removegroupscommand.cpp

   1 /*
   2  *  removegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "removegroupscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13 #include "sharedutilities.h"
  14 #include "inputdata.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> RemoveGroupsCommand::setParameters(){
  18         try {
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
  20                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
  21         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
  22         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);
  24         CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
  25                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
  26                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
  27                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
  28                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "RemoveGroupsCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string RemoveGroupsCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design or sharedfile.\n";
  46                 helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
  47                 helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group or count parameter is required, unless you have a current group or count file or are using a sharedfile.\n";
  48                 helpString += "You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n";
  49                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like removed.  You can separate group names with dashes.\n";
  50                 helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
  51                 helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
  52                 helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, amazon.groups).\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "RemoveGroupsCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string RemoveGroupsCommand::getOutputPattern(string type) {
  63     try {
  64         string pattern = "";
  65
  66         if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
  67         else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
  68         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
  69         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  70         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  71         else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
  72         else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
  73         else if (type == "design")      {   pattern = "[filename],pick,[extension]";    }
  74         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  75
  76         return pattern;
  77     }
  78     catch(exception& e) {
  79         m->errorOut(e, "RemoveGroupsCommand", "getOutputPattern");
  80         exit(1);
  81     }
  82 }
  83 //**********************************************************************************************************************
  84 RemoveGroupsCommand::RemoveGroupsCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["fasta"] = tempOutNames;
  90                 outputTypes["taxonomy"] = tempOutNames;
  91                 outputTypes["name"] = tempOutNames;
  92                 outputTypes["group"] = tempOutNames;
  93                 outputTypes["list"] = tempOutNames;
  94                 outputTypes["shared"] = tempOutNames;
  95         outputTypes["design"] = tempOutNames;
  96         outputTypes["count"] = tempOutNames;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107
 108                 //allow user to run help
 109                 if(option == "help") { help(); abort = true; calledHelp = true; }
 110                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 111
 112                 else {
 113                         vector<string> myArray = setParameters();
 114
 115                         OptionParser parser(option);
 116                         map<string,string> parameters = parser.getParameters();
 117
 118                         ValidParameters validParameter;
 119                         map<string,string>::iterator it;
 120
 121                         //check to make sure all parameters are valid for command
 122                         for (it = parameters.begin(); it != parameters.end(); it++) {
 123                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 124                         }
 125
 126                         //initialize outputTypes
 127                         vector<string> tempOutNames;
 128                         outputTypes["fasta"] = tempOutNames;
 129                         outputTypes["taxonomy"] = tempOutNames;
 130                         outputTypes["name"] = tempOutNames;
 131                         outputTypes["group"] = tempOutNames;
 132                         outputTypes["list"] = tempOutNames;
 133                         outputTypes["shared"] = tempOutNames;
 134             outputTypes["design"] = tempOutNames;
 135             outputTypes["count"] = tempOutNames;
 136
 137
 138                         //if the user changes the output directory command factory will send this info to us in the output parameter
 139                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 140
 141                         //if the user changes the input directory command factory will send this info to us in the output parameter
 142                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 143                         if (inputDir == "not found"){   inputDir = "";          }
 144                         else {
 145                                 string path;
 146                                 it = parameters.find("fasta");
 147                                 //user has given a template file
 148                                 if(it != parameters.end()){
 149                                         path = m->hasPath(it->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 152                                 }
 153
 154                                 it = parameters.find("accnos");
 155                                 //user has given a template file
 156                                 if(it != parameters.end()){
 157                                         path = m->hasPath(it->second);
 158                                         //if the user has not given a path then, add inputdir. else leave path alone.
 159                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 160                                 }
 161
 162                                 it = parameters.find("list");
 163                                 //user has given a template file
 164                                 if(it != parameters.end()){
 165                                         path = m->hasPath(it->second);
 166                                         //if the user has not given a path then, add inputdir. else leave path alone.
 167                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 168                                 }
 169
 170                                 it = parameters.find("name");
 171                                 //user has given a template file
 172                                 if(it != parameters.end()){
 173                                         path = m->hasPath(it->second);
 174                                         //if the user has not given a path then, add inputdir. else leave path alone.
