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 string SplitAbundCommand::getOutputFileNameTag(string type, string inputName=""){
  61         try {
  62         string outputFileName = "";
  63                 map<string, vector<string> >::iterator it;
  64
  65         //is this a type this command creates
  66         it = outputTypes.find(type);
  67         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  68         else {
  69             if (type == "fasta")            {   outputFileName =  "fasta";   }
  70             else if (type == "list")    {   outputFileName =  "list";   }
  71             else if (type == "name")        {   outputFileName =  "names";   }
  72             else if (type == "group")       {   outputFileName =  "groups";   }
  73             else if (type == "accnos")        {   outputFileName =  "accnos";   }
  74             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  75         }
  76         return outputFileName;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "SplitAbundCommand", "getOutputFileNameTag");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 SplitAbundCommand::SplitAbundCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["list"] = tempOutNames;
  90                 outputTypes["name"] = tempOutNames;
  91                 outputTypes["accnos"] = tempOutNames;
  92                 outputTypes["group"] = tempOutNames;
  93                 outputTypes["fasta"] = tempOutNames;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************
 101 SplitAbundCommand::SplitAbundCommand(string option)  {
 102         try {
 103                 abort = false; calledHelp = false;
 104                 allLines = 1;
 105
 106                 //allow user to run help
 107                 if(option == "help") { help(); abort = true; calledHelp = true; }
 108                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 109                 else {
 110                         vector<string> myArray = setParameters();
 111
 112                         OptionParser parser(option);
 113                         map<string, string> parameters = parser.getParameters();
 114
 115                         ValidParameters validParameter;
 116                         map<string, string>::iterator it;
 117
 118                         //check to make sure all parameters are valid for command
 119                         for (it = parameters.begin(); it != parameters.end(); it++) {
 120                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 121                         }
 122
 123                         //initialize outputTypes
 124                         vector<string> tempOutNames;
 125                         outputTypes["list"] = tempOutNames;
 126                         outputTypes["name"] = tempOutNames;
 127                         outputTypes["accnos"] = tempOutNames;
 128                         outputTypes["group"] = tempOutNames;
 129                         outputTypes["fasta"] = tempOutNames;
 130
 131                         //if the user changes the input directory command factory will send this info to us in the output parameter
 132                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 133                         if (inputDir == "not found"){   inputDir = "";          }
 134                         else {
 135                                 string path;
 136                                 it = parameters.find("list");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 142                                 }
 143
 144                                 it = parameters.find("group");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 150                                 }
 151
 152                                 it = parameters.find("fasta");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 158                                 }
 159
 160                                 it = parameters.find("name");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 166                                 }
 167
 168                         }
 169
 170
 171                         //if the user changes the output directory command factory will send this info to us in the output parameter
 172                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 173
 174                         //check for required parameters
 175                         listfile = validParameter.validFile(parameters, "list", true);
 176                         if (listfile == "not open") { abort = true; }
 177                         else if (listfile == "not found") { listfile = ""; }
 178                         else{ inputFile = listfile; m->setListFile(listfile); }
 179
 180                         namefile = validParameter.validFile(parameters, "name", true);
 181                         if (namefile == "not open") { abort = true; }
 182                         else if (namefile == "not found") { namefile = ""; }
 183                         else{ inputFile = namefile; m->setNameFile(namefile); }
 184
 185                         fastafile = validParameter.validFile(parameters, "fasta", true);
 186                         if (fastafile == "not open") { abort = true; }
 187                         else if (fastafile == "not found") {
 188                                 fastafile = m->getFastaFile();
 189                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 190                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 191                         }else { m->setFastaFile(fastafile); }
 192
 193                         groupfile = validParameter.validFile(parameters, "group", true);
 194                         if (groupfile == "not open") {  groupfile = ""; abort = true; }
 195                         else if (groupfile == "not found") { groupfile = ""; }
 196                         else {
 197                                 groupMap = new GroupMap(groupfile);
 198
 199                                 int error = groupMap->readMap();
 200                                 if (error == 1) { abort = true; }
 201                                 m->setGroupFile(groupfile);
 202                         }
 203
 204                         groups = validParameter.validFile(parameters, "groups", false);
 205                         if (groups == "not found") { groups = ""; }
 206                         else if (groups == "all") {
 207                                 if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  }
 208                                 else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
 209                         }else {
 210                                 m->splitAtDash(groups, Groups);
 211                         }
 212
 213                         if ((groupfile == "") && (groups != "")) {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";  Groups.clear(); }
 214
 215                         //do you have all files needed
 216                         if ((listfile == "") && (namefile == "")) {
 217                                 namefile = m->getNameFile();
 218                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 219                                 else {
 220                                         listfile = m->getListFile();
 221                                         if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 222                                         else {  m->mothurOut("You have no current list or namefile and the list or name parameter is required."); m->mothurOutEndLine(); abort = true; }
 223                                 }
 224                         }
 225
 226                         //check for optional parameter and set defaults
 227                         // ...at some point should added some additional type checking...
