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","fasta",false,false,true); parameters.push_back(pfasta);
  20                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
  21         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
  22         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);
  24         CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
  25                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
  26                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
  27                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
  28                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "RemoveGroupsCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string RemoveGroupsCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 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";
  46                 helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
  47                 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";
  48                 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";
  49                 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";
  50                 helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  51                 helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  52                 helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, amazon.groups).\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "RemoveGroupsCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string RemoveGroupsCommand::getOutputPattern(string type) {
  63     try {
  64         string pattern = "";
  65
  66         if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
  67         else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
  68         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
  69         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  70         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  71         else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
  72         else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
  73         else if (type == "design")      {   pattern = "[filename],pick,[extension]";    }
  74         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  75
  76         return pattern;
  77     }
  78     catch(exception& e) {
  79         m->errorOut(e, "RemoveGroupsCommand", "getOutputPattern");
  80         exit(1);
  81     }
  82 }
  83 //**********************************************************************************************************************
  84 RemoveGroupsCommand::RemoveGroupsCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["fasta"] = tempOutNames;
  90                 outputTypes["taxonomy"] = tempOutNames;
  91                 outputTypes["name"] = tempOutNames;
  92                 outputTypes["group"] = tempOutNames;
  93                 outputTypes["list"] = tempOutNames;
  94                 outputTypes["shared"] = tempOutNames;
  95         outputTypes["design"] = tempOutNames;
  96         outputTypes["count"] = tempOutNames;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107
 108                 //allow user to run help
 109                 if(option == "help") { help(); abort = true; calledHelp = true; }
 110                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 111
 112                 else {
 113                         vector<string> myArray = setParameters();
 114
 115                         OptionParser parser(option);
 116                         map<string,string> parameters = parser.getParameters();
 117
 118                         ValidParameters validParameter;
 119                         map<string,string>::iterator it;
 120
 121                         //check to make sure all parameters are valid for command
 122                         for (it = parameters.begin(); it != parameters.end(); it++) {
 123                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 124                         }
 125
 126                         //initialize outputTypes
 127                         vector<string> tempOutNames;
 128                         outputTypes["fasta"] = tempOutNames;
 129                         outputTypes["taxonomy"] = tempOutNames;
 130                         outputTypes["name"] = tempOutNames;
 131                         outputTypes["group"] = tempOutNames;
 132                         outputTypes["list"] = tempOutNames;
 133                         outputTypes["shared"] = tempOutNames;
 134             outputTypes["design"] = tempOutNames;
 135             outputTypes["count"] = tempOutNames;
 136
 137
 138                         //if the user changes the output directory command factory will send this info to us in the output parameter
 139                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 140
 141                         //if the user changes the input directory command factory will send this info to us in the output parameter
 142                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 143                         if (inputDir == "not found"){   inputDir = "";          }
 144                         else {
 145                                 string path;
 146                                 it = parameters.find("fasta");
 147                                 //user has given a template file
 148                                 if(it != parameters.end()){
 149                                         path = m->hasPath(it->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 152                                 }
 153
 154                                 it = parameters.find("accnos");
 155                                 //user has given a template file
 156                                 if(it != parameters.end()){
 157                                         path = m->hasPath(it->second);
 158                                         //if the user has not given a path then, add inputdir. else leave path alone.
 159                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 160                                 }
 161
 162                                 it = parameters.find("list");
 163                                 //user has given a template file
 164                                 if(it != parameters.end()){
 165                                         path = m->hasPath(it->second);
 166                                         //if the user has not given a path then, add inputdir. else leave path alone.
 167                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 168                                 }
 169
 170                                 it = parameters.find("name");
 171                                 //user has given a template file
 172                                 if(it != parameters.end()){
 173                                         path = m->hasPath(it->second);
 174                                         //if the user has not given a path then, add inputdir. else leave path alone.
