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