 228                         label = validParameter.validFile(parameters, "label", false);
 229                         if (label == "not found") { label = "";  allLines = 1; }
 230                         else {
 231                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 232                                 else { allLines = 1;  }
 233                         }
 234
 235                         string temp = validParameter.validFile(parameters, "accnos", false);            if (temp == "not found") { temp = "F"; }
 236                         accnos = m->isTrue(temp);
 237
 238                         temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
 239                         m->mothurConvert(temp, cutoff);
 240
 241                         if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 242                 }
 243
 244         }
 245         catch(exception& e) {
 246                 m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
 247                 exit(1);
 248         }
 249 }
 250 //**********************************************************************************************************************
 251 SplitAbundCommand::~SplitAbundCommand(){
 252         if (groupfile != "") {  delete groupMap;  }
 253 }
 254 //**********************************************************************************************************************
 255 int SplitAbundCommand::execute(){
 256         try {
 257
 258                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 259
 260                 if (listfile != "") { //you are using a listfile to determine abundance
 261                         if (outputDir == "") { outputDir = m->hasPath(listfile); }
 262
 263                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 264                         set<string> processedLabels;
 265                         set<string> userLabels = labels;
 266
 267                         input = new InputData(listfile, "list");
 268                         list = input->getListVector();
 269                         string lastLabel = list->getLabel();
 270
 271                         //do you have a namefile or do we need to similate one?
 272                         if (namefile != "") {  readNamesFile();         }
 273                         else                            { createNameMap(list);  }
 274
 275                         if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
 276
 277                         while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 278
 279                                 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
 280
 281                                 if(allLines == 1 || labels.count(list->getLabel()) == 1){
 282
 283                                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 284                                                 splitList(list);
 285
 286                                                 processedLabels.insert(list->getLabel());
 287                                                 userLabels.erase(list->getLabel());
 288                                 }
 289
 290                                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 291                                                 string saveLabel = list->getLabel();
 292
 293                                                 delete list;
 294                                                 list = input->getListVector(lastLabel); //get new list vector to process
 295
 296                                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 297                                                 splitList(list);
 298
 299                                                 processedLabels.insert(list->getLabel());
 300                                                 userLabels.erase(list->getLabel());
 301
 302                                                 //restore real lastlabel to save below
 303                                                 list->setLabel(saveLabel);
 304                                 }
 305
 306
 307                                 lastLabel = list->getLabel();
 308
 309                                 delete list;
 310                                 list = input->getListVector(); //get new list vector to process
 311                         }
 312
 313                         if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 314
 315                         //output error messages about any remaining user labels
 316                         set<string>::iterator it;
 317                         bool needToRun = false;
 318                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 319                                 m->mothurOut("Your file does not include the label " + *it);
 320                                 if (processedLabels.count(lastLabel) != 1) {
 321                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 322                                         needToRun = true;
 323                                 }else {
 324                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 325                                 }
 326
 327                         }
 328
 329                         if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 330
 331                         //run last label if you need to
 332                         if (needToRun == true)  {
 333                                 if (list != NULL) {     delete list;    }
 334                                 list = input->getListVector(lastLabel); //get new list vector to process
 335
 336                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 337                                 splitList(list);
 338
 339                                 delete list;
 340                         }
 341
 342                         delete input;
 343
 344                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }      return 0;       }
 345
 346                 }else { //you are using the namefile to determine abundance
 347                         if (outputDir == "") { outputDir = m->hasPath(namefile); }
 348
 349                         splitNames();
 350                         writeNames();
 351
 352                         string tag = "";
 353                         if (groupfile != "")                            {  parseGroup(tag);             }
 354                         if (accnos)                                                     {  writeAccnos(tag);    }
 355                         if (fastafile != "")                            {  parseFasta(tag);             }
 356                 }
 357
 358                 //set fasta file as new current fastafile
 359                 string current = "";
 360                 itTypes = outputTypes.find("fasta");
 361                 if (itTypes != outputTypes.end()) {
 362                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 363                 }
 364
 365                 itTypes = outputTypes.find("name");
