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::setParameters(){
  14         try {
  15                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
  17                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  18                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  19                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  20                 CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
  21                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  22                 CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(paccnos);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SplitAbundCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string SplitAbundCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n";
  40                 helpString += "The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n";
  41                 helpString += "The fasta and a list or name parameter are required, and you must provide a cutoff value.\n";
  42                 helpString += "The cutoff parameter is used to qualify what is abundant and rare.\n";
  43                 helpString += "The group parameter allows you to parse a group file into rare and abundant groups.\n";
  44                 helpString += "The label parameter is used to read specific labels in your listfile you want to use.\n";
  45                 helpString += "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";
  46                 helpString += "The groups parameter allows you to parse the files into rare and abundant files by group.  \n";
  47                 helpString += "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";
  48                 helpString += "If you want .abund and .rare files for all groups, set groups=all.  \n";
  49                 helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
  50                 helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "SplitAbundCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59
  60 //**********************************************************************************************************************
  61 SplitAbundCommand::SplitAbundCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["list"] = tempOutNames;
  67                 outputTypes["name"] = tempOutNames;
  68                 outputTypes["accnos"] = tempOutNames;
  69                 outputTypes["group"] = tempOutNames;
  70                 outputTypes["fasta"] = tempOutNames;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78 SplitAbundCommand::SplitAbundCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81                 allLines = 1;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85
  86                 else {
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string, string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string, string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["list"] = tempOutNames;
 103                         outputTypes["name"] = tempOutNames;
 104                         outputTypes["accnos"] = tempOutNames;
 105                         outputTypes["group"] = tempOutNames;
 106                         outputTypes["fasta"] = tempOutNames;
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("list");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 119                                 }
 120
 121                                 it = parameters.find("group");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 127                                 }
 128
 129                                 it = parameters.find("fasta");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 135                                 }
 136
 137                                 it = parameters.find("name");
 138                                 //user has given a template file
 139                                 if(it != parameters.end()){
 140                                         path = m->hasPath(it->second);
 141                                         //if the user has not given a path then, add inputdir. else leave path alone.
 142                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 143                                 }
 144
 145                         }
 146
 147
 148                         //if the user changes the output directory command factory will send this info to us in the output parameter
 149                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 150
 151                         //check for required parameters
 152                         listfile = validParameter.validFile(parameters, "list", true);
 153                         if (listfile == "not open") { abort = true; }
 154                         else if (listfile == "not found") { listfile = ""; }
 155                         else{ inputFile = listfile; }
 156
 157                         namefile = validParameter.validFile(parameters, "name", true);
 158                         if (namefile == "not open") { abort = true; }
 159                         else if (namefile == "not found") { namefile = ""; }
 160                         else{ inputFile = namefile; }
 161
 162                         fastafile = validParameter.validFile(parameters, "fasta", true);
 163                         if (fastafile == "not open") { abort = true; }
 164                         else if (fastafile == "not found") {
 165                                 fastafile = m->getFastaFile();
 166                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 167                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 168                         }
 169
 170                         groupfile = validParameter.validFile(parameters, "group", true);
 171                         if (groupfile == "not open") {  groupfile = ""; abort = true; }
 172                         else if (groupfile == "not found") { groupfile = ""; }
 173                         else {
 174                                 groupMap = new GroupMap(groupfile);
 175
 176                                 int error = groupMap->readMap();
 177                                 if (error == 1) { abort = true; }
 178
 179                         }
 180
 181                         groups = validParameter.validFile(parameters, "groups", false);
 182                         if (groups == "not found") { groups = ""; }
 183                         else if (groups == "all") {
 184                                 if (groupfile != "") {  Groups = groupMap->namesOfGroups;  }
 185                                 else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
 186                         }else {
 187                                 m->splitAtDash(groups, Groups);
 188                         }
 189
 190                         if ((groupfile == "") && (groups != "")) {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";  Groups.clear(); }
 191
 192                         //do you have all files needed
 193                         if ((listfile == "") && (namefile == "")) {
 194                                 namefile = m->getNameFile();
 195                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 196                                 else {
 197                                         listfile = m->getListFile();
 198                                         if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 199                                         else {  m->mothurOut("You have no current list or namefile and the list or name parameter is required."); m->mothurOutEndLine(); abort = true; }
 200                                 }
 201                         }
 202
 203                         //check for optional parameter and set defaults
 204                         // ...at some point should added some additional type checking...
