getgroupscommand.cpp

   1 /*
   2  *  getgroupscommand.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 "getgroupscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "sharedutilities.h"
  14 #include "inputdata.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> GetGroupsCommand::setParameters(){
  18         try {
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  20                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
  21                 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
  22                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
  23                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  24                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
  25                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  26                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  27                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  28                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  29
  30                 vector<string> myArray;
  31                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "GetGroupsCommand", "setParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 string GetGroupsCommand::getHelpString(){
  41         try {
  42                 string helpString = "";
  43                 helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or shared file.\n";
  44                 helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
  45                 helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
  46                 helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
  47                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n";
  48                 helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  49                 helpString += "Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  50                 helpString += "or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetGroupsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 GetGroupsCommand::GetGroupsCommand(){
  61         try {
  62                 abort = true; calledHelp = true;
  63                 setParameters();
  64                 vector<string> tempOutNames;
  65                 outputTypes["fasta"] = tempOutNames;
  66                 outputTypes["taxonomy"] = tempOutNames;
  67                 outputTypes["name"] = tempOutNames;
  68                 outputTypes["group"] = tempOutNames;
  69                 outputTypes["list"] = tempOutNames;
  70                 outputTypes["shared"] = tempOutNames;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78 GetGroupsCommand::GetGroupsCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; calledHelp = true; }
  84                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  85
  86                 else {
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string,string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["fasta"] = tempOutNames;
 103                         outputTypes["taxonomy"] = tempOutNames;
 104                         outputTypes["name"] = tempOutNames;
 105                         outputTypes["group"] = tempOutNames;
 106                         outputTypes["list"] = tempOutNames;
 107                         outputTypes["shared"] = tempOutNames;
 108
 109
 110                         //if the user changes the output directory command factory will send this info to us in the output parameter
 111                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 112
 113                         //if the user changes the input directory command factory will send this info to us in the output parameter
 114                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 115                         if (inputDir == "not found"){   inputDir = "";          }
 116                         else {
 117                                 string path;
 118                                 it = parameters.find("fasta");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 124                                 }
 125
 126                                 it = parameters.find("accnos");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 132                                 }
 133
 134                                 it = parameters.find("list");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 140                                 }
 141
 142                                 it = parameters.find("name");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 148                                 }
 149
 150                                 it = parameters.find("group");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 156                                 }
 157
 158                                 it = parameters.find("taxonomy");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 164                                 }
 165
 166                                 it = parameters.find("shared");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 172                                 }
 173                         }
 174
 175
 176                         //check for required parameters
 177                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 178                         if (accnosfile == "not open") { abort = true; }
 179                         else if (accnosfile == "not found") {  accnosfile = ""; }
 180                         else { m->setAccnosFile(accnosfile); }
 181
 182                         fastafile = validParameter.validFile(parameters, "fasta", true);
 183                         if (fastafile == "not open") { abort = true; }
 184                         else if (fastafile == "not found") {  fastafile = "";  }
 185                         else { m->setFastaFile(fastafile); }
 186
 187                         namefile = validParameter.validFile(parameters, "name", true);
 188                         if (namefile == "not open") { abort = true; }
 189                         else if (namefile == "not found") {  namefile = "";  }
 190                         else { m->setNameFile(namefile); }
 191
 192                         listfile = validParameter.validFile(parameters, "list", true);
 193                         if (listfile == "not open") { abort = true; }
 194                         else if (listfile == "not found") {  listfile = "";  }
 195                         else { m->setListFile(listfile); }
 196
 197                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 198                         if (taxfile == "not open") { abort = true; }
 199                         else if (taxfile == "not found") {  taxfile = "";  }
 200                         else { m->setTaxonomyFile(taxfile); }
 201
 202                         groups = validParameter.validFile(parameters, "groups", false);
 203                         if (groups == "not found") { groups = ""; }
 204                         else {
 205                                 m->splitAtDash(groups, Groups);
 206                                 m->setGroups(Groups);
 207                         }
 208
 209                         sharedfile = validParameter.validFile(parameters, "shared", true);
 210                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 211                         else if (sharedfile == "not found") {  sharedfile = "";  }
 212                         else { m->setSharedFile(sharedfile); }
 213
 214                         groupfile = validParameter.validFile(parameters, "group", true);
 215                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 216                         else if (groupfile == "not found") {    groupfile = ""; }
 217                         else { m->setGroupFile(groupfile); }
 218
 219                         if ((sharedfile == "") && (groupfile == "")) {
 220                                 //is there are current file available for any of these?