 366                 if (itTypes != outputTypes.end()) {
 367                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 368                 }
 369
 370                 itTypes = outputTypes.find("group");
 371                 if (itTypes != outputTypes.end()) {
 372                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 373                 }
 374
 375                 itTypes = outputTypes.find("list");
 376                 if (itTypes != outputTypes.end()) {
 377                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 378                 }
 379
 380                 itTypes = outputTypes.find("accnos");
 381                 if (itTypes != outputTypes.end()) {
 382                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 383                 }
 384
 385                 m->mothurOutEndLine();
 386                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 387                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 388                 m->mothurOutEndLine();
 389
 390                 return 0;
 391         }
 392         catch(exception& e) {
 393                 m->errorOut(e, "SplitAbundCommand", "execute");
 394                 exit(1);
 395         }
 396 }
 397 /**********************************************************************************************************************/
 398 int SplitAbundCommand::splitList(ListVector* thisList) {
 399         try {
 400                 rareNames.clear();
 401                 abundNames.clear();
 402
 403                 //get rareNames and abundNames
 404                 for (int i = 0; i < thisList->getNumBins(); i++) {
 405                         if (m->control_pressed) { return 0; }
 406
 407                         string bin = thisList->get(i);
 408
 409                         vector<string> names;
 410                         m->splitAtComma(bin, names);  //parses bin into individual sequence names
 411                         int size = names.size();
 412
 413                         if (size <= cutoff) {
 414                                 for (int j = 0; j < names.size(); j++) {  rareNames.insert(names[j]);  }
 415                         }else{
 416                                 for (int j = 0; j < names.size(); j++) {  abundNames.insert(names[j]);  }
 417                         }
 418                 }//end for
 419
 420
 421                 string tag = thisList->getLabel() + ".";
 422
 423                 writeList(thisList, tag);
 424
 425                 if (groupfile != "")                            {  parseGroup(tag);             }
 426                 if (accnos)                                                     {  writeAccnos(tag);    }
 427                 if (fastafile != "")                            {  parseFasta(tag);             }
 428
 429                 return 0;
 430
 431         }
 432         catch(exception& e) {
 433                 m->errorOut(e, "SplitAbundCommand", "splitList");
 434                 exit(1);
 435         }
 436 }
 437 /**********************************************************************************************************************/
 438 int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
 439         try {
 440
 441                 map<string, ofstream*> filehandles;
 442
 443                 if (Groups.size() == 0) {
 444                         SAbundVector* sabund = new SAbundVector();
 445                         *sabund = thisList->getSAbundVector();
 446
 447                         //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
 448                         // and don't have to store the bins until you are done with the whole vector, this save alot of space.
 449                         int numRareBins = 0;
 450                         for (int i = 0; i <= sabund->getMaxRank(); i++) {
 451                                 if (i > cutoff) { break; }
 452                                 numRareBins += sabund->get(i);
 453                         }
 454                         int numAbundBins = thisList->getNumBins() - numRareBins;
 455                         delete sabund;
 456
 457                         ofstream aout;
 458                         ofstream rout;
 459
 460                         string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list");
 461                         m->openOutputFile(rare, rout);
 462                         outputNames.push_back(rare); outputTypes["list"].push_back(rare);
 463
 464                         string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list");
 465                         m->openOutputFile(abund, aout);
 466                         outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 467
 468                         if (rareNames.size() != 0)      {  rout << thisList->getLabel() << '\t' << numRareBins << '\t';         }
 469                         if (abundNames.size() != 0) {   aout << thisList->getLabel() << '\t' << numAbundBins << '\t';   }
 470
 471                         for (int i = 0; i < thisList->getNumBins(); i++) {
 472                                 if (m->control_pressed) { break; }
 473
 474                                 string bin = list->get(i);
 475
 476                                 int size = m->getNumNames(bin);
 477
 478                                 if (size <= cutoff) {  rout << bin << '\t';  }
 479                                 else                            {  aout << bin << '\t'; }
 480                         }
 481
 482                         if (rareNames.size() != 0)      { rout << endl; }
 483                         if (abundNames.size() != 0) { aout << endl; }
 484
 485                         rout.close();
 486                         aout.close();
 487
 488                 }else{ //parse names by abundance and group
 489                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(listfile));
 490                         ofstream* temp;
 491                         ofstream* temp2;
 492                         //map<string, bool> wroteFile;
 493                         map<string, ofstream*> filehandles;
 494                         map<string, ofstream*>::iterator it3;
 495
 496                         for (int i=0; i<Groups.size(); i++) {
 497                                 temp = new ofstream;
 498                                 filehandles[Groups[i]+".rare"] = temp;
 499                                 temp2 = new ofstream;
 500                                 filehandles[Groups[i]+".abund"] = temp2;
 501
 502                 string rareGroupFileName = fileroot + Groups[i] + tag + ".rare." + getOutputFileNameTag("list");
 503                 string abundGroupFileName = fileroot + Groups[i] + tag + ".abund." + getOutputFileNameTag("list");
 504                                 m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
 505                                 m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
