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", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  22                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
  23         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, 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 parameter is required, unless you have a current group 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 == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "shared")      {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else if (type == "design")      {   outputFileName =  "pick" + m->getExtension(inputName);   }
  77             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  78         }
  79         return outputFileName;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "RemoveGroupsCommand", "getOutputFileNameTag");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87 RemoveGroupsCommand::RemoveGroupsCommand(){
  88         try {
  89                 abort = true; calledHelp = true;
  90                 setParameters();
  91                 vector<string> tempOutNames;
  92                 outputTypes["fasta"] = tempOutNames;
  93                 outputTypes["taxonomy"] = tempOutNames;
  94                 outputTypes["name"] = tempOutNames;
  95                 outputTypes["group"] = tempOutNames;
  96                 outputTypes["list"] = tempOutNames;
  97                 outputTypes["shared"] = tempOutNames;
  98         outputTypes["design"] = tempOutNames;
  99         }
 100         catch(exception& e) {
 101                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 102                 exit(1);
 103         }
 104 }
 105 //**********************************************************************************************************************
 106 RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 107         try {
 108                 abort = false; calledHelp = false;
 109
 110                 //allow user to run help
 111                 if(option == "help") { help(); abort = true; calledHelp = true; }
 112                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 113
 114                 else {
 115                         vector<string> myArray = setParameters();
 116
 117                         OptionParser parser(option);
 118                         map<string,string> parameters = parser.getParameters();
 119
 120                         ValidParameters validParameter;
 121                         map<string,string>::iterator it;
 122
 123                         //check to make sure all parameters are valid for command
 124                         for (it = parameters.begin(); it != parameters.end(); it++) {
 125                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 126                         }
 127
 128                         //initialize outputTypes
 129                         vector<string> tempOutNames;
 130                         outputTypes["fasta"] = tempOutNames;
 131                         outputTypes["taxonomy"] = tempOutNames;
 132                         outputTypes["name"] = tempOutNames;
 133                         outputTypes["group"] = tempOutNames;
 134                         outputTypes["list"] = tempOutNames;
 135                         outputTypes["shared"] = tempOutNames;
 136             outputTypes["design"] = tempOutNames;
 137
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 141
 142                         //if the user changes the input directory command factory will send this info to us in the output parameter
 143                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 144                         if (inputDir == "not found"){   inputDir = "";          }
 145                         else {
 146                                 string path;
 147                                 it = parameters.find("fasta");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 153                                 }
 154
 155                                 it = parameters.find("accnos");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 161                                 }
 162
 163                                 it = parameters.find("list");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 169                                 }
 170
 171                                 it = parameters.find("name");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 177                                 }
 178
 179                                 it = parameters.find("group");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 185                                 }
 186
 187                                 it = parameters.find("taxonomy");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 193                                 }
 194
 195                                 it = parameters.find("shared");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 201                                 }
 202
 203                 it = parameters.find("design");
 204                                 //user has given a template file
 205                                 if(it != parameters.end()){
 206                                         path = m->hasPath(it->second);
 207                                         //if the user has not given a path then, add inputdir. else leave path alone.
 208                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 209                                 }
 210                         }
 211
 212
 213                         //check for required parameters
 214                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 215                         if (accnosfile == "not open") { accnosfile = ""; abort = true; }
 216                         else if (accnosfile == "not found") {  accnosfile = ""; }
 217                         else { m->setAccnosFile(accnosfile); }
 218
 219                         fastafile = validParameter.validFile(parameters, "fasta", true);
 220                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 221                         else if (fastafile == "not found") {  fastafile = "";  }
 222                         else { m->setFastaFile(fastafile); }
 223
 224                         namefile = validParameter.validFile(parameters, "name", true);
 225                         if (namefile == "not open") { namefile = ""; abort = true; }
 226                         else if (namefile == "not found") {  namefile = "";  }
 227                         else { m->setNameFile(namefile); }
 228
 229                         groupfile = validParameter.validFile(parameters, "group", true);
 230                         if (groupfile == "not open") { groupfile = "";  abort = true; }
 231                         else if (groupfile == "not found") {    groupfile = "";         }
 232                         else { m->setGroupFile(groupfile); }
 233
 234                         listfile = validParameter.validFile(parameters, "list", true);
 235                         if (listfile == "not open") { listfile = ""; abort = true; }
 236                         else if (listfile == "not found") {  listfile = "";  }
 237                         else { m->setListFile(listfile); }
 238
 239                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 240                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 241                         else if (taxfile == "not found") {  taxfile = "";  }
 242                         else { m->setTaxonomyFile(taxfile); }
 243
 244             designfile = validParameter.validFile(parameters, "design", true);
 245                         if (designfile == "not open") { designfile = ""; abort = true; }
 246                         else if (designfile == "not found") {  designfile = "";  }
 247                         else { m->setDesignFile(designfile); }
 248
 249                         groups = validParameter.validFile(parameters, "groups", false);
 250                         if (groups == "not found") { groups = ""; }
 251                         else {
 252                                 m->splitAtDash(groups, Groups);
 253                                 m->setGroups(Groups);
 254                         }
 255
 256                         sharedfile = validParameter.validFile(parameters, "shared", true);
 257                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 258                         else if (sharedfile == "not found") {  sharedfile = "";  }
 259                         else { m->setSharedFile(sharedfile); }
 260
 261                         groupfile = validParameter.validFile(parameters, "group", true);
 262                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 263                         else if (groupfile == "not found") {    groupfile = ""; }
 264                         else { m->setGroupFile(groupfile); }
 265
 266                         if ((sharedfile == "") && (groupfile == "") && (designfile == "")) {
 267                                 //is there are current file available for any of these?