 175                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 176                                 }
 177
 178                                 it = parameters.find("group");
 179                                 //user has given a template file
 180                                 if(it != parameters.end()){
 181                                         path = m->hasPath(it->second);
 182                                         //if the user has not given a path then, add inputdir. else leave path alone.
 183                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 184                                 }
 185
 186                                 it = parameters.find("taxonomy");
 187                                 //user has given a template file
 188                                 if(it != parameters.end()){
 189                                         path = m->hasPath(it->second);
 190                                         //if the user has not given a path then, add inputdir. else leave path alone.
 191                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 192                                 }
 193
 194                                 it = parameters.find("shared");
 195                                 //user has given a template file
 196                                 if(it != parameters.end()){
 197                                         path = m->hasPath(it->second);
 198                                         //if the user has not given a path then, add inputdir. else leave path alone.
 199                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 200                                 }
 201
 202                 it = parameters.find("design");
 203                                 //user has given a template file
 204                                 if(it != parameters.end()){
 205                                         path = m->hasPath(it->second);
 206                                         //if the user has not given a path then, add inputdir. else leave path alone.
 207                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 208                                 }
 209
 210                 it = parameters.find("count");
 211                                 //user has given a template file
 212                                 if(it != parameters.end()){
 213                                         path = m->hasPath(it->second);
 214                                         //if the user has not given a path then, add inputdir. else leave path alone.
 215                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 216                                 }
 217                         }
 218
 219
 220                         //check for required parameters
 221                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 222                         if (accnosfile == "not open") { accnosfile = ""; abort = true; }
 223                         else if (accnosfile == "not found") {  accnosfile = ""; }
 224                         else { m->setAccnosFile(accnosfile); }
 225
 226                         fastafile = validParameter.validFile(parameters, "fasta", true);
 227                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 228                         else if (fastafile == "not found") {  fastafile = "";  }
 229                         else { m->setFastaFile(fastafile); }
 230
 231                         namefile = validParameter.validFile(parameters, "name", true);
 232                         if (namefile == "not open") { namefile = ""; abort = true; }
 233                         else if (namefile == "not found") {  namefile = "";  }
 234                         else { m->setNameFile(namefile); }
 235
 236                         groupfile = validParameter.validFile(parameters, "group", true);
 237                         if (groupfile == "not open") { groupfile = "";  abort = true; }
 238                         else if (groupfile == "not found") {    groupfile = "";         }
 239                         else { m->setGroupFile(groupfile); }
 240
 241                         listfile = validParameter.validFile(parameters, "list", true);
 242                         if (listfile == "not open") { listfile = ""; abort = true; }
 243                         else if (listfile == "not found") {  listfile = "";  }
 244                         else { m->setListFile(listfile); }
 245
 246                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 247                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 248                         else if (taxfile == "not found") {  taxfile = "";  }
 249                         else { m->setTaxonomyFile(taxfile); }
 250
 251             designfile = validParameter.validFile(parameters, "design", true);
 252                         if (designfile == "not open") { designfile = ""; abort = true; }
 253                         else if (designfile == "not found") {  designfile = "";  }
 254                         else { m->setDesignFile(designfile); }
 255
 256                         groups = validParameter.validFile(parameters, "groups", false);
 257                         if (groups == "not found") { groups = ""; }
 258                         else {
 259                                 m->splitAtDash(groups, Groups);
 260                                 m->setGroups(Groups);
 261                         }
 262
 263                         sharedfile = validParameter.validFile(parameters, "shared", true);
 264                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 265                         else if (sharedfile == "not found") {  sharedfile = "";  }
 266                         else { m->setSharedFile(sharedfile); }
 267
 268
 269                         countfile = validParameter.validFile(parameters, "count", true);
 270             if (countfile == "not open") { countfile = ""; abort = true; }
 271             else if (countfile == "not found") { countfile = "";  }
 272             else { m->setCountTableFile(countfile); }
 273
 274             if ((namefile != "") && (countfile != "")) {
 275                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 276             }
 277
 278             if ((groupfile != "") && (countfile != "")) {
 279                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 280             }
 281
 282
 283                         if ((sharedfile == "") && (groupfile == "") && (designfile == "") && (countfile == "")) {
 284                                 //is there are current file available for any of these?