 205                         label = validParameter.validFile(parameters, "label", false);
 206                         if (label == "not found") { label = "";  allLines = 1; }
 207                         else {
 208                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 209                                 else { allLines = 1;  }
 210                         }
 211
 212                         string temp = validParameter.validFile(parameters, "accnos", false);            if (temp == "not found") { temp = "F"; }
 213                         accnos = m->isTrue(temp);
 214
 215                         temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
 216                         convert(temp, cutoff);
 217
 218                         if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 219
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
 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) { if (calledHelp) { return 0; }  return 2;   }
 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                 //set fasta file as new current fastafile
 337                 string current = "";
 338                 itTypes = outputTypes.find("fasta");
 339                 if (itTypes != outputTypes.end()) {
 340                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 341                 }
 342
 343                 itTypes = outputTypes.find("name");
 344                 if (itTypes != outputTypes.end()) {
 345                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 346                 }
 347
 348                 itTypes = outputTypes.find("group");
 349                 if (itTypes != outputTypes.end()) {
 350                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 351                 }
 352
 353                 itTypes = outputTypes.find("list");
 354                 if (itTypes != outputTypes.end()) {
 355                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 356                 }
 357
 358                 itTypes = outputTypes.find("accnos");
 359                 if (itTypes != outputTypes.end()) {
 360                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 361                 }
 362
 363                 m->mothurOutEndLine();
 364                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 365                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 366                 m->mothurOutEndLine();
 367
 368                 return 0;
 369         }
 370         catch(exception& e) {
 371                 m->errorOut(e, "SplitAbundCommand", "execute");
 372                 exit(1);
 373         }
 374 }
 375 /**********************************************************************************************************************/
 376 int SplitAbundCommand::splitList(ListVector* thisList) {
 377         try {
 378                 rareNames.clear();
 379                 abundNames.clear();
 380
 381                 //get rareNames and abundNames
 382                 for (int i = 0; i < thisList->getNumBins(); i++) {
 383                         if (m->control_pressed) { return 0; }
 384
 385                         string bin = thisList->get(i);
 386
 387                         vector<string> names;
 388                         m->splitAtComma(bin, names);  //parses bin into individual sequence names
 389                         int size = names.size();
 390
 391                         if (size <= cutoff) {
 392                                 for (int j = 0; j < names.size(); j++) {  rareNames.insert(names[j]);  }
 393                         }else{
 394                                 for (int j = 0; j < names.size(); j++) {  abundNames.insert(names[j]);  }
 395                         }
 396                 }//end for
 397
 398
 399                 string tag = thisList->getLabel() + ".";
 400
 401                 writeList(thisList, tag);
 402
 403                 if (groupfile != "")                            {  parseGroup(tag);             }
 404                 if (accnos)                                                     {  writeAccnos(tag);    }
 405                 if (fastafile != "")                            {  parseFasta(tag);             }
 406
 407                 return 0;
 408
 409         }
 410         catch(exception& e) {
 411                 m->errorOut(e, "SplitAbundCommand", "splitList");
 412                 exit(1);
 413         }
 414 }
 415 /**********************************************************************************************************************/
 416 int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
 417         try {
 418
 419                 map<string, ofstream*> filehandles;
 420
 421                 if (Groups.size() == 0) {
 422                         SAbundVector* sabund = new SAbundVector();
 423                         *sabund = thisList->getSAbundVector();
 424
 425                         //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
 426                         // and don't have to store the bins until you are done with the whole vector, this save alot of space.