 506                                 outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName);
 507                                 outputNames.push_back(abundGroupFileName); outputTypes["list"].push_back(abundGroupFileName);
 508                         }
 509
 510                         map<string, string> groupVector;
 511                         map<string, string>::iterator itGroup;
 512                         map<string, int> groupNumBins;
 513
 514                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 515                                 groupNumBins[it3->first] = 0;
 516                                 groupVector[it3->first] = "";
 517                         }
 518
 519                         for (int i = 0; i < thisList->getNumBins(); i++) {
 520                                 if (m->control_pressed) { break; }
 521
 522                                 map<string, string> groupBins;
 523                                 string bin = list->get(i);
 524
 525                                 vector<string> names;
 526                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 527
 528                                 //parse bin into list of sequences in each group
 529                                 for (int j = 0; j < names.size(); j++) {
 530                                         string rareAbund;
 531                                         if (rareNames.count(names[j]) != 0) { //you are a rare name
 532                                                 rareAbund = ".rare";
 533                                         }else{ //you are a abund name
 534                                                 rareAbund = ".abund";
 535                                         }
 536
 537                                         string group = groupMap->getGroup(names[j]);
 538
 539                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 540                                                 itGroup = groupBins.find(group+rareAbund);
 541                                                 if(itGroup == groupBins.end()) {
 542                                                         groupBins[group+rareAbund] = names[j];  //add first name
 543                                                         groupNumBins[group+rareAbund]++;
 544                                                 }else{ //add another name
 545                                                         groupBins[group+rareAbund] +=  "," + names[j];
 546                                                 }
 547                                         }else if(group == "not found") {
 548                                                 m->mothurOut(names[j] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 549                                         }
 550                                 }
 551
 552
 553                                 for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
 554                                         groupVector[itGroup->first] +=  itGroup->second + '\t';
 555                                 }
 556                         }
 557
 558                         //end list vector
 559                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 560                                 (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl;  // label numBins  listvector for that group
 561                                 (*(filehandles[it3->first])).close();
 562                                 delete it3->second;
 563                         }
 564                 }
 565
 566                 return 0;
 567
 568         }
 569         catch(exception& e) {
 570                 m->errorOut(e, "SplitAbundCommand", "writeList");
 571                 exit(1);
 572         }
 573 }
 574 /**********************************************************************************************************************/
 575 int SplitAbundCommand::splitNames() { //namefile
 576         try {
 577
 578                 rareNames.clear();
 579                 abundNames.clear();
 580
 581                 //open input file
 582                 ifstream in;
 583                 m->openInputFile(namefile, in);
 584
 585                 while (!in.eof()) {
 586                         if (m->control_pressed) { break; }
 587
 588                         string firstCol, secondCol;
 589                         in >> firstCol >> secondCol; m->gobble(in);
 590
 591                         nameMap[firstCol] = secondCol;
 592
 593                         int size = m->getNumNames(secondCol);
 594
 595                         if (size <= cutoff) {
 596                                 rareNames.insert(firstCol);
 597                         }else{
 598                                 abundNames.insert(firstCol);
 599                         }
 600                 }
 601                 in.close();
 602
 603                 return 0;
 604
 605         }
 606         catch(exception& e) {
 607                 m->errorOut(e, "SplitAbundCommand", "splitNames");
 608                 exit(1);
 609         }
 610 }
 611 /**********************************************************************************************************************/
 612 int SplitAbundCommand::readNamesFile() {
 613         try {
 614                 //open input file
 615                 ifstream in;
 616                 m->openInputFile(namefile, in);
 617
 618                 while (!in.eof()) {
 619                         if (m->control_pressed) { break; }
 620
 621                         string firstCol, secondCol;
 622                         in >> firstCol >> secondCol; m->gobble(in);
 623
 624                         nameMap[firstCol] = secondCol;
 625                 }
 626                 in.close();
 627
 628                 return 0;
 629
 630         }
 631         catch(exception& e) {
 632                 m->errorOut(e, "SplitAbundCommand", "readNamesFile");
 633                 exit(1);
 634         }
 635 }
 636 /**********************************************************************************************************************/
 637 int SplitAbundCommand::createNameMap(ListVector* thisList) {
 638         try {
 639
 640                 if (thisList != NULL) {
 641                         for (int i = 0; i < thisList->getNumBins(); i++) {
 642                                 if (m->control_pressed) { return 0; }
 643
 644                                 string bin = thisList->get(i);
 645
 646                                 vector<string> names;
 647                                 m->splitAtComma(bin, names);  //parses bin into individual sequence names
 648
 649                                 for (int j = 0; j < names.size(); j++) {  nameMap[names[j]] = names[j];  }
 650                         }//end for
 651                 }
 652
 653                 return 0;
 654         }
 655         catch(exception& e) {
 656                 m->errorOut(e, "SplitAbundCommand", "createNameMap");
 657                 exit(1);
 658         }