 285                                 if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
 286                                         //give priority to group, then shared
 287                                         groupfile = m->getGroupFile();
 288                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 289                                         else {
 290                                                 sharedfile = m->getSharedFile();
 291                                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 292                                                 else {
 293                                                         countfile = m->getCountTableFile();
 294                             if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 295                             else {
 296                                 m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 297                             }
 298                                                 }
 299                                         }
 300                                 }else {
 301                                         //give priority to shared, then group
 302                                         sharedfile = m->getSharedFile();
 303                                         if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 304                                         else {
 305                                                 groupfile = m->getGroupFile();
 306                                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 307                                                 else {
 308                                                         designfile = m->getDesignFile();
 309                             if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 310                             else {
 311                                 countfile = m->getCountTableFile();
 312                                 if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
 313                                 else {
 314                                     m->mothurOut("You have no current groupfile, designfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 315                                 }
 316
 317                             }
 318                                                 }
 319                                         }
 320                                 }
 321                         }
 322
 323                         if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file containing group names or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
 324
 325                         if ((fastafile == "") && (namefile == "") && (countfile == "") && (groupfile == "")  && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design, count or list."); m->mothurOutEndLine(); abort = true; }
 326                         if (((groupfile == "") && (countfile == "")) && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group or count file."); m->mothurOutEndLine(); abort = true; }
 327
 328             if (countfile == "") {
 329                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 330                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 331                     parser.getNameFile(files);
 332                 }
 333             }
 334                 }
 335
 336         }
 337         catch(exception& e) {
 338                 m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
 339                 exit(1);
 340         }
 341 }
 342 //**********************************************************************************************************************
 343
 344 int RemoveGroupsCommand::execute(){
 345         try {
 346
 347                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 348
 349                 //get groups you want to remove
 350                 if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
 351
 352                 if (groupfile != "") {
 353                         groupMap = new GroupMap(groupfile);
 354                         groupMap->readMap();
 355
 356                         //make sure groups are valid
 357                         //takes care of user setting groupNames that are invalid or setting groups=all
 358                         SharedUtil* util = new SharedUtil();
 359                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 360                         util->setGroups(Groups, namesGroups);
 361                         delete util;
 362
 363                         //fill names with names of sequences that are from the groups we want to remove
 364                         fillNames();
 365
 366                         delete groupMap;
 367                 }else if (countfile != ""){
 368             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 369                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
 370             }
 371             CountTable ct;
 372             ct.readTable(countfile);
 373             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
 374
 375             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
 376             SharedUtil util;
 377             util.setGroups(Groups, gNamesOfGroups);
 378             vector<string> namesOfSeqs = ct.getNamesOfSeqs();
 379             sort(Groups.begin(), Groups.end());
 380
 381             for (int i = 0; i < namesOfSeqs.size(); i++) {
 382                 vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
 383                 if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
 384                     names.insert(namesOfSeqs[i]);
 385                 }
 386             }
 387         }
 388
 389
 390                 if (m->control_pressed) { return 0; }
 391
 392                 //read through the correct file and output lines you want to keep
 393                 if (namefile != "")                     {               readName();             }
 394                 if (fastafile != "")            {               readFasta();    }