 175                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 176                                 }
 177
 178                                 it = parameters.find("group");
 179                                 //user has given a template file
 180                                 if(it != parameters.end()){
 181                                         path = m->hasPath(it->second);
 182                                         //if the user has not given a path then, add inputdir. else leave path alone.
 183                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 184                                 }
 185
 186                                 it = parameters.find("taxonomy");
 187                                 //user has given a template file
 188                                 if(it != parameters.end()){
 189                                         path = m->hasPath(it->second);
 190                                         //if the user has not given a path then, add inputdir. else leave path alone.
 191                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 192                                 }
 193
 194                                 it = parameters.find("shared");
 195                                 //user has given a template file
 196                                 if(it != parameters.end()){
 197                                         path = m->hasPath(it->second);
 198                                         //if the user has not given a path then, add inputdir. else leave path alone.
 199                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 200                                 }
 201
 202                 it = parameters.find("design");
 203                                 //user has given a template file
 204                                 if(it != parameters.end()){
 205                                         path = m->hasPath(it->second);
 206                                         //if the user has not given a path then, add inputdir. else leave path alone.
 207                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 208                                 }
 209
 210                 it = parameters.find("count");
 211                                 //user has given a template file
 212                                 if(it != parameters.end()){
 213                                         path = m->hasPath(it->second);
 214                                         //if the user has not given a path then, add inputdir. else leave path alone.
 215                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 216                                 }
 217                         }
 218
 219
 220                         //check for required parameters
 221                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 222                         if (accnosfile == "not open") { accnosfile = ""; abort = true; }
 223                         else if (accnosfile == "not found") {  accnosfile = ""; }
 224                         else { m->setAccnosFile(accnosfile); }
 225
 226                         fastafile = validParameter.validFile(parameters, "fasta", true);
 227                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 228                         else if (fastafile == "not found") {  fastafile = "";  }
 229                         else { m->setFastaFile(fastafile); }
 230
 231                         namefile = validParameter.validFile(parameters, "name", true);
 232                         if (namefile == "not open") { namefile = ""; abort = true; }
 233                         else if (namefile == "not found") {  namefile = "";  }
 234                         else { m->setNameFile(namefile); }
 235
 236                         groupfile = validParameter.validFile(parameters, "group", true);
 237                         if (groupfile == "not open") { groupfile = "";  abort = true; }
 238                         else if (groupfile == "not found") {    groupfile = "";         }
 239                         else { m->setGroupFile(groupfile); }
 240
 241                         listfile = validParameter.validFile(parameters, "list", true);
 242                         if (listfile == "not open") { listfile = ""; abort = true; }
 243                         else if (listfile == "not found") {  listfile = "";  }
 244                         else { m->setListFile(listfile); }
 245
 246                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 247                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 248                         else if (taxfile == "not found") {  taxfile = "";  }
 249                         else { m->setTaxonomyFile(taxfile); }
 250
 251             designfile = validParameter.validFile(parameters, "design", true);
 252                         if (designfile == "not open") { designfile = ""; abort = true; }
 253                         else if (designfile == "not found") {  designfile = "";  }
 254                         else { m->setDesignFile(designfile); }
 255
 256                         groups = validParameter.validFile(parameters, "groups", false);
 257                         if (groups == "not found") { groups = ""; }
 258                         else {
 259                                 m->splitAtDash(groups, Groups);
 260                                 m->setGroups(Groups);
 261                         }
 262
 263                         sharedfile = validParameter.validFile(parameters, "shared", true);
 264                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 265                         else if (sharedfile == "not found") {  sharedfile = "";  }
 266                         else { m->setSharedFile(sharedfile); }
 267
 268
 269                         countfile = validParameter.validFile(parameters, "count", true);
 270             if (countfile == "not open") { countfile = ""; abort = true; }
 271             else if (countfile == "not found") { countfile = "";  }
 272             else { m->setCountTableFile(countfile); }
 273
 274             if ((namefile != "") && (countfile != "")) {
 275                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 276             }
 277
 278             if ((groupfile != "") && (countfile != "")) {
 279                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 280             }
 281
 282
 283                         if ((sharedfile == "") && (groupfile == "") && (designfile == "") && (countfile == "")) {
 284                                 //is there are current file available for any of these?