 268                                 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
 269                                         //give priority to group, then shared
 270                                         groupfile = m->getGroupFile();
 271                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 272                                         else {
 273                                                 sharedfile = m->getSharedFile();
 274                                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 275                                                 else {
 276                                                         m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 277                                                 }
 278                                         }
 279                                 }else {
 280                                         //give priority to shared, then group
 281                                         sharedfile = m->getSharedFile();
 282                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 283                                         else {
 284                                                 groupfile = m->getGroupFile();
 285                                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 286                                                 else {
 287                                                         designfile = m->getDesignFile();
 288                             if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 289                             else {
 290                                 m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true;
 291                             }
 292                                                 }
 293                                         }
 294                                 }
 295                         }
 296
 297                         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; }
 298
 299                         if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (sharedfile == "") && (designfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; }
 300                         if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
 301
 302                         if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 303                                 vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 304                                 parser.getNameFile(files);
 305                         }
 306
 307                 }
 308
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 312                 exit(1);
 313         }
 314 }
 315 //**********************************************************************************************************************
 316
 317 int RemoveGroupsCommand::execute(){
 318         try {
 319
 320                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 321
 322                 //get groups you want to remove
 323                 if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
 324
 325                 if (groupfile != "") {
 326                         groupMap = new GroupMap(groupfile);
 327                         groupMap->readMap();
 328
 329                         //make sure groups are valid
 330                         //takes care of user setting groupNames that are invalid or setting groups=all
 331                         SharedUtil* util = new SharedUtil();
 332                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 333                         util->setGroups(Groups, namesGroups);
 334                         delete util;
 335
 336                         //fill names with names of sequences that are from the groups we want to remove
 337                         fillNames();
 338
 339                         delete groupMap;
 340                 }
 341
 342                 if (m->control_pressed) { return 0; }
 343
 344                 //read through the correct file and output lines you want to keep
 345                 if (namefile != "")                     {               readName();             }
 346                 if (fastafile != "")            {               readFasta();    }
 347                 if (groupfile != "")            {               readGroup();    }
 348                 if (listfile != "")                     {               readList();             }
 349                 if (taxfile != "")                      {               readTax();              }
 350                 if (sharedfile != "")           {               readShared();   }
 351         if (designfile != "")           {               readDesign();   }
 352
 353                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 354
 355                 if (outputNames.size() != 0) {
 356                         m->mothurOutEndLine();
 357                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 358                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 359                         m->mothurOutEndLine();
 360
 361                         //set fasta file as new current fastafile
 362                         string current = "";
 363                         itTypes = outputTypes.find("fasta");
 364                         if (itTypes != outputTypes.end()) {
 365                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 366                         }
 367
 368                         itTypes = outputTypes.find("name");
 369                         if (itTypes != outputTypes.end()) {
 370                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 371                         }
 372
 373                         itTypes = outputTypes.find("group");
 374                         if (itTypes != outputTypes.end()) {
 375                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 376                         }
 377
 378                         itTypes = outputTypes.find("list");
 379                         if (itTypes != outputTypes.end()) {
 380                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 381                         }
 382
 383                         itTypes = outputTypes.find("taxonomy");
 384                         if (itTypes != outputTypes.end()) {
 385                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 386                         }
 387
 388                         itTypes = outputTypes.find("shared");
 389                         if (itTypes != outputTypes.end()) {
 390                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 391                         }
 392
 393             itTypes = outputTypes.find("design");
 394                         if (itTypes != outputTypes.end()) {
 395                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
 396                         }
 397                 }
 398
 399                 return 0;
 400         }
 401
 402         catch(exception& e) {
 403                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 404                 exit(1);
 405         }
 406 }
 407
 408 //**********************************************************************************************************************