 395                 if (groupfile != "")            {               readGroup();    }
 396         if (countfile != "")            {               readCount();    }
 397                 if (listfile != "")                     {               readList();             }
 398                 if (taxfile != "")                      {               readTax();              }
 399                 if (sharedfile != "")           {               readShared();   }
 400         if (designfile != "")           {               readDesign();   }
 401
 402                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 403
 404                 if (outputNames.size() != 0) {
 405                         m->mothurOutEndLine();
 406                         m->mothurOut("Output File names: "); m->mothurOutEndLine();
 407                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 408                         m->mothurOutEndLine();
 409
 410                         //set fasta file as new current fastafile
 411                         string current = "";
 412                         itTypes = outputTypes.find("fasta");
 413                         if (itTypes != outputTypes.end()) {
 414                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 415                         }
 416
 417                         itTypes = outputTypes.find("name");
 418                         if (itTypes != outputTypes.end()) {
 419                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 420                         }
 421
 422                         itTypes = outputTypes.find("group");
 423                         if (itTypes != outputTypes.end()) {
 424                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 425                         }
 426
 427                         itTypes = outputTypes.find("list");
 428                         if (itTypes != outputTypes.end()) {
 429                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 430                         }
 431
 432                         itTypes = outputTypes.find("taxonomy");
 433                         if (itTypes != outputTypes.end()) {
 434                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 435                         }
 436
 437                         itTypes = outputTypes.find("shared");
 438                         if (itTypes != outputTypes.end()) {
 439                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 440                         }
 441
 442             itTypes = outputTypes.find("design");
 443                         if (itTypes != outputTypes.end()) {
 444                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
 445                         }
 446
 447             itTypes = outputTypes.find("count");
 448                         if (itTypes != outputTypes.end()) {
 449                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 450                         }
 451                 }
 452
 453                 return 0;
 454         }
 455
 456         catch(exception& e) {
 457                 m->errorOut(e, "RemoveGroupsCommand", "execute");
 458                 exit(1);
 459         }
 460 }
 461
 462 //**********************************************************************************************************************
 463 int RemoveGroupsCommand::readFasta(){
 464         try {
 465                 string thisOutputDir = outputDir;
 466                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 467         map<string, string> variables;
 468         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 469         variables["[extension]"] = m->getExtension(fastafile);
 470                 string outputFileName = getOutputFileName("fasta", variables);
 471
 472                 ofstream out;
 473                 m->openOutputFile(outputFileName, out);
 474
 475                 ifstream in;
 476                 m->openInputFile(fastafile, in);
 477                 string name;
 478
 479                 bool wroteSomething = false;
 480                 int removedCount = 0;
 481
 482                 while(!in.eof()){
 483                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 484
 485                         Sequence currSeq(in);
 486                         name = currSeq.getName();
 487
 488                         if (name != "") {
 489                                 //if this name is in the accnos file
 490                                 if (names.count(name) == 0) {
 491                                         wroteSomething = true;
 492                                         currSeq.printSequence(out);
 493                                 }else {
 494                                         //if you are not in the accnos file check if you are a name that needs to be changed
 495                                         map<string, string>::iterator it = uniqueToRedundant.find(name);
 496                                         if (it != uniqueToRedundant.end()) {
 497                                                 wroteSomething = true;
 498                                                 currSeq.setName(it->second);
 499                                                 currSeq.printSequence(out);
 500                                         }else { removedCount++; }
 501                                 }
 502                         }
 503                         m->gobble(in);
 504                 }
 505                 in.close();
 506                 out.close();
 507
 508                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 509                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 510
 511                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 512
 513                 return 0;
 514
 515         }
 516         catch(exception& e) {
 517                 m->errorOut(e, "RemoveGroupsCommand", "readFasta");
 518                 exit(1);
 519         }
 520 }
 521 //**********************************************************************************************************************