 285                                 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
 286                                         //give priority to group, then shared
 287                                         groupfile = m->getGroupFile();
 288                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 289                                         else {
 290                                                 sharedfile = m->getSharedFile();
 291                                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 292                                                 else {
 293                                                         countfile = m->getCountTableFile();
 294                             if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 295                             else {
 296                                 m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 297                             }
 298                                                 }
 299                                         }
 300                                 }else {
 301                                         //give priority to shared, then group
 302                                         sharedfile = m->getSharedFile();
 303                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 304                                         else {
 305                                                 groupfile = m->getGroupFile();
 306                                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 307                                                 else {
 308                                                         designfile = m->getDesignFile();
 309                             if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 310                             else {
 311                                 countfile = m->getCountTableFile();
 312                                 if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 313                                 else {
 314                                     m->mothurOut("You have no current groupfile, designfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 315                                 }
 316
 317                             }
 318                                                 }
 319                                         }
 320                                 }
 321                         }
 322
 323                         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; }
 324
 325                         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; }
 326                         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; }
 327
 328             if (countfile == "") {
 329                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 330                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 331                     parser.getNameFile(files);
 332                 }
 333             }
 334                 }
 335
 336         }
 337         catch(exception& e) {
 338                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 339                 exit(1);
 340         }
 341 }
 342 //**********************************************************************************************************************
 343
 344 int RemoveGroupsCommand::execute(){
 345         try {
 346
 347                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 348
 349                 //get groups you want to remove
 350                 if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
 351
 352                 if (groupfile != "") {
 353                         groupMap = new GroupMap(groupfile);
 354                         groupMap->readMap();
 355
 356                         //make sure groups are valid
 357                         //takes care of user setting groupNames that are invalid or setting groups=all
 358                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 359                         vector<string> checkedGroups;
 360             for (int i = 0; i < Groups.size(); i++) {
 361                 if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
 362                 else {  m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
 363             }
 364
 365             if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
 366                         else {
 367                 Groups = checkedGroups;
 368                 m->setGroups(Groups);
 369             }
 370
 371                         //fill names with names of sequences that are from the groups we want to remove
 372                         fillNames();
 373
 374                         delete groupMap;
 375                 }else if (countfile != ""){
 376             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 377                 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");
 378             }
 379             CountTable ct;
 380             ct.readTable(countfile, true);
 381             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
 382
 383             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
 384             SharedUtil util;
 385             util.setGroups(Groups, gNamesOfGroups);
 386             vector<string> namesOfSeqs = ct.getNamesOfSeqs();
 387             sort(Groups.begin(), Groups.end());
 388
 389             for (int i = 0; i < namesOfSeqs.size(); i++) {
 390                 vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
 391                 if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
 392                     names.insert(namesOfSeqs[i]);
 393                 }
 394             }
 395         }
 396
 397
 398                 if (m->control_pressed) { return 0; }
 399
 400                 //read through the correct file and output lines you want to keep
 401                 if (namefile != "")                     {               readName();             }
 402                 if (fastafile != "")            {               readFasta();    }