 221                                 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
 222                                         //give priority to group, then shared
 223                                         groupfile = m->getGroupFile();
 224                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 225                                         else {
 226                                                 sharedfile = m->getSharedFile();
 227                                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 228                                                 else {
 229                                                         m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 230                                                 }
 231                                         }
 232                                 }else {
 233                                         //give priority to shared, then group
 234                                         sharedfile = m->getSharedFile();
 235                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 236                                         else {
 237                                                 groupfile = m->getGroupFile();
 238                                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 239                                                 else {
 240                                                         m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 241                                                 }
 242                                         }
 243                                 }
 244                         }
 245
 246                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 247
 248                         if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
 249                         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; }
 250
 251                 }
 252
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
 256                 exit(1);
 257         }
 258 }
 259 //**********************************************************************************************************************
 260
 261 int GetGroupsCommand::execute(){
 262         try {
 263
 264                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 265
 266                 //get groups you want to remove
 267                 if (accnosfile != "") { readAccnos(); }
 268
 269                 if (groupfile != "") {
 270                         groupMap = new GroupMap(groupfile);
 271                         groupMap->readMap();
 272
 273                         //make sure groups are valid
 274                         //takes care of user setting groupNames that are invalid or setting groups=all
 275                         SharedUtil* util = new SharedUtil();
 276                         vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
 277                         util->setGroups(Groups, gNamesOfGroups);
 278                         groupMap->setNamesOfGroups(gNamesOfGroups);
 279                         delete util;
 280
 281                         //fill names with names of sequences that are from the groups we want to remove
 282                         fillNames();
 283
 284                         delete groupMap;
 285                 }
 286
 287                 if (m->control_pressed) { return 0; }
 288
 289                 //read through the correct file and output lines you want to keep
 290                 if (namefile != "")                     {               readName();             }
 291                 if (fastafile != "")            {               readFasta();    }
 292                 if (groupfile != "")            {               readGroup();    }
 293                 if (listfile != "")                     {               readList();             }
 294                 if (taxfile != "")                      {               readTax();              }
 295                 if (sharedfile != "")           {               readShared();   }
 296
 297                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 298
 299
 300                 if (outputNames.size() != 0) {
 301                         m->mothurOutEndLine();
 302                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 303                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 304                         m->mothurOutEndLine();
 305
 306                         //set fasta file as new current fastafile
 307                         string current = "";
 308                         itTypes = outputTypes.find("fasta");
 309                         if (itTypes != outputTypes.end()) {
 310                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 311                         }
 312
 313                         itTypes = outputTypes.find("name");
 314                         if (itTypes != outputTypes.end()) {
 315                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 316                         }
 317
 318                         itTypes = outputTypes.find("group");
 319                         if (itTypes != outputTypes.end()) {
 320                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 321                         }
 322
 323                         itTypes = outputTypes.find("list");
 324                         if (itTypes != outputTypes.end()) {
 325                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 326                         }
 327
 328                         itTypes = outputTypes.find("taxonomy");
 329                         if (itTypes != outputTypes.end()) {
 330                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 331                         }
 332
 333                         itTypes = outputTypes.find("shared");
 334                         if (itTypes != outputTypes.end()) {
 335                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 336                         }
 337                 }
 338
 339                 return 0;
 340         }
 341
 342         catch(exception& e) {
 343                 m->errorOut(e, "GetGroupsCommand", "execute");
 344                 exit(1);
 345         }
 346 }
 347
 348 //**********************************************************************************************************************
 349 int GetGroupsCommand::readFasta(){
 350         try {
 351                 string thisOutputDir = outputDir;
 352                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 353                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
 354
 355                 ofstream out;
 356                 m->openOutputFile(outputFileName, out);
 357
 358                 ifstream in;
 359                 m->openInputFile(fastafile, in);
 360                 string name;
 361
 362                 bool wroteSomething = false;
 363                 int selectedCount = 0;
 364
 365                 while(!in.eof()){
 366                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 367
 368                         Sequence currSeq(in);
 369                         name = currSeq.getName();
 370
 371                         if (name != "") {
 372                                 //if this name is in the accnos file
 373                                 if (names.count(name) != 0) {
 374                                         wroteSomething = true;
 375
 376                                         currSeq.printSequence(out);
 377                                         selectedCount++;
 378                                 }