 409 int RemoveGroupsCommand::readFasta(){
 410         try {
 411                 string thisOutputDir = outputDir;
 412                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 413                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 414
 415                 ofstream out;
 416                 m->openOutputFile(outputFileName, out);
 417
 418                 ifstream in;
 419                 m->openInputFile(fastafile, in);
 420                 string name;
 421
 422                 bool wroteSomething = false;
 423                 int removedCount = 0;
 424
 425                 while(!in.eof()){
 426                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 427
 428                         Sequence currSeq(in);
 429                         name = currSeq.getName();
 430
 431                         if (name != "") {
 432                                 //if this name is in the accnos file
 433                                 if (names.count(name) == 0) {
 434                                         wroteSomething = true;
 435                                         currSeq.printSequence(out);
 436                                 }else {
 437                                         //if you are not in the accnos file check if you are a name that needs to be changed
 438                                         map<string, string>::iterator it = uniqueToRedundant.find(name);
 439                                         if (it != uniqueToRedundant.end()) {
 440                                                 wroteSomething = true;
 441                                                 currSeq.setName(it->second);
 442                                                 currSeq.printSequence(out);
 443                                         }else { removedCount++; }
 444                                 }
 445                         }
 446                         m->gobble(in);
 447                 }
 448                 in.close();
 449                 out.close();
 450
 451                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 452                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 453
 454                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 455
 456                 return 0;
 457
 458         }
 459         catch(exception& e) {
 460                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 461                 exit(1);
 462         }
 463 }
 464 //**********************************************************************************************************************
 465 int RemoveGroupsCommand::readShared(){
 466         try {
 467                 string thisOutputDir = outputDir;
 468                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 469
 470                 //get group names from sharedfile so we can set Groups to the groupNames we want to keep
 471                 //that way we can take advantage of the reads in inputdata and sharedRabundVector
 472                 InputData* tempInput = new InputData(sharedfile, "sharedfile");
 473                 vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
 474
 475                 //save m->Groups
 476                 vector<string> allGroupsNames = m->getAllGroups();
 477                 vector<string> mothurOutGroups = m->getGroups();
 478
 479                 vector<string> groupsToKeep;
 480                 for (int i = 0; i < allGroupsNames.size(); i++) {
 481                         if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
 482                                 groupsToKeep.push_back(allGroupsNames[i]);
 483                         }
 484                 }
 485
 486                 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; }
 487
 488                 //reset read
 489                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 490                 delete tempInput;
 491                 m->setGroups(groupsToKeep);
 492                 m->clearAllGroups();
 493                 m->saveNextLabel = "";
 494                 m->printedHeaders = false;
 495                 m->currentBinLabels.clear();
 496                 m->binLabelsInFile.clear();
 497
 498                 InputData input(sharedfile, "sharedfile");
 499                 lookup = input.getSharedRAbundVectors();
 500
 501                 bool wroteSomething = false;
 502
 503                 while(lookup[0] != NULL) {
 504
 505                         string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
 506                         ofstream out;
 507                         m->openOutputFile(outputFileName, out);
 508                         outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 509
 510                         if (m->control_pressed) { out.close();  m->mothurRemove(outputFileName);  for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
 511
 512                         lookup[0]->printHeaders(out);
 513
 514                         for (int i = 0; i < lookup.size(); i++) {
 515                                 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
 516                                 lookup[i]->print(out);
 517                                 wroteSomething = true;
 518
 519                         }
 520
 521                         //get next line to process
 522                         //prevent memory leak
 523                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 524                         lookup = input.getSharedRAbundVectors();
 525
 526                         out.close();
 527                 }
 528
 529
 530                 m->setGroups(mothurOutGroups);
 531
 532                 if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 533
 534                 string groupsString = "";
 535                 for (int i = 0; i < Groups.size()-1; i++) {     groupsString += Groups[i] + ", "; }
 536                 groupsString += Groups[Groups.size()-1];
 537
 538                 m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
 539
 540                 return 0;
 541
 542         }
 543         catch(exception& e) {
 544                 m->errorOut(e, "RemoveGroupsCommand", "readShared");
 545                 exit(1);
 546         }
 547 }
 548 //**********************************************************************************************************************
 549 int RemoveGroupsCommand::readList(){
 550         try {
 551                 string thisOutputDir = outputDir;
 552                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 553                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 554
 555                 ofstream out;
 556                 m->openOutputFile(outputFileName, out);
 557
 558                 ifstream in;
 559                 m->openInputFile(listfile, in);
 560
 561                 bool wroteSomething = false;
 562                 int removedCount = 0;
 563
 564                 while(!in.eof()){
 565
 566                         removedCount = 0;
 567
 568                         //read in list vector
 569                         ListVector list(in);
 570
 571                         //make a new list vector