 403                 if (groupfile != "")            {               readGroup();    }
 404         if (countfile != "")            {               readCount();    }
 405                 if (listfile != "")                     {               readList();             }
 406                 if (taxfile != "")                      {               readTax();              }
 407                 if (sharedfile != "")           {               readShared();   }
 408         if (designfile != "")           {               readDesign();   }
 409
 410                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 411
 412                 if (outputNames.size() != 0) {
 413                         m->mothurOutEndLine();
 414                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 415                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 416                         m->mothurOutEndLine();
 417
 418                         //set fasta file as new current fastafile
 419                         string current = "";
 420                         itTypes = outputTypes.find("fasta");
 421                         if (itTypes != outputTypes.end()) {
 422                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 423                         }
 424
 425                         itTypes = outputTypes.find("name");
 426                         if (itTypes != outputTypes.end()) {
 427                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 428                         }
 429
 430                         itTypes = outputTypes.find("group");
 431                         if (itTypes != outputTypes.end()) {
 432                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 433                         }
 434
 435                         itTypes = outputTypes.find("list");
 436                         if (itTypes != outputTypes.end()) {
 437                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 438                         }
 439
 440                         itTypes = outputTypes.find("taxonomy");
 441                         if (itTypes != outputTypes.end()) {
 442                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 443                         }
 444
 445                         itTypes = outputTypes.find("shared");
 446                         if (itTypes != outputTypes.end()) {
 447                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 448                         }
 449
 450             itTypes = outputTypes.find("design");
 451                         if (itTypes != outputTypes.end()) {
 452                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
 453                         }
 454
 455             itTypes = outputTypes.find("count");
 456                         if (itTypes != outputTypes.end()) {
 457                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 458                         }
 459                 }
 460
 461                 return 0;
 462         }
 463
 464         catch(exception& e) {
 465                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 466                 exit(1);
 467         }
 468 }
 469
 470 //**********************************************************************************************************************
 471 int RemoveGroupsCommand::readFasta(){
 472         try {
 473                 string thisOutputDir = outputDir;
 474                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 475         map<string, string> variables;
 476         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 477         variables["[extension]"] = m->getExtension(fastafile);
 478                 string outputFileName = getOutputFileName("fasta", variables);
 479
 480                 ofstream out;
 481                 m->openOutputFile(outputFileName, out);
 482
 483                 ifstream in;
 484                 m->openInputFile(fastafile, in);
 485                 string name;
 486
 487                 bool wroteSomething = false;
 488                 int removedCount = 0;
 489
 490                 while(!in.eof()){
 491                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 492
 493                         Sequence currSeq(in);
 494                         name = currSeq.getName();
 495
 496                         if (name != "") {
 497                                 //if this name is in the accnos file
 498                                 if (names.count(name) == 0) {
 499                                         wroteSomething = true;
 500                                         currSeq.printSequence(out);
 501                                 }else {
 502                                         //if you are not in the accnos file check if you are a name that needs to be changed
 503                                         map<string, string>::iterator it = uniqueToRedundant.find(name);
 504                                         if (it != uniqueToRedundant.end()) {
 505                                                 wroteSomething = true;
 506                                                 currSeq.setName(it->second);
 507                                                 currSeq.printSequence(out);
 508                                         }else { removedCount++; }
 509                                 }
 510                         }
 511                         m->gobble(in);
 512                 }
 513                 in.close();
 514                 out.close();
 515
 516                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 517                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 518
 519                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 520
 521                 return 0;
 522
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 526                 exit(1);
 527         }
 528 }
 529 //**********************************************************************************************************************