 379                         }
 380                         m->gobble(in);
 381                 }
 382                 in.close();
 383                 out.close();
 384
 385                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 386                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 387
 388                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 389
 390
 391                 return 0;
 392
 393         }
 394         catch(exception& e) {
 395                 m->errorOut(e, "GetGroupsCommand", "readFasta");
 396                 exit(1);
 397         }
 398 }
 399 //**********************************************************************************************************************
 400 int GetGroupsCommand::readShared(){
 401         try {
 402                 string thisOutputDir = outputDir;
 403                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 404
 405                 InputData input(sharedfile, "sharedfile");
 406                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 407
 408                 bool wroteSomething = false;
 409
 410                 while(lookup[0] != NULL) {
 411
 412                         string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".pick" + m->getExtension(sharedfile);
 413                         ofstream out;
 414                         m->openOutputFile(outputFileName, out);
 415                         outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 416
 417                         if (m->control_pressed) { out.close();  m->mothurRemove(outputFileName);  for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
 418
 419                         lookup[0]->printHeaders(out);
 420
 421                         for (int i = 0; i < lookup.size(); i++) {
 422                                 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
 423                                 lookup[i]->print(out);
 424                                 wroteSomething = true;
 425
 426                         }
 427
 428                         //get next line to process
 429                         //prevent memory leak
 430                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 431                         lookup = input.getSharedRAbundVectors();
 432
 433                         out.close();
 434                 }
 435
 436                 if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 437
 438                 string groupsString = "";
 439                 for (int i = 0; i < Groups.size()-1; i++) {     groupsString += Groups[i] + ", "; }
 440                 groupsString += Groups[Groups.size()-1];
 441
 442                 m->mothurOut("Selected groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
 443
 444                 return 0;
 445
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "GetGroupsCommand", "readShared");
 449                 exit(1);
 450         }
 451 }
 452 //**********************************************************************************************************************
 453 int GetGroupsCommand::readList(){
 454         try {
 455                 string thisOutputDir = outputDir;
 456                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 457                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 458
 459                 ofstream out;
 460                 m->openOutputFile(outputFileName, out);
 461
 462                 ifstream in;
 463                 m->openInputFile(listfile, in);
 464
 465                 bool wroteSomething = false;
 466                 int selectedCount = 0;
 467
 468                 while(!in.eof()){
 469
 470                         selectedCount = 0;
 471
 472                         //read in list vector
 473                         ListVector list(in);
 474
 475                         //make a new list vector
 476                         ListVector newList;
 477                         newList.setLabel(list.getLabel());
 478
 479                         //for each bin
 480                         for (int i = 0; i < list.getNumBins(); i++) {
 481                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 482
 483                                 //parse out names that are in accnos file
 484                                 string binnames = list.get(i);
 485
 486                                 string newNames = "";
 487                                 while (binnames.find_first_of(',') != -1) {
 488                                         string name = binnames.substr(0,binnames.find_first_of(','));
 489                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 490
 491                                         //if that name is in the .accnos file, add it
 492                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++;  }
 493                                 }
 494
 495                                 //get last name
 496                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  }
 497
 498                                 //if there are names in this bin add to new list
 499                                 if (newNames != "") {
 500                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 501                                         newList.push_back(newNames);
 502                                 }
 503                         }
 504
 505                         //print new listvector
 506                         if (newList.getNumBins() != 0) {
 507                                 wroteSomething = true;
 508                                 newList.print(out);
 509                         }
 510
 511                         m->gobble(in);
 512                 }
 513                 in.close();
 514                 out.close();
 515
 516                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 517                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 518
 519                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 520
 521                 return 0;
 522
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "GetGroupsCommand", "readList");
 526                 exit(1);
 527         }
 528 }
 529 //**********************************************************************************************************************
 530 int GetGroupsCommand::readName(){
 531         try {
 532                 string thisOutputDir = outputDir;
 533                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 534                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 535
 536                 ofstream out;
 537                 m->openOutputFile(outputFileName, out);
 538
 539                 ifstream in;
 540                 m->openInputFile(namefile, in);
 541                 string name, firstCol, secondCol;
 542
 543                 bool wroteSomething = false;
 544                 int selectedCount = 0;
 545
 546                 while(!in.eof()){
 547                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 548
 549                         in >> firstCol;         m->gobble(in);
 550                         in >> secondCol;
 551
 552                         vector<string> parsedNames;
 553                         m->splitAtComma(secondCol, parsedNames);
 554
 555                         vector<string> validSecond;  validSecond.clear();
 556                         for (int i = 0; i < parsedNames.size(); i++) {
 557                                 if (names.count(parsedNames[i]) != 0) {
 558                                         validSecond.push_back(parsedNames[i]);