 427                         int numRareBins = 0;
 428                         for (int i = 0; i <= sabund->getMaxRank(); i++) {
 429                                 if (i > cutoff) { break; }
 430                                 numRareBins += sabund->get(i);
 431                         }
 432                         int numAbundBins = thisList->getNumBins() - numRareBins;
 433                         delete sabund;
 434
 435                         ofstream aout;
 436                         ofstream rout;
 437
 438                         string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare.list";
 439                         m->openOutputFile(rare, rout);
 440                         outputNames.push_back(rare); outputTypes["list"].push_back(rare);
 441
 442                         string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund.list";
 443                         m->openOutputFile(abund, aout);
 444                         outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 445
 446                         if (rareNames.size() != 0)      {  rout << thisList->getLabel() << '\t' << numRareBins << '\t';         }
 447                         if (abundNames.size() != 0) {   aout << thisList->getLabel() << '\t' << numAbundBins << '\t';   }
 448
 449                         for (int i = 0; i < thisList->getNumBins(); i++) {
 450                                 if (m->control_pressed) { break; }
 451
 452                                 string bin = list->get(i);
 453
 454                                 int size = m->getNumNames(bin);
 455
 456                                 if (size <= cutoff) {  rout << bin << '\t';  }
 457                                 else                            {  aout << bin << '\t'; }
 458                         }
 459
 460                         if (rareNames.size() != 0)      { rout << endl; }
 461                         if (abundNames.size() != 0) { aout << endl; }
 462
 463                         rout.close();
 464                         aout.close();
 465
 466                 }else{ //parse names by abundance and group
 467                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(listfile));
 468                         ofstream* temp;
 469                         ofstream* temp2;
 470                         //map<string, bool> wroteFile;
 471                         map<string, ofstream*> filehandles;
 472                         map<string, ofstream*>::iterator it3;
 473
 474                         for (int i=0; i<Groups.size(); i++) {
 475                                 temp = new ofstream;
 476                                 filehandles[Groups[i]+".rare"] = temp;
 477                                 temp2 = new ofstream;
 478                                 filehandles[Groups[i]+".abund"] = temp2;
 479
 480                                 m->openOutputFile(fileroot + Groups[i] + tag + ".rare.list", *(filehandles[Groups[i]+".rare"]));
 481                                 m->openOutputFile(fileroot + Groups[i] + tag + ".abund.list", *(filehandles[Groups[i]+".abund"]));
 482                                 outputNames.push_back(fileroot + Groups[i] + tag + ".rare.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".rare.list");
 483                                 outputNames.push_back(fileroot + Groups[i] + tag + ".abund.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".abund.list");
 484                         }
 485
 486                         map<string, string> groupVector;
 487                         map<string, string>::iterator itGroup;
 488                         map<string, int> groupNumBins;
 489
 490                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 491                                 groupNumBins[it3->first] = 0;
 492                                 groupVector[it3->first] = "";
 493                         }
 494
 495                         for (int i = 0; i < thisList->getNumBins(); i++) {
 496                                 if (m->control_pressed) { break; }
 497
 498                                 map<string, string> groupBins;
 499                                 string bin = list->get(i);
 500
 501                                 vector<string> names;
 502                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 503
 504                                 //parse bin into list of sequences in each group
 505                                 for (int j = 0; j < names.size(); j++) {
 506                                         string rareAbund;
 507                                         if (rareNames.count(names[j]) != 0) { //you are a rare name
 508                                                 rareAbund = ".rare";
 509                                         }else{ //you are a abund name
 510                                                 rareAbund = ".abund";
 511                                         }
 512
 513                                         string group = groupMap->getGroup(names[j]);
 514
 515                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 516                                                 itGroup = groupBins.find(group+rareAbund);
 517                                                 if(itGroup == groupBins.end()) {
 518                                                         groupBins[group+rareAbund] = names[j];  //add first name
 519                                                         groupNumBins[group+rareAbund]++;
 520                                                 }else{ //add another name
 521                                                         groupBins[group+rareAbund] +=  "," + names[j];
 522                                                 }
 523                                         }else if(group == "not found") {
 524                                                 m->mothurOut(names[j] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 525                                         }
 526                                 }
 527
 528
 529                                 for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