 530 int RemoveGroupsCommand::readShared(){
 531         try {
 532                 string thisOutputDir = outputDir;
 533                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 534
 535                 //get group names from sharedfile so we can set Groups to the groupNames we want to keep
 536                 //that way we can take advantage of the reads in inputdata and sharedRabundVector
 537                 InputData* tempInput = new InputData(sharedfile, "sharedfile");
 538                 vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
 539
 540         map<string, string> variables;
 541         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 542         variables["[extension]"] = m->getExtension(sharedfile);
 543
 544                 //save m->Groups
 545                 vector<string> allGroupsNames = m->getAllGroups();
 546                 vector<string> mothurOutGroups = m->getGroups();
 547
 548                 vector<string> groupsToKeep;
 549                 for (int i = 0; i < allGroupsNames.size(); i++) {
 550                         if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
 551                                 groupsToKeep.push_back(allGroupsNames[i]);
 552                         }
 553                 }
 554
 555                 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; }
 556
 557                 //reset read
 558                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 559                 delete tempInput;
 560                 m->setGroups(groupsToKeep);
 561                 m->clearAllGroups();
 562                 m->saveNextLabel = "";
 563                 m->printedHeaders = false;
 564                 m->currentBinLabels.clear();
 565                 m->binLabelsInFile.clear();
 566
 567                 InputData input(sharedfile, "sharedfile");
 568                 lookup = input.getSharedRAbundVectors();
 569
 570                 bool wroteSomething = false;
 571
 572                 while(lookup[0] != NULL) {
 573
 574                         variables["[tag]"] = lookup[0]->getLabel();
 575             string outputFileName = getOutputFileName("shared", variables);
 576                         ofstream out;
 577                         m->openOutputFile(outputFileName, out);
 578                         outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 579
 580                         if (m->control_pressed) { out.close();  m->mothurRemove(outputFileName);  for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
 581
 582                         lookup[0]->printHeaders(out);
 583
 584                         for (int i = 0; i < lookup.size(); i++) {
 585                                 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
 586                                 lookup[i]->print(out);
 587                                 wroteSomething = true;
 588
 589                         }
 590
 591                         //get next line to process
 592                         //prevent memory leak
 593                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 594                         lookup = input.getSharedRAbundVectors();
 595
 596                         out.close();
 597                 }
 598
 599
 600                 m->setGroups(mothurOutGroups);
 601
 602                 if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 603
 604                 string groupsString = "";
 605                 for (int i = 0; i < Groups.size()-1; i++) {     groupsString += Groups[i] + ", "; }
 606                 groupsString += Groups[Groups.size()-1];
 607
 608                 m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
 609
 610                 return 0;
 611
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "RemoveGroupsCommand", "readShared");
 615                 exit(1);
 616         }
 617 }
 618 //**********************************************************************************************************************
 619 int RemoveGroupsCommand::readList(){
 620         try {
 621                 string thisOutputDir = outputDir;
 622                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 623                 map<string, string> variables;
 624         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 625         variables["[extension]"] = m->getExtension(listfile);
 626                 string outputFileName = getOutputFileName("list", variables);
 627
 628
 629                 ofstream out;
 630                 m->openOutputFile(outputFileName, out);
 631
 632                 ifstream in;
 633                 m->openInputFile(listfile, in);
 634
 635                 bool wroteSomething = false;
 636                 int removedCount = 0;
 637
 638                 while(!in.eof()){
 639
 640                         removedCount = 0;
 641
 642                         //read in list vector
 643                         ListVector list(in);
 644
 645                         //make a new list vector
 646                         ListVector newList;
 647                         newList.setLabel(list.getLabel());
 648
 649                         //for each bin
 650                         for (int i = 0; i < list.getNumBins(); i++) {
 651                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 652
 653                                 //parse out names that are in accnos file
 654                                 string binnames = list.get(i);
 655
 656                                 string newNames = "";
 657                                 while (binnames.find_first_of(',') != -1) {
 658                                         string name = binnames.substr(0,binnames.find_first_of(','));
 659                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 660
 661                                         //if that name is in the .accnos file, add it
 662                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 663                                         else {
