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