception& e) {
 899                 m->errorOut(e, "RemoveGroupsCommand", "readCount");
 900                 exit(1);
 901         }
 902 }
 903 //**********************************************************************************************************************
 904 int RemoveGroupsCommand::readDesign(){
 905         try {
 906                 string thisOutputDir = outputDir;
 907                 if (outputDir == "") {  thisOutputDir += m->hasPath(designfile);  }
 908                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
 909
 910                 ofstream out;
 911                 m->openOutputFile(outputFileName, out);
 912
 913                 ifstream in;
 914                 m->openInputFile(designfile, in);
 915                 string name, group;
 916
 917                 bool wroteSomething = false;
 918                 int removedCount = 0;
 919
 920                 while(!in.eof()){
 921                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 922
 923                         in >> name;                             //read from first column
 924                         in >> group;                    //read from second column
 925
 926                         //if this name is in the accnos file
 927                         if (!(m->inUsersGroups(name, Groups))) {
 928                                 wroteSomething = true;
 929                                 out << name << '\t' << group << endl;
 930                         }else {  removedCount++;  }
 931
 932                         m->gobble(in);
 933                 }
 934                 in.close();
 935                 out.close();
 936
 937                 if (wroteSomething == false) {  m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine();  }
 938                 outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
 939
 940                 m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
 941
 942
 943                 return 0;
 944         }
 945         catch(exception& e) {
 946                 m->errorOut(e, "RemoveGroupsCommand", "readDesign");
 947                 exit(1);
 948         }
 949 }
 950
 951 //**********************************************************************************************************************
 952 int RemoveGroupsCommand::readTax(){
 953         try {
 954                 string thisOutputDir = outputDir;
 955                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 956                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 957                 ofstream out;
 958                 m->openOutputFile(outputFileName, out);
 959
 960                 ifstream in;
 961                 m->openInputFile(taxfile, in);
 962                 string name, tax;
 963
 964                 bool wroteSomething = false;
 965                 int removedCount = 0;
 966
 967                 while(!in.eof()){
 968                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 969
 970                         in >> name;                             //read from first column
 971                         in >> tax;                      //read from second column
 972
 973                         //if this name is in the accnos file
 974                         if (names.count(name) == 0) {
 975                                 wroteSomething = true;
 976                                 out << name << '\t' << tax << endl;
 977                         }else {  //if you are not in the accnos file check if you are a name that needs to be changed
 978                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 979                                 if (it != uniqueToRedundant.end()) {
 980                                         wroteSomething = true;
 981                                         out << it->second << '\t' << tax << endl;
 982                                 }else { removedCount++; }  }
 983
 984                         m->gobble(in);
 985                 }
 986                 in.close();
 987                 out.close();
 988
 989                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 990                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 991
 992                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 993
 994                 return 0;
 995         }
 996         catch(exception& e) {
 997                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
 998                 exit(1);
 999         }
1000 }
1001 //**********************************************************************************************************************
1002 int RemoveGroupsCommand::fillNames(){
1003         try {
1004                 vector<string> seqs = groupMap->getNamesSeqs();
1005
1006                 for (int i = 0; i < seqs.size(); i++) {
1007
1008                         if (m->control_pressed) { return 0; }
1009
1010                         string group = groupMap->getGroup(seqs[i]);
1011
1012                         if (m->inUsersGroups(group, Groups)) {
1013                                 names.insert(seqs[i]);
1014                         }
1015                 }
1016
1017                 return 0;
1018         }
1019         catch(exception& e) {
1020                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
1021                 exit(1);
1022         }
1023 }
1024
1025 //**********************************************************************************************************************
1026
1027
1028