 664                                                 //if you are not in the accnos file check if you are a name that needs to be changed
 665                                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 666                                                 if (it != uniqueToRedundant.end()) {
 667                                                         newNames += it->second + ",";
 668                                                 }else { removedCount++; }
 669                                         }
 670                                 }
 671
 672                                 //get last name
 673                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 674                                 else { //if you are not in the accnos file check if you are a name that needs to be changed
 675                                         map<string, string>::iterator it = uniqueToRedundant.find(binnames);
 676                                         if (it != uniqueToRedundant.end()) {
 677                                                 newNames += it->second + ",";
 678                                         }else { removedCount++; }
 679                                 }
 680
 681                                 //if there are names in this bin add to new list
 682                                 if (newNames != "") {
 683                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 684                                         newList.push_back(newNames);
 685                                 }
 686                         }
 687
 688                         //print new listvector
 689                         if (newList.getNumBins() != 0) {
 690                                 wroteSomething = true;
 691                                 newList.print(out);
 692                         }
 693
 694                         m->gobble(in);
 695                 }
 696                 in.close();
 697                 out.close();
 698
 699                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 700                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 701
 702                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
 703
 704                 return 0;
 705
 706         }
 707         catch(exception& e) {
 708                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 709                 exit(1);
 710         }
 711 }
 712 //**********************************************************************************************************************
 713 int RemoveGroupsCommand::readName(){
 714         try {
 715                 string thisOutputDir = outputDir;
 716                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 717                 map<string, string> variables;
 718                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 719         variables["[extension]"] = m->getExtension(namefile);
 720                 string outputFileName = getOutputFileName("name", variables);
 721                 ofstream out;
 722                 m->openOutputFile(outputFileName, out);
 723
 724                 ifstream in;
 725                 m->openInputFile(namefile, in);
 726                 string name, firstCol, secondCol;
 727
 728                 bool wroteSomething = false;
 729                 int removedCount = 0;
 730
 731                 while(!in.eof()){
 732                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 733
 734                         in >> firstCol;         m->gobble(in);
 735                         in >> secondCol;
 736
 737                         vector<string> parsedNames;
 738                         m->splitAtComma(secondCol, parsedNames);
 739
 740                         vector<string> validSecond;  validSecond.clear();
 741                         for (int i = 0; i < parsedNames.size(); i++) {
 742                                 if (names.count(parsedNames[i]) == 0) {
 743                                         validSecond.push_back(parsedNames[i]);
 744                                 }
 745                         }
 746
 747                         removedCount += parsedNames.size()-validSecond.size();
 748
 749                         //if the name in the first column is in the set then print it and any other names in second column also in set
 750                         if (names.count(firstCol) == 0) {
 751
 752                                 wroteSomething = true;
 753
 754                                 out << firstCol << '\t';
 755
 756                                 //you know you have at least one valid second since first column is valid
 757                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 758                                 out << validSecond[validSecond.size()-1] << endl;
 759
 760                                 //make first name in set you come to first column and then add the remaining names to second column
 761                         }else {
 762
 763                                 //you want part of this row
 764                                 if (validSecond.size() != 0) {
 765
 766                                         wroteSomething = true;
 767
 768                                         out << validSecond[0] << '\t';
 769
 770                                         //you know you have at least one valid second since first column is valid
 771                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 772                                         out << validSecond[validSecond.size()-1] << endl;
 773                                         uniqueToRedundant[firstCol] = validSecond[0];
 774                                 }
 775                         }
 776
 777                         m->gobble(in);
 778                 }
 779                 in.close();
 780                 out.close();
 781
 782                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 783                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 784
 785                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
