splitabundcommand.cpp

   1 /*
   2  *  splitabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/17/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "splitabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SplitAbundCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "SplitAbundCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 SplitAbundCommand::SplitAbundCommand(){
  26         try {
  27                 //initialize outputTypes
  28                 vector<string> tempOutNames;
  29                 outputTypes["list"] = tempOutNames;
  30                 outputTypes["name"] = tempOutNames;
  31                 outputTypes["accnos"] = tempOutNames;
  32                 outputTypes["group"] = tempOutNames;
  33                 outputTypes["fasta"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> SplitAbundCommand::getRequiredParameters(){
  42         try {
  43                 string Array[] =  {"fasta","list","name","or"};
  44                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "SplitAbundCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 vector<string> SplitAbundCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "SplitAbundCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64 SplitAbundCommand::SplitAbundCommand(string option)  {
  65         try {
  66                 abort = false;
  67                 allLines = 1;
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["list"] = tempOutNames;
  91                         outputTypes["name"] = tempOutNames;
  92                         outputTypes["accnos"] = tempOutNames;
  93                         outputTypes["group"] = tempOutNames;
  94                         outputTypes["fasta"] = tempOutNames;
  95
  96                         //if the user changes the input directory command factory will send this info to us in the output parameter
  97                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  98                         if (inputDir == "not found"){   inputDir = "";          }
  99                         else {
 100                                 string path;
 101                                 it = parameters.find("list");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 107                                 }
 108
 109                                 it = parameters.find("group");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 115                                 }
 116
 117                                 it = parameters.find("fasta");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 123                                 }
 124
 125                                 it = parameters.find("name");
 126                                 //user has given a template file
 127                                 if(it != parameters.end()){
 128                                         path = m->hasPath(it->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 131                                 }
 132
 133                         }
 134
 135
 136                         //if the user changes the output directory command factory will send this info to us in the output parameter
 137                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 138
 139                         //check for required parameters
 140                         listfile = validParameter.validFile(parameters, "list", true);
 141                         if (listfile == "not open") { abort = true; }
 142                         else if (listfile == "not found") { listfile = ""; }
 143                         else{ inputFile = listfile; }
 144
 145                         namefile = validParameter.validFile(parameters, "name", true);
 146                         if (namefile == "not open") { abort = true; }
 147                         else if (namefile == "not found") { namefile = ""; }
 148                         else{ inputFile = namefile; }
 149
 150                         fastafile = validParameter.validFile(parameters, "fasta", true);
 151                         if (fastafile == "not open") { abort = true; }
 152                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 153
 154                         groupfile = validParameter.validFile(parameters, "group", true);
 155                         if (groupfile == "not open") {  groupfile = ""; abort = true; }
 156                         else if (groupfile == "not found") { groupfile = ""; }
 157                         else {
 158                                 groupMap = new GroupMap(groupfile);
 159
 160                                 int error = groupMap->readMap();
 161                                 if (error == 1) { abort = true; }
 162
 163                         }
 164
 165                         groups = validParameter.validFile(parameters, "groups", false);
 166                         if (groups == "not found") { groups = ""; }
 167                         else if (groups == "all") {
 168                                 if (groupfile != "") {  Groups = groupMap->namesOfGroups;  }
 169                                 else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
 170                         }else {
 171                                 m->splitAtDash(groups, Groups);
 172                         }
 173
 174                         if ((groupfile == "") && (groups != "")) {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";  Groups.clear(); }
 175
 176                         //do you have all files needed
 177                         if ((listfile == "") && (namefile == "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 178
 179                         //check for optional parameter and set defaults
 180                         // ...at some point should added some additional type checking...