 522 int RemoveGroupsCommand::readShared(){
 523         try {
 524                 string thisOutputDir = outputDir;
 525                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 526
 527                 //get group names from sharedfile so we can set Groups to the groupNames we want to keep
 528                 //that way we can take advantage of the reads in inputdata and sharedRabundVector
 529                 InputData* tempInput = new InputData(sharedfile, "sharedfile");
 530                 vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
 531
 532         map<string, string> variables;
 533         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 534         variables["[extension]"] = m->getExtension(sharedfile);
 535
 536                 //save m->Groups
 537                 vector<string> allGroupsNames = m->getAllGroups();
 538                 vector<string> mothurOutGroups = m->getGroups();
 539
 540                 vector<string> groupsToKeep;
 541                 for (int i = 0; i < allGroupsNames.size(); i++) {
 542                         if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
 543                                 groupsToKeep.push_back(allGroupsNames[i]);
 544                         }
 545                 }
 546
 547                 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; }
 548
 549                 //reset read
 550                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 551                 delete tempInput;
 552                 m->setGroups(groupsToKeep);
 553                 m->clearAllGroups();
 554                 m->saveNextLabel = "";
 555                 m->printedHeaders = false;
 556                 m->currentBinLabels.clear();
 557                 m->binLabelsInFile.clear();
 558
 559                 InputData input(sharedfile, "sharedfile");
 560                 lookup = input.getSharedRAbundVectors();
 561
 562                 bool wroteSomething = false;
 563
 564                 while(lookup[0] != NULL) {
 565
 566                         variables["[tag]"] = lookup[0]->getLabel();
 567             string outputFileName = getOutputFileName("shared", variables);
 568                         ofstream out;
 569                         m->openOutputFile(outputFileName, out);
 570                         outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 571
 572                         if (m->control_pressed) { out.close();  m->mothurRemove(outputFileName);  for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
 573
 574                         lookup[0]->printHeaders(out);
 575
 576                         for (int i = 0; i < lookup.size(); i++) {
 577                                 out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
 578                                 lookup[i]->print(out);
 579                                 wroteSomething = true;
 580
 581                         }
 582
 583                         //get next line to process
 584                         //prevent memory leak
 585                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 586                         lookup = input.getSharedRAbundVectors();
 587
 588                         out.close();
 589                 }
 590
 591
 592                 m->setGroups(mothurOutGroups);
 593
 594                 if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 595
 596                 string groupsString = "";
 597                 for (int i = 0; i < Groups.size()-1; i++) {     groupsString += Groups[i] + ", "; }
 598                 groupsString += Groups[Groups.size()-1];
 599
 600                 m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
 601
 602                 return 0;
 603
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "RemoveGroupsCommand", "readShared");
 607                 exit(1);
 608         }
 609 }
 610 //**********************************************************************************************************************
 611 int RemoveGroupsCommand::readList(){
 612         try {
 613                 string thisOutputDir = outputDir;
 614                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 615                 map<string, string> variables;
 616         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 617         variables["[extension]"] = m->getExtension(listfile);
 618                 string outputFileName = getOutputFileName("list", variables);
 619
 620
 621                 ofstream out;
 622                 m->openOutputFile(outputFileName, out);
 623
 624                 ifstream in;
 625                 m->openInputFile(listfile, in);
 626
 627                 bool wroteSomething = false;
 628                 int removedCount = 0;
 629
 630                 while(!in.eof()){
 631
 632                         removedCount = 0;
 633
 634                         //read in list vector
 635                         ListVector list(in);
 636
 637                         //make a new list vector
 638                         ListVector newList;
 639                         newList.setLabel(list.getLabel());
 640
 641                         //for each bin
 642                         for (int i = 0; i < list.getNumBins(); i++) {
 643                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 644
 645                                 //parse out names that are in accnos file
 646                                 string binnames = list.get(i);
 647
 648                                 string newNames = "";
 649                                 while (binnames.find_first_of(',') != -1) {
 650                                         string name = binnames.substr(0,binnames.find_first_of(','));
 651                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 652
 653                                         //if that name is in the .accnos file, add it
 654                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 655                                         else {