 786
 787                 return 0;
 788         }
 789         catch(exception& e) {
 790                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 791                 exit(1);
 792         }
 793 }
 794
 795 //**********************************************************************************************************************
 796 int RemoveGroupsCommand::readGroup(){
 797         try {
 798                 string thisOutputDir = outputDir;
 799                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 800         map<string, string> variables;
 801                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 802         variables["[extension]"] = m->getExtension(groupfile);
 803                 string outputFileName = getOutputFileName("group", variables);
 804                 ofstream out;
 805                 m->openOutputFile(outputFileName, out);
 806
 807                 ifstream in;
 808                 m->openInputFile(groupfile, in);
 809                 string name, group;
 810
 811                 bool wroteSomething = false;
 812                 int removedCount = 0;
 813
 814                 while(!in.eof()){
 815                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 816
 817                         in >> name;                             //read from first column
 818                         in >> group;                    //read from second column
 819
 820                         //if this name is in the accnos file
 821                         if (names.count(name) == 0) {
 822                                 wroteSomething = true;
 823                                 out << name << '\t' << group << endl;
 824                         }else {  removedCount++;  }
 825
 826                         m->gobble(in);
 827                 }
 828                 in.close();
 829                 out.close();
 830
 831                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 832                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 833
 834                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
 835
 836
 837                 return 0;
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 841                 exit(1);
 842         }
 843 }
 844 //**********************************************************************************************************************
 845 int RemoveGroupsCommand::readCount(){
 846         try {
 847                 string thisOutputDir = outputDir;
 848                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 849                 map<string, string> variables;
 850                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 851         variables["[extension]"] = m->getExtension(countfile);
 852                 string outputFileName = getOutputFileName("count", variables);
 853
 854                 ofstream out;
 855                 m->openOutputFile(outputFileName, out);
 856
 857                 ifstream in;
 858                 m->openInputFile(countfile, in);
 859
 860                 bool wroteSomething = false;
 861                 int removedCount = 0;
 862
 863         string headers = m->getline(in); m->gobble(in);
 864         vector<string> columnHeaders = m->splitWhiteSpace(headers);
 865
 866         vector<string> groups;
 867         map<int, string> originalGroupIndexes;
 868         map<string, int> GroupIndexes;
 869         set<int> indexOfGroupsChosen;
 870         for (int i = 2; i < columnHeaders.size(); i++) {  groups.push_back(columnHeaders[i]);  originalGroupIndexes[i-2] = columnHeaders[i]; }
 871         //sort groups to keep consistent with how we store the groups in groupmap
 872         sort(groups.begin(), groups.end());
 873         for (int i = 0; i < groups.size(); i++) {  GroupIndexes[groups[i]] = i; }
 874
 875                 vector<string> groupsToKeep;
 876                 for (int i = 0; i < groups.size(); i++) {
 877                         if (!m->inUsersGroups(groups[i], Groups)) { groupsToKeep.push_back(groups[i]); }
 878                 }
 879         sort(groupsToKeep.begin(), groupsToKeep.end());
 880         out << "Representative_Sequence\ttotal\t";
 881         for (int i = 0; i < groupsToKeep.size(); i++) { out << groupsToKeep[i] << '\t'; indexOfGroupsChosen.insert(GroupIndexes[groupsToKeep[i]]); }
 882         out << endl;
 883
 884         string name; int oldTotal;
 885         while (!in.eof()) {
 886
 887             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 888
 889             in >> name; m->gobble(in); in >> oldTotal; m->gobble(in);
 890             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(oldTotal) + "\n"); }
 891
 892             if (names.count(name) == 0) {
 893                 //if group info, then read it
 894                 vector<int> selectedCounts; int thisTotal = 0; int temp;
 895                 for (int i = 0; i < groups.size(); i++) {
 896                     int thisIndex = GroupIndexes[originalGroupIndexes[i]];
 897                     in >> temp;  m->gobble(in);
 898                     if (indexOfGroupsChosen.count(thisIndex) != 0) { //we want this group
 899                         selectedCounts.push_back(temp); thisTotal += temp;
 900                     }
 901                 }
 902
 903                 out << name << '\t' << thisTotal << '\t';
 904                 for (int i = 0; i < selectedCounts.size(); i++) {  out << selectedCounts[i] << '\t'; }
 905                 out << endl;
 906
 907                 wroteSomething = true;
 908                 removedCount+= (oldTotal - thisTotal);
 909             }else {  m->getline(in); removedCount += oldTotal; }
 910
 911             m->gobble(in);
 912         }
 913         in.close();
 914                 out.close();
 915
 916                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 917                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 918