 181                         label = validParameter.validFile(parameters, "label", false);
 182                         if (label == "not found") { label = "";  allLines = 1; }
 183                         else {
 184                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 185                                 else { allLines = 1;  }
 186                         }
 187
 188                         string temp = validParameter.validFile(parameters, "accnos", false);            if (temp == "not found") { temp = "F"; }
 189                         accnos = m->isTrue(temp);
 190
 191                         temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
 192                         convert(temp, cutoff);
 193
 194                         if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 195
 196                 }
 197
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
 201                 exit(1);
 202         }
 203 }
 204 //**********************************************************************************************************************
 205 void SplitAbundCommand::help(){
 206         try {
 207                 m->mothurOut("The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n");
 208                 m->mothurOut("The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n");
 209                 m->mothurOut("The fasta and a list or name parameter are required, and you must provide a cutoff value.\n");
 210                 m->mothurOut("The cutoff parameter is used to qualify what is abundant and rare.\n");
 211                 m->mothurOut("The group parameter allows you to parse a group file into rare and abundant groups.\n");
 212                 m->mothurOut("The label parameter is used to read specific labels in your listfile you want to use.\n");
 213                 m->mothurOut("The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.\n");
 214                 m->mothurOut("The groups parameter allows you to parse the files into rare and abundant files by group.  \n");
 215                 m->mothurOut("For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files.  \n");
 216                 m->mothurOut("If you want .abund and .rare files for all groups, set groups=all.  \n");
 217                 m->mothurOut("The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
 218                 m->mothurOut("Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
 219                 m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "SplitAbundCommand", "help");
 224                 exit(1);
 225         }
 226 }
 227 //**********************************************************************************************************************
 228 SplitAbundCommand::~SplitAbundCommand(){
 229         if (groupfile != "") {  delete groupMap;  }
 230 }
 231 //**********************************************************************************************************************
 232 int SplitAbundCommand::execute(){
 233         try {
 234
 235                 if (abort == true) {    return 0;       }
 236
 237                 if (listfile != "") { //you are using a listfile to determine abundance
 238                         if (outputDir == "") { outputDir = m->hasPath(listfile); }
 239
 240                         //remove old files so you can append later....
 241                         string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
 242                         if (Groups.size() == 0) {
 243                                 remove((fileroot + "rare.list").c_str());
 244                                 remove((fileroot + "abund.list").c_str());
 245
 246                                 outputNames.push_back((fileroot + "rare.list"));
 247                                 outputNames.push_back((fileroot + "abund.list"));
 248                                 outputTypes["list"].push_back((fileroot + "rare.list"));
 249                                 outputTypes["list"].push_back((fileroot + "abund.list"));
 250                         }else{
 251                                 for (int i=0; i<Groups.size(); i++) {
 252                                         remove((fileroot + Groups[i] + ".rare.list").c_str());
 253                                         remove((fileroot + Groups[i] + ".abund.list").c_str());
 254
 255                                         outputNames.push_back((fileroot + Groups[i] + ".rare.list"));
 256                                         outputNames.push_back((fileroot + Groups[i] + ".abund.list"));
 257                                         outputTypes["list"].push_back((fileroot + Groups[i] + ".rare.list"));
 258                                         outputTypes["list"].push_back((fileroot + Groups[i] + ".abund.list"));
 259                                 }
 260                         }
 261
 262                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 263                         set<string> processedLabels;
 264                         set<string> userLabels = labels;
 265
 266                         input = new InputData(listfile, "list");
 267                         list = input->getListVector();
 268                         string lastLabel = list->getLabel();
 269
 270                         //do you have a namefile or do we need to similate one?