 559                                 }
 560                         }
 561
 562                         selectedCount += validSecond.size();
 563
 564                         //if the name in the first column is in the set then print it and any other names in second column also in set
 565                         if (names.count(firstCol) != 0) {
 566
 567                                 wroteSomething = true;
 568
 569                                 out << firstCol << '\t';
 570
 571                                 //you know you have at least one valid second since first column is valid
 572                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 573                                 out << validSecond[validSecond.size()-1] << endl;
 574
 575                                 //make first name in set you come to first column and then add the remaining names to second column
 576                         }else {
 577
 578                                 //you want part of this row
 579                                 if (validSecond.size() != 0) {
 580
 581                                         wroteSomething = true;
 582
 583                                         out << validSecond[0] << '\t';
 584
 585                                         //you know you have at least one valid second since first column is valid
 586                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 587                                         out << validSecond[validSecond.size()-1] << endl;
 588                                 }
 589                         }
 590
 591                         m->gobble(in);
 592                 }
 593                 in.close();
 594                 out.close();
 595
 596                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 597                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 598
 599                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 600
 601                 return 0;
 602         }
 603         catch(exception& e) {
 604                 m->errorOut(e, "GetGroupsCommand", "readName");
 605                 exit(1);
 606         }
 607 }
 608
 609 //**********************************************************************************************************************
 610 int GetGroupsCommand::readGroup(){
 611         try {
 612                 string thisOutputDir = outputDir;
 613                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 614                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 615
 616                 ofstream out;
 617                 m->openOutputFile(outputFileName, out);
 618
 619                 ifstream in;
 620                 m->openInputFile(groupfile, in);
 621                 string name, group;
 622
 623                 bool wroteSomething = false;
 624                 int selectedCount = 0;
 625
 626                 while(!in.eof()){
 627                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 628
 629                         in >> name;                             //read from first column
 630                         in >> group;                    //read from second column
 631
 632                         //if this name is in the accnos file
 633                         if (names.count(name) != 0) {
 634                                 wroteSomething = true;
 635                                 out << name << '\t' << group << endl;
 636                                 selectedCount++;
 637                         }
 638
 639                         m->gobble(in);
 640                 }
 641                 in.close();
 642                 out.close();
 643
 644                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 645                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 646
 647                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 648
 649                 return 0;
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "GetGroupsCommand", "readGroup");
 653                 exit(1);
 654         }
 655 }
 656 //**********************************************************************************************************************
 657 int GetGroupsCommand::readTax(){
 658         try {
 659                 string thisOutputDir = outputDir;
 660                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 661                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 662                 ofstream out;
 663                 m->openOutputFile(outputFileName, out);
 664
 665                 ifstream in;
 666                 m->openInputFile(taxfile, in);
 667                 string name, tax;
 668
 669                 bool wroteSomething = false;
 670
 671                 while(!in.eof()){
 672                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 673
 674                         in >> name;                             //read from first column
 675                         in >> tax;                      //read from second column
 676
 677                         //if this name is in the accnos file
 678                         if (names.count(name) != 0) {
 679                                 wroteSomething = true;
 680                                 out << name << '\t' << tax << endl;
 681                         }
 682
 683                         m->gobble(in);
 684                 }
 685                 in.close();
 686                 out.close();
 687
 688                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 689                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
 690
 691                 return 0;
 692         }
 693         catch(exception& e) {
 694                 m->errorOut(e, "GetGroupsCommand", "readTax");
 695                 exit(1);
 696         }
 697 }
 698 //**********************************************************************************************************************
 699 void GetGroupsCommand::readAccnos(){
 700         try {
 701                 Groups.clear();
 702
 703                 ifstream in;
 704                 m->openInputFile(accnosfile, in);
 705                 string name;
 706
 707                 while(!in.eof()){
 708                         in >> name;
 709
 710                         Groups.push_back(name);
 711
 712                         m->gobble(in);
 713                 }
 714                 in.close();
 715
 716                 m->setGroups(Groups);
 717
 718         }
 719         catch(exception& e) {
 720                 m->errorOut(e, "GetGroupsCommand", "readAccnos");
 721                 exit(1);
 722         }
 723 }
 724 //**********************************************************************************************************************
 725 int GetGroupsCommand::fillNames(){
 726         try {
 727                 vector<string> seqs = groupMap->getNamesSeqs();
 728
 729                 for (int i = 0; i < seqs.size(); i++) {
 730
 731                         if (m->control_pressed) { return 0; }
 732
 733                         string group = groupMap->getGroup(seqs[i]);
 734
 735                         if (m->inUsersGroups(group, Groups)) {
 736                                 names.insert(seqs[i]);
 737                         }
 738                 }
 739
 740                 return 0;
 741         }
 742         catch(exception& e) {
 743                 m->errorOut(e, "GetGroupsCommand", "fillNames");
 744                 exit(1);
 745         }
 746 }
 747
 748 //**********************************************************************************************************************
 749
 750