 572                         ListVector newList;
 573                         newList.setLabel(list.getLabel());
 574
 575                         //for each bin
 576                         for (int i = 0; i < list.getNumBins(); i++) {
 577                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 578
 579                                 //parse out names that are in accnos file
 580                                 string binnames = list.get(i);
 581
 582                                 string newNames = "";
 583                                 while (binnames.find_first_of(',') != -1) {
 584                                         string name = binnames.substr(0,binnames.find_first_of(','));
 585                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 586
 587                                         //if that name is in the .accnos file, add it
 588                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 589                                         else {
 590                                                 //if you are not in the accnos file check if you are a name that needs to be changed
 591                                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 592                                                 if (it != uniqueToRedundant.end()) {
 593                                                         newNames += it->second + ",";
 594                                                 }else { removedCount++; }
 595                                         }
 596                                 }
 597
 598                                 //get last name
 599                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 600                                 else { //if you are not in the accnos file check if you are a name that needs to be changed
 601                                         map<string, string>::iterator it = uniqueToRedundant.find(binnames);
 602                                         if (it != uniqueToRedundant.end()) {
 603                                                 newNames += it->second + ",";
 604                                         }else { removedCount++; }
 605                                 }
 606
 607                                 //if there are names in this bin add to new list
 608                                 if (newNames != "") {
 609                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 610                                         newList.push_back(newNames);
 611                                 }
 612                         }
 613
 614                         //print new listvector
 615                         if (newList.getNumBins() != 0) {
 616                                 wroteSomething = true;
 617                                 newList.print(out);
 618                         }
 619
 620                         m->gobble(in);
 621                 }
 622                 in.close();
 623                 out.close();
 624
 625                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 626                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 627
 628                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
 629
 630                 return 0;
 631
 632         }
 633         catch(exception& e) {
 634                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 635                 exit(1);
 636         }
 637 }
 638 //**********************************************************************************************************************
 639 int RemoveGroupsCommand::readName(){
 640         try {
 641                 string thisOutputDir = outputDir;
 642                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 643                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 644                 ofstream out;
 645                 m->openOutputFile(outputFileName, out);
 646
 647                 ifstream in;
 648                 m->openInputFile(namefile, in);
 649                 string name, firstCol, secondCol;
 650
 651                 bool wroteSomething = false;
 652                 int removedCount = 0;
 653
 654                 while(!in.eof()){
 655                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 656
 657                         in >> firstCol;         m->gobble(in);
 658                         in >> secondCol;
 659
 660                         vector<string> parsedNames;
 661                         m->splitAtComma(secondCol, parsedNames);
 662
 663                         vector<string> validSecond;  validSecond.clear();
 664                         for (int i = 0; i < parsedNames.size(); i++) {
 665                                 if (names.count(parsedNames[i]) == 0) {
 666                                         validSecond.push_back(parsedNames[i]);
 667                                 }
 668                         }
 669
 670                         removedCount += parsedNames.size()-validSecond.size();
 671
 672                         //if the name in the first column is in the set then print it and any other names in second column also in set
 673                         if (names.count(firstCol) == 0) {
 674
 675                                 wroteSomething = true;
 676
 677                                 out << firstCol << '\t';
 678
 679                                 //you know you have at least one valid second since first column is valid
 680                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 681                                 out << validSecond[validSecond.size()-1] << endl;
 682
 683                                 //make first name in set you come to first column and then add the remaining names to second column
 684                         }else {
 685
 686                                 //you want part of this row
 687                                 if (validSecond.size() != 0) {
 688
 689                                         wroteSomething = true;
 690
 691                                         out << validSecond[0] << '\t';
 692
 693                                         //you know you have at least one valid second since first column is valid
 694                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 695                                         out << validSecond[validSecond.size()-1] << endl;
 696                                         uniqueToRedundant[firstCol] = validSecond[0];
 697                                 }
 698                         }
 699
 700                         m->gobble(in);
 701                 }
 702                 in.close();
 703                 out.close();
 704
 705                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 706                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 707
 708                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
 709
 710                 return 0;
 711         }
 712         catch(exception& e) {
 713                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 714                 exit(1);
 715         }
 716 }
 717
 718 //**********************************************************************************************************************