 530                                         groupVector[itGroup->first] +=  itGroup->second + '\t';
 531                                 }
 532                         }
 533
 534                         //end list vector
 535                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 536                                 (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl;  // label numBins  listvector for that group
 537                                 (*(filehandles[it3->first])).close();
 538                                 delete it3->second;
 539                         }
 540                 }
 541
 542                 return 0;
 543
 544         }
 545         catch(exception& e) {
 546                 m->errorOut(e, "SplitAbundCommand", "writeList");
 547                 exit(1);
 548         }
 549 }
 550 /**********************************************************************************************************************/
 551 int SplitAbundCommand::splitNames() { //namefile
 552         try {
 553
 554                 rareNames.clear();
 555                 abundNames.clear();
 556
 557                 //open input file
 558                 ifstream in;
 559                 m->openInputFile(namefile, in);
 560
 561                 while (!in.eof()) {
 562                         if (m->control_pressed) { break; }
 563
 564                         string firstCol, secondCol;
 565                         in >> firstCol >> secondCol; m->gobble(in);
 566
 567                         nameMap[firstCol] = secondCol;
 568
 569                         int size = m->getNumNames(secondCol);
 570
 571                         if (size <= cutoff) {
 572                                 rareNames.insert(firstCol);
 573                         }else{
 574                                 abundNames.insert(firstCol);
 575                         }
 576                 }
 577                 in.close();
 578
 579                 return 0;
 580
 581         }
 582         catch(exception& e) {
 583                 m->errorOut(e, "SplitAbundCommand", "splitNames");
 584                 exit(1);
 585         }
 586 }
 587 /**********************************************************************************************************************/
 588 int SplitAbundCommand::readNamesFile() {
 589         try {
 590                 //open input file
 591                 ifstream in;
 592                 m->openInputFile(namefile, in);
 593
 594                 while (!in.eof()) {
 595                         if (m->control_pressed) { break; }
 596
 597                         string firstCol, secondCol;
 598                         in >> firstCol >> secondCol; m->gobble(in);
 599
 600                         nameMap[firstCol] = secondCol;
 601                 }
 602                 in.close();
 603
 604                 return 0;
 605
 606         }
 607         catch(exception& e) {
 608                 m->errorOut(e, "SplitAbundCommand", "readNamesFile");
 609                 exit(1);
 610         }
 611 }
 612 /**********************************************************************************************************************/
 613 int SplitAbundCommand::createNameMap(ListVector* thisList) {
 614         try {
 615
 616                 if (thisList != NULL) {
 617                         for (int i = 0; i < thisList->getNumBins(); i++) {
 618                                 if (m->control_pressed) { return 0; }
 619
 620                                 string bin = thisList->get(i);
 621
 622                                 vector<string> names;
 623                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 624
 625                                 for (int j = 0; j < names.size(); j++) {  nameMap[names[j]] = names[j];  }
 626                         }//end for
 627                 }
 628
 629                 return 0;
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "SplitAbundCommand", "createNameMap");
 633                 exit(1);
 634         }
 635 }
 636 /**********************************************************************************************************************/
 637 int SplitAbundCommand::writeNames() { //namefile
 638         try {
 639
 640                 map<string, ofstream*> filehandles;
 641
 642                 if (Groups.size() == 0) {
 643                         ofstream aout;
 644                         ofstream rout;
 645
 646                         string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare.names";
 647                         m->openOutputFile(rare, rout);
 648                         outputNames.push_back(rare); outputTypes["name"].push_back(rare);
 649
 650                         string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund.names";
 651                         m->openOutputFile(abund, aout);
 652                         outputNames.push_back(abund); outputTypes["name"].push_back(abund);
 653
 654                         if (rareNames.size() != 0) {
 655                                 for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 656                                         rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
 657                                 }
 658                         }
 659                         rout.close();
 660
 661                         if (abundNames.size() != 0) {
 662                                 for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 663                                         aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
 664                                 }
 665                         }
 666                         aout.close();
 667
 668                 }else{ //parse names by abundance and group
 669                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(namefile));
 670                         ofstream* temp;
 671                         ofstream* temp2;
 672                         map<string, ofstream*> filehandles;
 673                         map<string, ofstream*>::iterator it3;
 674