 919                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your count file."); m->mothurOutEndLine();
 920
 921                 return 0;
 922         }
 923         catch(exception& e) {
 924                 m->errorOut(e, "RemoveGroupsCommand", "readCount");
 925                 exit(1);
 926         }
 927 }
 928 //**********************************************************************************************************************
 929 int RemoveGroupsCommand::readDesign(){
 930         try {
 931                 string thisOutputDir = outputDir;
 932                 if (outputDir == "") {  thisOutputDir += m->hasPath(designfile);  }
 933         map<string, string> variables;
 934                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
 935         variables["[extension]"] = m->getExtension(designfile);
 936                 string outputFileName = getOutputFileName("design", variables);
 937
 938                 ofstream out;
 939                 m->openOutputFile(outputFileName, out);
 940
 941                 ifstream in;
 942                 m->openInputFile(designfile, in);
 943                 string name, group;
 944
 945                 bool wroteSomething = false;
 946                 int removedCount = 0;
 947
 948                 while(!in.eof()){
 949                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 950
 951                         in >> name;                             //read from first column
 952                         in >> group;                    //read from second column
 953
 954                         //if this name is in the accnos file
 955                         if (!(m->inUsersGroups(name, Groups))) {
 956                                 wroteSomething = true;
 957                                 out << name << '\t' << group << endl;
 958                         }else {  removedCount++;  }
 959
 960                         m->gobble(in);
 961                 }
 962                 in.close();
 963                 out.close();
 964
 965                 if (wroteSomething == false) {  m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine();  }
 966                 outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
 967
 968                 m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
 969
 970
 971                 return 0;
 972         }
 973         catch(exception& e) {
 974                 m->errorOut(e, "RemoveGroupsCommand", "readDesign");
 975                 exit(1);
 976         }
 977 }
 978
 979 //**********************************************************************************************************************
 980 int RemoveGroupsCommand::readTax(){
 981         try {
 982                 string thisOutputDir = outputDir;
 983                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 984                 map<string, string> variables;
 985                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
 986         variables["[extension]"] = m->getExtension(taxfile);
 987                 string outputFileName = getOutputFileName("taxonomy", variables);
 988                 ofstream out;
 989                 m->openOutputFile(outputFileName, out);
 990
 991                 ifstream in;
 992                 m->openInputFile(taxfile, in);
 993                 string name, tax;
 994
 995                 bool wroteSomething = false;
 996                 int removedCount = 0;
 997
 998                 while(!in.eof()){
 999                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
1000
1001                         in >> name;                             //read from first column
1002                         in >> tax;                      //read from second column
1003
1004                         //if this name is in the accnos file
1005                         if (names.count(name) == 0) {
1006                                 wroteSomething = true;
1007                                 out << name << '\t' << tax << endl;
1008                         }else {  //if you are not in the accnos file check if you are a name that needs to be changed
1009                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
1010                                 if (it != uniqueToRedundant.end()) {
1011                                         wroteSomething = true;
1012                                         out << it->second << '\t' << tax << endl;
1013                                 }else { removedCount++; }  }
1014
1015                         m->gobble(in);
1016                 }
1017                 in.close();
1018                 out.close();
1019
1020                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
1021                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
1022
1023                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
1024
1025                 return 0;
1026         }
1027         catch(exception& e) {
1028                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
1029                 exit(1);
1030         }
1031 }
1032 //**********************************************************************************************************************
1033 int RemoveGroupsCommand::fillNames(){
1034         try {
1035                 vector<string> seqs = groupMap->getNamesSeqs();
1036
1037                 for (int i = 0; i < seqs.size(); i++) {
1038
1039                         if (m->control_pressed) { return 0; }
1040
1041                         string group = groupMap->getGroup(seqs[i]);
1042
1043                         if (m->inUsersGroups(group, Groups)) {
1044                                 names.insert(seqs[i]);
1045                         }
1046                 }
1047
1048                 return 0;
1049         }
1050         catch(exception& e) {
1051                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
1052                 exit(1);
1053         }
1054 }
1055
1056 //**********************************************************************************************************************
1057
1058
1059