 271                         if (namefile != "") {  readNamesFile();         }
 272                         else                            { createNameMap(list);  }
 273
 274                         if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
 275
 276                         while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 277
 278                                 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
 279
 280                                 if(allLines == 1 || labels.count(list->getLabel()) == 1){
 281
 282                                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 283                                                 splitList(list);
 284
 285                                                 processedLabels.insert(list->getLabel());
 286                                                 userLabels.erase(list->getLabel());
 287                                 }
 288
 289                                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 290                                                 string saveLabel = list->getLabel();
 291
 292                                                 delete list;
 293                                                 list = input->getListVector(lastLabel); //get new list vector to process
 294
 295                                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 296                                                 splitList(list);
 297
 298                                                 processedLabels.insert(list->getLabel());
 299                                                 userLabels.erase(list->getLabel());
 300
 301                                                 //restore real lastlabel to save below
 302                                                 list->setLabel(saveLabel);
 303                                 }
 304
 305
 306                                 lastLabel = list->getLabel();
 307
 308                                 delete list;
 309                                 list = input->getListVector(); //get new list vector to process
 310                         }
 311
 312                         if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 313
 314                         //output error messages about any remaining user labels
 315                         set<string>::iterator it;
 316                         bool needToRun = false;
 317                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 318                                 m->mothurOut("Your file does not include the label " + *it);
 319                                 if (processedLabels.count(lastLabel) != 1) {
 320                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 321                                         needToRun = true;
 322                                 }else {
 323                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 324                                 }
 325
 326                         }
 327
 328                         if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 329
 330                         //run last label if you need to
 331                         if (needToRun == true)  {
 332                                 if (list != NULL) {     delete list;    }
 333                                 list = input->getListVector(lastLabel); //get new list vector to process
 334
 335                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 336                                 splitList(list);
 337
 338                                 delete list;
 339                         }
 340
 341                         delete input;
 342
 343                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); }       return 0;       }
 344
 345                 }else { //you are using the namefile to determine abundance
 346                         if (outputDir == "") { outputDir = m->hasPath(namefile); }
 347
 348                         splitNames();
 349                         writeNames();
 350
 351                         string tag = "";
 352                         if (groupfile != "")                            {  parseGroup(tag);             }
 353                         if (accnos)                                                     {  writeAccnos(tag);    }
 354                         if (fastafile != "")                            {  parseFasta(tag);             }
 355                 }
 356
 357                 m->mothurOutEndLine();
 358                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 359                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 360                 m->mothurOutEndLine();
 361
 362                 return 0;
 363         }
 364         catch(exception& e) {
 365                 m->errorOut(e, "SplitAbundCommand", "execute");
 366                 exit(1);
 367         }
 368 }
 369 /**********************************************************************************************************************/
 370 int SplitAbundCommand::splitList(ListVector* thisList) {
 371         try {
 372                 rareNames.clear();
 373                 abundNames.clear();
 374
 375                 //get rareNames and abundNames
 376                 for (int i = 0; i < thisList->getNumBins(); i++) {
 377                         if (m->control_pressed) { return 0; }
 378
 379                         string bin = thisList->get(i);
 380
 381                         vector<string> names;
 382                         m->splitAtComma(bin, names);  //parses bin into individual sequence names
 383                         int size = names.size();
 384
 385                         if (size <= cutoff) {
 386                                 for (int j = 0; j < names.size(); j++) {  rareNames.insert(names[j]);  }
 387                         }else{
 388                                 for (int j = 0; j < names.size(); j++) {  abundNames.insert(names[j]);  }
 389                         }
 390                 }//end for
 391
 392                 writeList(thisList);
 393
 394                 string tag = thisList->getLabel() + ".";
 395                 if (groupfile != "")                            {  parseGroup(tag);             }
 396                 if (accnos)                                                     {  writeAccnos(tag);    }
 397                 if (fastafile != "")                            {  parseFasta(tag);             }
 398
 399                 return 0;
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "SplitAbundCommand", "splitList");
 404                 exit(1);
 405         }
 406 }
 407 /**********************************************************************************************************************/
 408 int SplitAbundCommand::writeList(ListVector* thisList) {
 409         try {
 410
 411                 map<string, ofstream*> filehandles;
 412
 413                 if (Groups.size() == 0) {
 414                         SAbundVector* sabund = new SAbundVector();
 415                         *sabund = thisList->getSAbundVector();
 416
 417                         //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
 418                         // and don't have to store the bins until you are done with the whole vector, this save alot of space.