 675                         for (int i=0; i<Groups.size(); i++) {
 676                                 temp = new ofstream;
 677                                 filehandles[Groups[i]+".rare"] = temp;
 678                                 temp2 = new ofstream;
 679                                 filehandles[Groups[i]+".abund"] = temp2;
 680
 681                                 m->openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"]));
 682                                 m->openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"]));
 683                         }
 684
 685                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 686                                 vector<string> names;
 687                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 688
 689                                 string rareAbund;
 690                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 691                                                 rareAbund = ".rare";
 692                                 }else{ //you are a abund name
 693                                                 rareAbund = ".abund";
 694                                 }
 695
 696                                 map<string, string> outputStrings;
 697                                 map<string, string>::iterator itout;
 698                                 for (int i = 0; i < names.size(); i++) {
 699
 700                                         string group = groupMap->getGroup(names[i]);
 701
 702                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 703                                                 itout = outputStrings.find(group+rareAbund);
 704                                                 if (itout == outputStrings.end()) {
 705                                                         outputStrings[group+rareAbund] = names[i] + '\t' + names[i];
 706                                                 }else {   outputStrings[group+rareAbund] += "," + names[i]; }
 707                                         }else if(group == "not found") {
 708                                                 m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 709                                         }
 710                                 }
 711
 712                                 for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) { *(filehandles[itout->first]) << itout->second << endl;     }
 713                         }
 714
 715
 716                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 717                                 (*(filehandles[it3->first])).close();
 718                                 outputNames.push_back(fileroot + it3->first + ".names");  outputTypes["name"].push_back(fileroot + it3->first + ".names");
 719                                 delete it3->second;
 720                         }
 721                 }
 722
 723                 return 0;
 724
 725         }
 726         catch(exception& e) {
 727                 m->errorOut(e, "SplitAbundCommand", "writeNames");
 728                 exit(1);
 729         }
 730 }
 731 /**********************************************************************************************************************/
 732 //just write the unique names - if a namesfile is given
 733 int SplitAbundCommand::writeAccnos(string tag) {
 734         try {
 735
 736                 map<string, ofstream*> filehandles;
 737
 738                 if (Groups.size() == 0) {
 739                         ofstream aout;
 740                         ofstream rout;
 741
 742
 743                         string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare.accnos";
 744                         m->openOutputFile(rare, rout);
 745                         outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
 746
 747                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 748                                 rout << (*itRare) << endl;
 749                         }
 750                         rout.close();
 751
 752                         string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund.accnos";
 753                         m->openOutputFile(abund, aout);
 754                         outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
 755
 756                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 757                                 aout << (*itAbund) << endl;
 758                         }
 759                         aout.close();
 760
 761                 }else{ //parse names by abundance and group
 762                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(inputFile));
 763                         ofstream* temp;
 764                         ofstream* temp2;
 765                         map<string, ofstream*> filehandles;
 766                         map<string, ofstream*>::iterator it3;
 767
 768                         for (int i=0; i<Groups.size(); i++) {
 769                                 temp = new ofstream;
 770                                 filehandles[Groups[i]+".rare"] = temp;
 771                                 temp2 = new ofstream;
 772                                 filehandles[Groups[i]+".abund"] = temp2;
 773
 774                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"]));
 775                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"]));
 776                         }
 777
 778                         //write rare
 779                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 780                                         string group = groupMap->getGroup(*itRare);
 781
 782                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 783                                                 *(filehandles[group+".rare"]) << *itRare << endl;
 784                                         }
 785                         }
 786
 787                         //write abund
 788                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 789                                         string group = groupMap->getGroup(*itAbund);
 790