 719 int RemoveGroupsCommand::readGroup(){
 720         try {
 721                 string thisOutputDir = outputDir;
 722                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 723                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 724                 ofstream out;
 725                 m->openOutputFile(outputFileName, out);
 726
 727                 ifstream in;
 728                 m->openInputFile(groupfile, in);
 729                 string name, group;
 730
 731                 bool wroteSomething = false;
 732                 int removedCount = 0;
 733
 734                 while(!in.eof()){
 735                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 736
 737                         in >> name;                             //read from first column
 738                         in >> group;                    //read from second column
 739
 740                         //if this name is in the accnos file
 741                         if (names.count(name) == 0) {
 742                                 wroteSomething = true;
 743                                 out << name << '\t' << group << endl;
 744                         }else {  removedCount++;  }
 745
 746                         m->gobble(in);
 747                 }
 748                 in.close();
 749                 out.close();
 750
 751                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 752                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 753
 754                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
 755
 756
 757                 return 0;
 758         }
 759         catch(exception& e) {
 760                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 761                 exit(1);
 762         }
 763 }
 764 //**********************************************************************************************************************
 765 int RemoveGroupsCommand::readDesign(){
 766         try {
 767                 string thisOutputDir = outputDir;
 768                 if (outputDir == "") {  thisOutputDir += m->hasPath(designfile);  }
 769                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
 770
 771                 ofstream out;
 772                 m->openOutputFile(outputFileName, out);
 773
 774                 ifstream in;
 775                 m->openInputFile(designfile, in);
 776                 string name, group;
 777
 778                 bool wroteSomething = false;
 779                 int removedCount = 0;
 780
 781                 while(!in.eof()){
 782                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 783
 784                         in >> name;                             //read from first column
 785                         in >> group;                    //read from second column
 786
 787                         //if this name is in the accnos file
 788                         if (!(m->inUsersGroups(name, Groups))) {
 789                                 wroteSomething = true;
 790                                 out << name << '\t' << group << endl;
 791                         }else {  removedCount++;  }
 792
 793                         m->gobble(in);
 794                 }
 795                 in.close();
 796                 out.close();
 797
 798                 if (wroteSomething == false) {  m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine();  }
 799                 outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
 800
 801                 m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
 802
 803
 804                 return 0;
 805         }
 806         catch(exception& e) {
 807                 m->errorOut(e, "RemoveGroupsCommand", "readDesign");
 808                 exit(1);
 809         }
 810 }
 811
 812 //**********************************************************************************************************************
 813 int RemoveGroupsCommand::readTax(){
 814         try {
 815                 string thisOutputDir = outputDir;
 816                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 817                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 818                 ofstream out;
 819                 m->openOutputFile(outputFileName, out);
 820
 821                 ifstream in;
 822                 m->openInputFile(taxfile, in);
 823                 string name, tax;
 824
 825                 bool wroteSomething = false;
 826                 int removedCount = 0;
 827
 828                 while(!in.eof()){
 829                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 830
 831                         in >> name;                             //read from first column
 832                         in >> tax;                      //read from second column
 833
 834                         //if this name is in the accnos file
 835                         if (names.count(name) == 0) {
 836                                 wroteSomething = true;
 837                                 out << name << '\t' << tax << endl;
 838                         }else {  //if you are not in the accnos file check if you are a name that needs to be changed
 839                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 840                                 if (it != uniqueToRedundant.end()) {
 841                                         wroteSomething = true;
 842                                         out << it->second << '\t' << tax << endl;
 843                                 }else { removedCount++; }  }
 844
 845                         m->gobble(in);
 846                 }
 847                 in.close();
 848                 out.close();
 849
 850                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 851                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 852
 853                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 854
 855                 return 0;
 856         }
 857         catch(exception& e) {
 858                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
 859                 exit(1);
 860         }
 861 }
 862 //**********************************************************************************************************************
 863 int RemoveGroupsCommand::fillNames(){
 864         try {
 865                 vector<string> seqs = groupMap->getNamesSeqs();
 866
 867                 for (int i = 0; i < seqs.size(); i++) {
 868
 869                         if (m->control_pressed) { return 0; }
 870
 871                         string group = groupMap->getGroup(seqs[i]);
 872
 873                         if (m->inUsersGroups(group, Groups)) {
 874                                 names.insert(seqs[i]);
 875                         }
 876                 }
 877
 878                 return 0;
 879         }
 880         catch(exception& e) {
 881                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
 882                 exit(1);
 883         }
 884 }
 885
 886 //**********************************************************************************************************************
 887
 888
 889