 419                         int numRareBins = 0;
 420                         for (int i = 0; i <= sabund->getMaxRank(); i++) {
 421                                 if (i > cutoff) { break; }
 422                                 numRareBins += sabund->get(i);
 423                         }
 424                         int numAbundBins = thisList->getNumBins() - numRareBins;
 425                         delete sabund;
 426
 427                         ofstream aout;
 428                         ofstream rout;
 429
 430                         string rare = outputDir + m->getRootName(m->getSimpleName(listfile))  + "rare.list";
 431                         m->openOutputFileAppend(rare, rout);
 432                         //outputNames.push_back(rare);
 433
 434                         string abund = outputDir + m->getRootName(m->getSimpleName(listfile))  + "abund.list";
 435                         m->openOutputFileAppend(abund, aout);
 436                         //outputNames.push_back(abund);
 437
 438                         if (rareNames.size() != 0)      {  rout << thisList->getLabel() << '\t' << numRareBins << '\t';         }
 439                         if (abundNames.size() != 0) {   aout << thisList->getLabel() << '\t' << numAbundBins << '\t';   }
 440
 441                         for (int i = 0; i < thisList->getNumBins(); i++) {
 442                                 if (m->control_pressed) { break; }
 443
 444                                 string bin = list->get(i);
 445
 446                                 int size = m->getNumNames(bin);
 447
 448                                 if (size <= cutoff) {  rout << bin << '\t';  }
 449                                 else                            {  aout << bin << '\t'; }
 450                         }
 451
 452                         if (rareNames.size() != 0)      { rout << endl; }
 453                         if (abundNames.size() != 0) { aout << endl; }
 454
 455                         rout.close();
 456                         aout.close();
 457
 458                 }else{ //parse names by abundance and group
 459                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(listfile));
 460                         ofstream* temp;
 461                         ofstream* temp2;
 462                         //map<string, bool> wroteFile;
 463                         map<string, ofstream*> filehandles;
 464                         map<string, ofstream*>::iterator it3;
 465
 466                         for (int i=0; i<Groups.size(); i++) {
 467                                 temp = new ofstream;
 468                                 filehandles[Groups[i]+".rare"] = temp;
 469                                 temp2 = new ofstream;
 470                                 filehandles[Groups[i]+".abund"] = temp2;
 471
 472                                 m->openOutputFileAppend(fileroot + Groups[i] + ".rare.list", *(filehandles[Groups[i]+".rare"]));
 473                                 m->openOutputFileAppend(fileroot + Groups[i] + ".abund.list", *(filehandles[Groups[i]+".abund"]));
 474                         }
 475
 476                         map<string, string> groupVector;
 477                         map<string, string>::iterator itGroup;
 478                         map<string, int> groupNumBins;
 479
 480                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 481                                 groupNumBins[it3->first] = 0;
 482                                 groupVector[it3->first] = "";
 483                         }
 484
 485                         for (int i = 0; i < thisList->getNumBins(); i++) {
 486                                 if (m->control_pressed) { break; }
 487
 488                                 map<string, string> groupBins;
 489                                 string bin = list->get(i);
 490
 491                                 vector<string> names;
 492                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 493
 494                                 //parse bin into list of sequences in each group
 495                                 for (int j = 0; j < names.size(); j++) {
 496                                         string rareAbund;
 497                                         if (rareNames.count(names[j]) != 0) { //you are a rare name
 498                                                 rareAbund = ".rare";
 499                                         }else{ //you are a abund name
 500                                                 rareAbund = ".abund";
 501                                         }
 502
 503                                         string group = groupMap->getGroup(names[j]);
 504
 505                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 506                                                 itGroup = groupBins.find(group+rareAbund);
 507                                                 if(itGroup == groupBins.end()) {
 508                                                         groupBins[group+rareAbund] = names[j];  //add first name
 509                                                         groupNumBins[group+rareAbund]++;
 510                                                 }else{ //add another name
 511                                                         groupBins[group+rareAbund] +=  "," + names[j];
 512                                                 }
 513                                         }else if(group == "not found") {
 514                                                 m->mothurOut(names[j] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 515                                         }
 516                                 }
 517
 518
 519                                 for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
 520                                         groupVector[itGroup->first] +=  itGroup->second + '\t';
 521                                 }
 522                         }
 523
 524                         //end list vector