 656                                                 //if you are not in the accnos file check if you are a name that needs to be changed
 657                                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
 658                                                 if (it != uniqueToRedundant.end()) {
 659                                                         newNames += it->second + ",";
 660                                                 }else { removedCount++; }
 661                                         }
 662                                 }
 663
 664                                 //get last name
 665                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 666                                 else { //if you are not in the accnos file check if you are a name that needs to be changed
 667                                         map<string, string>::iterator it = uniqueToRedundant.find(binnames);
 668                                         if (it != uniqueToRedundant.end()) {
 669                                                 newNames += it->second + ",";
 670                                         }else { removedCount++; }
 671                                 }
 672
 673                                 //if there are names in this bin add to new list
 674                                 if (newNames != "") {
 675                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 676                                         newList.push_back(newNames);
 677                                 }
 678                         }
 679
 680                         //print new listvector
 681                         if (newList.getNumBins() != 0) {
 682                                 wroteSomething = true;
 683                                 newList.print(out);
 684                         }
 685
 686                         m->gobble(in);
 687                 }
 688                 in.close();
 689                 out.close();
 690
 691                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 692                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 693
 694                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
 695
 696                 return 0;
 697
 698         }
 699         catch(exception& e) {
 700                 m->errorOut(e, "RemoveGroupsCommand", "readList");
 701                 exit(1);
 702         }
 703 }
 704 //**********************************************************************************************************************
 705 int RemoveGroupsCommand::readName(){
 706         try {
 707                 string thisOutputDir = outputDir;
 708                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 709                 map<string, string> variables;
 710                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 711         variables["[extension]"] = m->getExtension(namefile);
 712                 string outputFileName = getOutputFileName("name", variables);
 713                 ofstream out;
 714                 m->openOutputFile(outputFileName, out);
 715
 716                 ifstream in;
 717                 m->openInputFile(namefile, in);
 718                 string name, firstCol, secondCol;
 719
 720                 bool wroteSomething = false;
 721                 int removedCount = 0;
 722
 723                 while(!in.eof()){
 724                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 725
 726                         in >> firstCol;         m->gobble(in);
 727                         in >> secondCol;
 728
 729                         vector<string> parsedNames;
 730                         m->splitAtComma(secondCol, parsedNames);
 731
 732                         vector<string> validSecond;  validSecond.clear();
 733                         for (int i = 0; i < parsedNames.size(); i++) {
 734                                 if (names.count(parsedNames[i]) == 0) {
 735                                         validSecond.push_back(parsedNames[i]);
 736                                 }
 737                         }
 738
 739                         removedCount += parsedNames.size()-validSecond.size();
 740
 741                         //if the name in the first column is in the set then print it and any other names in second column also in set
 742                         if (names.count(firstCol) == 0) {
 743
 744                                 wroteSomething = true;
 745
 746                                 out << firstCol << '\t';
 747
 748                                 //you know you have at least one valid second since first column is valid
 749                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 750                                 out << validSecond[validSecond.size()-1] << endl;
 751
 752                                 //make first name in set you come to first column and then add the remaining names to second column
 753                         }else {
 754
 755                                 //you want part of this row
 756                                 if (validSecond.size() != 0) {
 757
 758                                         wroteSomething = true;
 759
 760                                         out << validSecond[0] << '\t';
 761
 762                                         //you know you have at least one valid second since first column is valid
 763                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 764                                         out << validSecond[validSecond.size()-1] << endl;
 765                                         uniqueToRedundant[firstCol] = validSecond[0];
 766                                 }
 767                         }
 768
 769                         m->gobble(in);
 770                 }
 771                 in.close();
 772                 out.close();
 773
 774                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 775                 outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
 776
 777                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