 791                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 792                                                 *(filehandles[group+".abund"]) << *itAbund << endl;
 793                                         }
 794                         }
 795
 796                         //close files
 797                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 798                                 (*(filehandles[it3->first])).close();
 799                                 outputNames.push_back(fileroot + tag + it3->first + ".accnos");  outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos");
 800                                 delete it3->second;
 801                         }
 802                 }
 803
 804                 return 0;
 805
 806         }
 807         catch(exception& e) {
 808                 m->errorOut(e, "SplitAbundCommand", "writeAccnos");
 809                 exit(1);
 810         }
 811 }
 812 /**********************************************************************************************************************/
 813 int SplitAbundCommand::parseGroup(string tag) { //namefile
 814         try {
 815
 816                 map<string, ofstream*> filehandles;
 817
 818                 if (Groups.size() == 0) {
 819                         ofstream aout;
 820                         ofstream rout;
 821
 822                         string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare.groups";
 823                         m->openOutputFile(rare, rout);
 824                         outputNames.push_back(rare); outputTypes["group"].push_back(rare);
 825
 826                         string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund.groups";
 827                         m->openOutputFile(abund, aout);
 828                         outputNames.push_back(abund); outputTypes["group"].push_back(abund);
 829
 830                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 831                                 vector<string> names;
 832                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 833
 834                                 for (int i = 0; i < names.size(); i++) {
 835
 836                                         string group = groupMap->getGroup(names[i]);
 837
 838                                         if (group == "not found") {
 839                                                 m->mothurOut(names[i] + " is not in your groupfile, ignoring, please correct."); m->mothurOutEndLine();
 840                                         }else {
 841                                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 842                                                         rout << names[i] << '\t' << group << endl;
 843                                                 }else{ //you are a abund name
 844                                                         aout << names[i] << '\t' << group << endl;
 845                                                 }
 846                                         }
 847                                 }
 848                         }
 849
 850                         rout.close();
 851                         aout.close();
 852
 853                 }else{ //parse names by abundance and group
 854                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(groupfile));
 855                         ofstream* temp;
 856                         ofstream* temp2;
 857                         map<string, ofstream*> filehandles;
 858                         map<string, ofstream*>::iterator it3;
 859
 860                         for (int i=0; i<Groups.size(); i++) {
 861                                 temp = new ofstream;
 862                                 filehandles[Groups[i]+".rare"] = temp;
 863                                 temp2 = new ofstream;
 864                                 filehandles[Groups[i]+".abund"] = temp2;
 865
 866                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"]));
 867                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"]));
 868                         }
 869
 870                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 871                                 vector<string> names;
 872                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 873
 874                                 string rareAbund;
 875                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 876                                         rareAbund = ".rare";
 877                                 }else{ //you are a abund name
 878                                         rareAbund = ".abund";
 879                                 }
 880
 881                                 for (int i = 0; i < names.size(); i++) {
 882
 883                                         string group = groupMap->getGroup(names[i]);
 884
 885                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 886                                                 *(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
 887                                         }
 888                                 }
 889                         }
 890
 891                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 892                                 (*(filehandles[it3->first])).close();
 893                                 outputNames.push_back(fileroot + tag + it3->first + ".groups");  outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups");
 894                                 delete it3->second;
 895                         }
 896                 }
 897
 898                 return 0;
 899
 900         }
 901         catch(exception& e) {
 902                 m->errorOut(e, "SplitAbundCommand", "parseGroups");
 903                 exit(1);
 904         }
 905 }
 906 /**********************************************************************************************************************/
 907 int SplitAbundCommand::parseFasta(string tag) { //namefile
 908         try {
 909
 910                 map<string, ofstream*> filehandles;
 911
 912                 if (Groups.size() == 0) {