 525                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 526                                 (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl;  // label numBins  listvector for that group
 527                                 (*(filehandles[it3->first])).close();
 528                                 delete it3->second;
 529                         }
 530                 }
 531
 532                 return 0;
 533
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "SplitAbundCommand", "writeList");
 537                 exit(1);
 538         }
 539 }
 540 /**********************************************************************************************************************/
 541 int SplitAbundCommand::splitNames() { //namefile
 542         try {
 543
 544                 rareNames.clear();
 545                 abundNames.clear();
 546
 547                 //open input file
 548                 ifstream in;
 549                 m->openInputFile(namefile, in);
 550
 551                 while (!in.eof()) {
 552                         if (m->control_pressed) { break; }
 553
 554                         string firstCol, secondCol;
 555                         in >> firstCol >> secondCol; m->gobble(in);
 556
 557                         nameMap[firstCol] = secondCol;
 558
 559                         int size = m->getNumNames(secondCol);
 560
 561                         if (size <= cutoff) {
 562                                 rareNames.insert(firstCol);
 563                         }else{
 564                                 abundNames.insert(firstCol);
 565                         }
 566                 }
 567                 in.close();
 568
 569                 return 0;
 570
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "SplitAbundCommand", "splitNames");
 574                 exit(1);
 575         }
 576 }
 577 /**********************************************************************************************************************/
 578 int SplitAbundCommand::readNamesFile() {
 579         try {
 580                 //open input file
 581                 ifstream in;
 582                 m->openInputFile(namefile, in);
 583
 584                 while (!in.eof()) {
 585                         if (m->control_pressed) { break; }
 586
 587                         string firstCol, secondCol;
 588                         in >> firstCol >> secondCol; m->gobble(in);
 589
 590                         nameMap[firstCol] = secondCol;
 591                 }
 592                 in.close();
 593
 594                 return 0;
 595
 596         }
 597         catch(exception& e) {
 598                 m->errorOut(e, "SplitAbundCommand", "readNamesFile");
 599                 exit(1);
 600         }
 601 }
 602 /**********************************************************************************************************************/
 603 int SplitAbundCommand::createNameMap(ListVector* thisList) {
 604         try {
 605
 606                 if (thisList != NULL) {
 607                         for (int i = 0; i < thisList->getNumBins(); i++) {
 608                                 if (m->control_pressed) { return 0; }
 609
 610                                 string bin = thisList->get(i);
 611
 612                                 vector<string> names;
 613                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 614
 615                                 for (int j = 0; j < names.size(); j++) {  nameMap[names[j]] = names[j];  }
 616                         }//end for
 617                 }
 618
 619                 return 0;
 620         }
 621         catch(exception& e) {
 622                 m->errorOut(e, "SplitAbundCommand", "createNameMap");
 623                 exit(1);
 624         }
 625 }
 626 /**********************************************************************************************************************/
 627 int SplitAbundCommand::writeNames() { //namefile
 628         try {
 629
 630                 map<string, ofstream*> filehandles;
 631
 632                 if (Groups.size() == 0) {
 633                         ofstream aout;
 634                         ofstream rout;
 635
 636                         string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare.names";
 637                         m->openOutputFile(rare, rout);
 638                         outputNames.push_back(rare); outputTypes["name"].push_back(rare);
 639
 640                         string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund.names";
 641                         m->openOutputFile(abund, aout);
 642                         outputNames.push_back(abund); outputTypes["name"].push_back(abund);
 643
 644                         if (rareNames.size() != 0) {
 645                                 for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 646                                         rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
 647                                 }
 648                         }
 649                         rout.close();
 650
 651                         if (abundNames.size() != 0) {
 652                                 for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 653                                         aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
 654                                 }
 655                         }
 656                         aout.close();
 657
 658                 }else{ //parse names by abundance and group
 659                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(namefile));
 660                         ofstream* temp;
 661                         ofstream* temp2;
 662                         map<string, ofstream*> filehandles;
 663                         map<string, ofstream*>::iterator it3;
 664
 665                         for (int i=0; i<Groups.size(); i++) {
 666                                 temp = new ofstream;
 667                                 filehandles[Groups[i]+".rare"] = temp;
 668                                 temp2 = new ofstream;