 778
 779                 return 0;
 780         }
 781         catch(exception& e) {
 782                 m->errorOut(e, "RemoveGroupsCommand", "readName");
 783                 exit(1);
 784         }
 785 }
 786
 787 //**********************************************************************************************************************
 788 int RemoveGroupsCommand::readGroup(){
 789         try {
 790                 string thisOutputDir = outputDir;
 791                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 792         map<string, string> variables;
 793                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 794         variables["[extension]"] = m->getExtension(groupfile);
 795                 string outputFileName = getOutputFileName("group", variables);
 796                 ofstream out;
 797                 m->openOutputFile(outputFileName, out);
 798
 799                 ifstream in;
 800                 m->openInputFile(groupfile, in);
 801                 string name, group;
 802
 803                 bool wroteSomething = false;
 804                 int removedCount = 0;
 805
 806                 while(!in.eof()){
 807                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 808
 809                         in >> name;                             //read from first column
 810                         in >> group;                    //read from second column
 811
 812                         //if this name is in the accnos file
 813                         if (names.count(name) == 0) {
 814                                 wroteSomething = true;
 815                                 out << name << '\t' << group << endl;
 816                         }else {  removedCount++;  }
 817
 818                         m->gobble(in);
 819                 }
 820                 in.close();
 821                 out.close();
 822
 823                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
 824                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 825
 826                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
 827
 828
 829                 return 0;
 830         }
 831         catch(exception& e) {
 832                 m->errorOut(e, "RemoveGroupsCommand", "readGroup");
 833                 exit(1);
 834         }
 835 }
 836 //**********************************************************************************************************************
 837 int RemoveGroupsCommand::readCount(){
 838         try {
 839                 string thisOutputDir = outputDir;
 840                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 841                 map<string, string> variables;
 842                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 843         variables["[extension]"] = m->getExtension(countfile);
 844                 string outputFileName = getOutputFileName("count", variables);
 845
 846                 ofstream out;
 847                 m->openOutputFile(outputFileName, out);
 848
 849                 ifstream in;
 850                 m->openInputFile(countfile, in);
 851
 852                 bool wroteSomething = false;
 853                 int removedCount = 0;
 854
 855         string headers = m->getline(in); m->gobble(in);
 856         vector<string> columnHeaders = m->splitWhiteSpace(headers);
 857
 858         vector<string> groups;
 859         map<int, string> originalGroupIndexes;
 860         map<string, int> GroupIndexes;
 861         set<int> indexOfGroupsChosen;
 862         for (int i = 2; i < columnHeaders.size(); i++) {  groups.push_back(columnHeaders[i]);  originalGroupIndexes[i-2] = columnHeaders[i]; }
 863         //sort groups to keep consistent with how we store the groups in groupmap
 864         sort(groups.begin(), groups.end());
 865         for (int i = 0; i < groups.size(); i++) {  GroupIndexes[groups[i]] = i; }
 866
 867                 vector<string> groupsToKeep;
 868                 for (int i = 0; i < groups.size(); i++) {
 869                         if (!m->inUsersGroups(groups[i], Groups)) { groupsToKeep.push_back(groups[i]); }
 870                 }
 871         sort(groupsToKeep.begin(), groupsToKeep.end());
 872         out << "Representative_Sequence\ttotal\t";
 873         for (int i = 0; i < groupsToKeep.size(); i++) { out << groupsToKeep[i] << '\t'; indexOfGroupsChosen.insert(GroupIndexes[groupsToKeep[i]]); }
 874         out << endl;
 875
 876         string name; int oldTotal;
 877         while (!in.eof()) {
 878
 879             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 880
 881             in >> name; m->gobble(in); in >> oldTotal; m->gobble(in);
 882             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(oldTotal) + "\n"); }
 883
 884             if (names.count(name) == 0) {
 885                 //if group info, then read it
 886                 vector<int> selectedCounts; int thisTotal = 0; int temp;
 887                 for (int i = 0; i < groups.size(); i++) {
 888                     int thisIndex = GroupIndexes[originalGroupIndexes[i]];
 889                     in >> temp;  m->gobble(in);
 890                     if (indexOfGroupsChosen.count(thisIndex) != 0) { //we want this group
 891                         selectedCounts.push_back(temp); thisTotal += temp;
 892                     }
 893                 }
 894
 895                 out << name << '\t' << thisTotal << '\t';
 896                 for (int i = 0; i < selectedCounts.size(); i++) {  out << selectedCounts[i] << '\t'; }
 897                 out << endl;
 898
 899                 wroteSomething = true;
 900                 removedCount+= (oldTotal - thisTotal);
 901             }else {  m->getline(in); removedCount += oldTotal; }
 902
 903             m->gobble(in);
 904         }
 905         in.close();
 906                 out.close();
 907
 908                 if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
 909                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 910