 913                         ofstream aout;
 914                         ofstream rout;
 915
 916                         string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare.fasta";
 917                         m->openOutputFile(rare, rout);
 918                         outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
 919
 920                         string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund.fasta";
 921                         m->openOutputFile(abund, aout);
 922                         outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
 923
 924                         //open input file
 925                         ifstream in;
 926                         m->openInputFile(fastafile, in);
 927
 928                         while (!in.eof()) {
 929                                 if (m->control_pressed) { break; }
 930
 931                                 Sequence seq(in); m->gobble(in);
 932
 933                                 if (seq.getName() != "") {
 934
 935                                         map<string, string>::iterator itNames;
 936
 937                                         itNames = nameMap.find(seq.getName());
 938
 939                                         if (itNames == nameMap.end()) {
 940                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
 941                                         }else{
 942                                                 if (rareNames.count(seq.getName()) != 0) { //you are a rare name
 943                                                         seq.printSequence(rout);
 944                                                 }else{ //you are a abund name
 945                                                         seq.printSequence(aout);
 946                                                 }
 947                                         }
 948                                 }
 949                         }
 950                         in.close();
 951                         rout.close();
 952                         aout.close();
 953
 954                 }else{ //parse names by abundance and group
 955                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(fastafile));
 956                         ofstream* temp;
 957                         ofstream* temp2;
 958                         map<string, ofstream*> filehandles;
 959                         map<string, ofstream*>::iterator it3;
 960
 961                         for (int i=0; i<Groups.size(); i++) {
 962                                 temp = new ofstream;
 963                                 filehandles[Groups[i]+".rare"] = temp;
 964                                 temp2 = new ofstream;
 965                                 filehandles[Groups[i]+".abund"] = temp2;
 966
 967                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"]));
 968                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"]));
 969                         }
 970
 971                         //open input file
 972                         ifstream in;
 973                         m->openInputFile(fastafile, in);
 974
 975                         while (!in.eof()) {
 976                                 if (m->control_pressed) { break; }
 977
 978                                 Sequence seq(in); m->gobble(in);
 979
 980                                 if (seq.getName() != "") {
 981                                         map<string, string>::iterator itNames = nameMap.find(seq.getName());
 982
 983                                         if (itNames == nameMap.end()) {
 984                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
 985                                         }else{
 986                                                 vector<string> names;
 987                                                 m->splitAtComma(itNames->second, names);  //parses bin into individual sequence names
 988
 989                                                 string rareAbund;
 990                                                 if (rareNames.count(itNames->first) != 0) { //you are a rare name
 991                                                         rareAbund = ".rare";
 992                                                 }else{ //you are a abund name
 993                                                         rareAbund = ".abund";
 994                                                 }
 995
 996                                                 for (int i = 0; i < names.size(); i++) {
 997
 998                                                         string group = groupMap->getGroup(seq.getName());
 999
1000                                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
1001                                                                 seq.printSequence(*(filehandles[group+rareAbund]));
1002                                                         }else if(group == "not found") {
1003                                                                 m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
1004                                                         }
1005                                                 }
1006                                         }
1007                                 }
1008                         }
1009                         in.close();
1010
1011                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
1012                                 (*(filehandles[it3->first])).close();
1013                                 outputNames.push_back(fileroot + tag + it3->first + ".fasta");  outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta");
1014                                 delete it3->second;
1015                         }
1016                 }
1017
1018                 return 0;
1019
1020         }
1021         catch(exception& e) {
1022                 m->errorOut(e, "SplitAbundCommand", "parseFasta");
1023                 exit(1);
1024         }
1025 }
1026 /**********************************************************************************************************************/
1027