 669                                 filehandles[Groups[i]+".abund"] = temp2;
 670
 671                                 m->openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"]));
 672                                 m->openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"]));
 673                         }
 674
 675                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 676                                 vector<string> names;
 677                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 678
 679                                 string rareAbund;
 680                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 681                                                 rareAbund = ".rare";
 682                                 }else{ //you are a abund name
 683                                                 rareAbund = ".abund";
 684                                 }
 685
 686                                 map<string, string> outputStrings;
 687                                 map<string, string>::iterator itout;
 688                                 for (int i = 0; i < names.size(); i++) {
 689
 690                                         string group = groupMap->getGroup(names[i]);
 691
 692                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 693                                                 itout = outputStrings.find(group+rareAbund);
 694                                                 if (itout == outputStrings.end()) {
 695                                                         outputStrings[group+rareAbund] = names[i] + '\t' + names[i];
 696                                                 }else {   outputStrings[group+rareAbund] += "," + names[i]; }
 697                                         }else if(group == "not found") {
 698                                                 m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 699                                         }
 700                                 }
 701
 702                                 for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) { *(filehandles[itout->first]) << itout->second << endl;     }
 703                         }
 704
 705
 706                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 707                                 (*(filehandles[it3->first])).close();
 708                                 outputNames.push_back(fileroot + it3->first + ".names");  outputTypes["name"].push_back(fileroot + it3->first + ".names");
 709                                 delete it3->second;
 710                         }
 711                 }
 712
 713                 return 0;
 714
 715         }
 716         catch(exception& e) {
 717                 m->errorOut(e, "SplitAbundCommand", "writeNames");
 718                 exit(1);
 719         }
 720 }
 721 /**********************************************************************************************************************/
 722 //just write the unique names - if a namesfile is given
 723 int SplitAbundCommand::writeAccnos(string tag) {
 724         try {
 725
 726                 map<string, ofstream*> filehandles;
 727
 728                 if (Groups.size() == 0) {
 729                         ofstream aout;
 730                         ofstream rout;
 731
 732
 733                         string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare.accnos";
 734                         m->openOutputFile(rare, rout);
 735                         outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
 736
 737                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 738                                 rout << (*itRare) << endl;
 739                         }
 740                         rout.close();
 741
 742                         string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund.accnos";
 743                         m->openOutputFile(abund, aout);
 744                         outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
 745
 746                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 747                                 aout << (*itAbund) << endl;
 748                         }
 749                         aout.close();
 750
 751                 }else{ //parse names by abundance and group
 752                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(inputFile));
 753                         ofstream* temp;
 754                         ofstream* temp2;
 755                         map<string, ofstream*> filehandles;
 756                         map<string, ofstream*>::iterator it3;
 757
 758                         for (int i=0; i<Groups.size(); i++) {
 759                                 temp = new ofstream;
 760                                 filehandles[Groups[i]+".rare"] = temp;
 761                                 temp2 = new ofstream;
 762                                 filehandles[Groups[i]+".abund"] = temp2;
 763
 764                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"]));
 765                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"]));
 766                         }
 767
 768                         //write rare
 769                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 770                                         string group = groupMap->getGroup(*itRare);
 771
 772                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 773                                                 *(filehandles[group+".rare"]) << *itRare << endl;
 774                                         }
 775                         }
 776
 777                         //write abund
 778                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 779                                         string group = groupMap->getGroup(*itAbund);
 780
 781                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 782                                                 *(filehandles[group+".abund"]) << *itAbund << endl;