 911                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your count file."); m->mothurOutEndLine();
 912
 913                 return 0;
 914         }
 915         catch(exception& e) {
 916                 m->errorOut(e, "RemoveGroupsCommand", "readCount");
 917                 exit(1);
 918         }
 919 }
 920 //**********************************************************************************************************************
 921 int RemoveGroupsCommand::readDesign(){
 922         try {
 923                 string thisOutputDir = outputDir;
 924                 if (outputDir == "") {  thisOutputDir += m->hasPath(designfile);  }
 925         map<string, string> variables;
 926                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
 927         variables["[extension]"] = m->getExtension(designfile);
 928                 string outputFileName = getOutputFileName("design", variables);
 929
 930                 ofstream out;
 931                 m->openOutputFile(outputFileName, out);
 932
 933                 ifstream in;
 934                 m->openInputFile(designfile, in);
 935                 string name, group;
 936
 937                 bool wroteSomething = false;
 938                 int removedCount = 0;
 939
 940                 while(!in.eof()){
 941                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 942
 943                         in >> name;                             //read from first column
 944                         in >> group;                    //read from second column
 945
 946                         //if this name is in the accnos file
 947                         if (!(m->inUsersGroups(name, Groups))) {
 948                                 wroteSomething = true;
 949                                 out << name << '\t' << group << endl;
 950                         }else {  removedCount++;  }
 951
 952                         m->gobble(in);
 953                 }
 954                 in.close();
 955                 out.close();
 956
 957                 if (wroteSomething == false) {  m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine();  }
 958                 outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
 959
 960                 m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
 961
 962
 963                 return 0;
 964         }
 965         catch(exception& e) {
 966                 m->errorOut(e, "RemoveGroupsCommand", "readDesign");
 967                 exit(1);
 968         }
 969 }
 970
 971 //**********************************************************************************************************************
 972 int RemoveGroupsCommand::readTax(){
 973         try {
 974                 string thisOutputDir = outputDir;
 975                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 976                 map<string, string> variables;
 977                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
 978         variables["[extension]"] = m->getExtension(taxfile);
 979                 string outputFileName = getOutputFileName("taxonomy", variables);
 980                 ofstream out;
 981                 m->openOutputFile(outputFileName, out);
 982
 983                 ifstream in;
 984                 m->openInputFile(taxfile, in);
 985                 string name, tax;
 986
 987                 bool wroteSomething = false;
 988                 int removedCount = 0;
 989
 990                 while(!in.eof()){
 991                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 992
 993                         in >> name;                             //read from first column
 994                         in >> tax;                      //read from second column
 995
 996                         //if this name is in the accnos file
 997                         if (names.count(name) == 0) {
 998                                 wroteSomething = true;
 999                                 out << name << '\t' << tax << endl;
1000                         }else {  //if you are not in the accnos file check if you are a name that needs to be changed
1001                                 map<string, string>::iterator it = uniqueToRedundant.find(name);
1002                                 if (it != uniqueToRedundant.end()) {
1003                                         wroteSomething = true;
1004                                         out << it->second << '\t' << tax << endl;
1005                                 }else { removedCount++; }  }
1006
1007                         m->gobble(in);
1008                 }
1009                 in.close();
1010                 out.close();
1011
1012                 if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
1013                 outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
1014
1015                 m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
1016
1017                 return 0;
1018         }
1019         catch(exception& e) {
1020                 m->errorOut(e, "RemoveGroupsCommand", "readTax");
1021                 exit(1);
1022         }
1023 }
1024 //**********************************************************************************************************************
1025 int RemoveGroupsCommand::fillNames(){
1026         try {
1027                 vector<string> seqs = groupMap->getNamesSeqs();
1028
1029                 for (int i = 0; i < seqs.size(); i++) {
1030
1031                         if (m->control_pressed) { return 0; }
1032
1033                         string group = groupMap->getGroup(seqs[i]);
1034
1035                         if (m->inUsersGroups(group, Groups)) {
1036                                 names.insert(seqs[i]);
1037                         }
1038                 }
1039
1040                 return 0;
1041         }
1042         catch(exception& e) {
1043                 m->errorOut(e, "RemoveGroupsCommand", "fillNames");
1044                 exit(1);
1045         }
1046 }
1047
1048 //**********************************************************************************************************************
1049
1050
1051