 783                                         }
 784                         }
 785
 786                         //close files
 787                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 788                                 (*(filehandles[it3->first])).close();
 789                                 outputNames.push_back(fileroot + tag + it3->first + ".accnos");  outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos");
 790                                 delete it3->second;
 791                         }
 792                 }
 793
 794                 return 0;
 795
 796         }
 797         catch(exception& e) {
 798                 m->errorOut(e, "SplitAbundCommand", "writeAccnos");
 799                 exit(1);
 800         }
 801 }
 802 /**********************************************************************************************************************/
 803 int SplitAbundCommand::parseGroup(string tag) { //namefile
 804         try {
 805
 806                 map<string, ofstream*> filehandles;
 807
 808                 if (Groups.size() == 0) {
 809                         ofstream aout;
 810                         ofstream rout;
 811
 812                         string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare.groups";
 813                         m->openOutputFile(rare, rout);
 814                         outputNames.push_back(rare); outputTypes["group"].push_back(rare);
 815
 816                         string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund.groups";
 817                         m->openOutputFile(abund, aout);
 818                         outputNames.push_back(abund); outputTypes["group"].push_back(abund);
 819
 820                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 821                                 vector<string> names;
 822                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 823
 824                                 for (int i = 0; i < names.size(); i++) {
 825
 826                                         string group = groupMap->getGroup(names[i]);
 827
 828                                         if (group == "not found") {
 829                                                 m->mothurOut(names[i] + " is not in your groupfile, ignoring, please correct."); m->mothurOutEndLine();
 830                                         }else {
 831                                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 832                                                         rout << names[i] << '\t' << group << endl;
 833                                                 }else{ //you are a abund name
 834                                                         aout << names[i] << '\t' << group << endl;
 835                                                 }
 836                                         }
 837                                 }
 838                         }
 839
 840                         rout.close();
 841                         aout.close();
 842
 843                 }else{ //parse names by abundance and group
 844                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(groupfile));
 845                         ofstream* temp;
 846                         ofstream* temp2;
 847                         map<string, ofstream*> filehandles;
 848                         map<string, ofstream*>::iterator it3;
 849
 850                         for (int i=0; i<Groups.size(); i++) {
 851                                 temp = new ofstream;
 852                                 filehandles[Groups[i]+".rare"] = temp;
 853                                 temp2 = new ofstream;
 854                                 filehandles[Groups[i]+".abund"] = temp2;
 855
 856                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"]));
 857                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"]));
 858                         }
 859
 860                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 861                                 vector<string> names;
 862                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 863
 864                                 string rareAbund;
 865                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 866                                         rareAbund = ".rare";
 867                                 }else{ //you are a abund name
 868                                         rareAbund = ".abund";
 869                                 }
 870
 871                                 for (int i = 0; i < names.size(); i++) {
 872
 873                                         string group = groupMap->getGroup(names[i]);
 874
 875                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 876                                                 *(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
 877                                         }
 878                                 }
 879                         }
 880
 881                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 882                                 (*(filehandles[it3->first])).close();
 883                                 outputNames.push_back(fileroot + tag + it3->first + ".groups");  outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups");
 884                                 delete it3->second;
 885                         }
 886                 }
 887
 888                 return 0;
 889
 890         }
 891         catch(exception& e) {
 892                 m->errorOut(e, "SplitAbundCommand", "parseGroups");
 893                 exit(1);
 894         }
 895 }
 896 /**********************************************************************************************************************/
 897 int SplitAbundCommand::parseFasta(string tag) { //namefile
 898         try {
 899
 900                 map<string, ofstream*> filehandles;
 901
 902                 if (Groups.size() == 0) {
 903                         ofstream aout;
 904                         ofstream rout;
 905
 906                         string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare.fasta";
 907                         m->openOutputFile(rare, rout);
 908                         outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
 909
 910                         string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund.fasta";
 911                         m->openOutputFile(abund, aout);
 912                         outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
 913
 914                         //open input file
 915                         ifstream in;
 916                         m->openInputFile(fastafile, in);
 917
 918                         while (!in.eof()) {
 919                                 if (m->control_pressed) { break; }
 920
 921                                 Sequence seq(in); m->gobble(in);
 922
 923                                 if (seq.getName() != "") {
 924
 925                                         map<string, string>::iterator itNames;
 926
 927                                         itNames = nameMap.find(seq.getName());
 928
 929                                         if (itNames == nameMap.end()) {
 930                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
 931                                         }else{
 932                                                 if (rareNames.count(seq.getName()) != 0) { //you are a rare name
 933                                                         seq.printSequence(rout);
 934                                                 }else{ //you are a abund name
 935                                                         seq.printSequence(aout);
 936                                                 }
 937                                         }
 938                                 }
 939                         }
 940                         in.close();
 941                         rout.close();
 942                         aout.close();
 943
 944                 }else{ //parse names by abundance and group
 945                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(fastafile));
 946                         ofstream* temp;
 947                         ofstream* temp2;
 948                         map<string, ofstream*> filehandles;
 949                         map<string, ofstream*>::iterator it3;
 950
 951                         for (int i=0; i<Groups.size(); i++) {
 952                                 temp = new ofstream;
 953                                 filehandles[Groups[i]+".rare"] = temp;
 954                                 temp2 = new ofstream;
 955                                 filehandles[Groups[i]+".abund"] = temp2;
 956
 957                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"]));
 958                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"]));
 959                         }
 960
 961                         //open input file
 962                         ifstream in;
 963                         m->openInputFile(fastafile, in);
 964
 965                         while (!in.eof()) {
 966                                 if (m->control_pressed) { break; }
 967
 968                                 Sequence seq(in); m->gobble(in);
 969
 970                                 if (seq.getName() != "") {
 971                                         map<string, string>::iterator itNames = nameMap.find(seq.getName());
 972
 973                                         if (itNames == nameMap.end()) {
 974                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
 975                                         }else{
 976                                                 vector<string> names;
 977                                                 m->splitAtComma(itNames->second, names);  //parses bin into individual sequence names
 978
 979                                                 string rareAbund;
 980                                                 if (rareNames.count(itNames->first) != 0) { //you are a rare name
 981                                                         rareAbund = ".rare";
 982                                                 }else{ //you are a abund name
 983                                                         rareAbund = ".abund";
 984                                                 }
 985
 986                                                 for (int i = 0; i < names.size(); i++) {
 987
 988                                                         string group = groupMap->getGroup(seq.getName());
 989
 990                                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 991                                                                 seq.printSequence(*(filehandles[group+rareAbund]));
 992                                                         }else if(group == "not found") {
 993                                                                 m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 994                                                         }
 995                                                 }
 996                                         }
 997                                 }
 998                         }
 999                         in.close();
1000
1001                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
1002                                 (*(filehandles[it3->first])).close();
1003                                 outputNames.push_back(fileroot + tag + it3->first + ".fasta");  outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta");
1004                                 delete it3->second;
1005                         }
1006                 }
1007
1008                 return 0;
1009
1010         }
1011         catch(exception& e) {
1012                 m->errorOut(e, "SplitAbundCommand", "parseFasta");
1013                 exit(1);
1014         }
1015 }
1016 /**********************************************************************************************************************/
1017