 659 }
 660 /**********************************************************************************************************************/
 661 int SplitAbundCommand::writeNames() { //namefile
 662         try {
 663
 664                 map<string, ofstream*> filehandles;
 665
 666                 if (Groups.size() == 0) {
 667                         ofstream aout;
 668                         ofstream rout;
 669
 670                         string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare." + getOutputFileNameTag("name");
 671                         m->openOutputFile(rare, rout);
 672                         outputNames.push_back(rare); outputTypes["name"].push_back(rare);
 673
 674                         string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund." + getOutputFileNameTag("name");
 675                         m->openOutputFile(abund, aout);
 676                         outputNames.push_back(abund); outputTypes["name"].push_back(abund);
 677
 678                         if (rareNames.size() != 0) {
 679                                 for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 680                                         rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
 681                                 }
 682                         }
 683                         rout.close();
 684
 685                         if (abundNames.size() != 0) {
 686                                 for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 687                                         aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
 688                                 }
 689                         }
 690                         aout.close();
 691
 692                 }else{ //parse names by abundance and group
 693                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(namefile));
 694                         ofstream* temp;
 695                         ofstream* temp2;
 696                         map<string, ofstream*> filehandles;
 697                         map<string, ofstream*>::iterator it3;
 698
 699                         for (int i=0; i<Groups.size(); i++) {
 700                                 temp = new ofstream;
 701                                 filehandles[Groups[i]+".rare"] = temp;
 702                                 temp2 = new ofstream;
 703                                 filehandles[Groups[i]+".abund"] = temp2;
 704
 705                 string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name");
 706                 string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name");
 707                                 m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
 708                                 m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
 709                         }
 710
 711                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 712                                 vector<string> names;
 713                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 714
 715                                 string rareAbund;
 716                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 717                                                 rareAbund = ".rare";
 718                                 }else{ //you are a abund name
 719                                                 rareAbund = ".abund";
 720                                 }
 721
 722                                 map<string, string> outputStrings;
 723                                 map<string, string>::iterator itout;
 724                                 for (int i = 0; i < names.size(); i++) {
 725
 726                                         string group = groupMap->getGroup(names[i]);
 727
 728                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 729                                                 itout = outputStrings.find(group+rareAbund);
 730                                                 if (itout == outputStrings.end()) {
 731                                                         outputStrings[group+rareAbund] = names[i] + '\t' + names[i];
 732                                                 }else {   outputStrings[group+rareAbund] += "," + names[i]; }
 733                                         }else if(group == "not found") {
 734                                                 m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 735                                         }
 736                                 }
 737
 738                                 for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) { *(filehandles[itout->first]) << itout->second << endl;     }
 739                         }
 740
 741
 742                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 743                                 (*(filehandles[it3->first])).close();
 744                                 outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));  outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));
 745                                 delete it3->second;
 746                         }
 747                 }
 748
 749                 return 0;
 750
 751         }
 752         catch(exception& e) {
 753                 m->errorOut(e, "SplitAbundCommand", "writeNames");
 754                 exit(1);
 755         }
 756 }
 757 /**********************************************************************************************************************/
 758 //just write the unique names - if a namesfile is given
 759 int SplitAbundCommand::writeAccnos(string tag) {
 760         try {
 761
 762                 map<string, ofstream*> filehandles;
 763
 764                 if (Groups.size() == 0) {
 765                         ofstream aout;
 766                         ofstream rout;
 767
 768
 769                         string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare." + getOutputFileNameTag("accnos");
 770                         m->openOutputFile(rare, rout);
 771                         outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
 772
 773                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 774                                 rout << (*itRare) << endl;
 775                         }
 776                         rout.close();
 777
 778                         string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund." + getOutputFileNameTag("accnos");
 779                         m->openOutputFile(abund, aout);
 780                         outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
 781
 782                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 783                                 aout << (*itAbund) << endl;
 784                         }
 785                         aout.close();
 786
 787                 }else{ //parse names by abundance and group
 788                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(inputFile));
 789                         ofstream* temp;
 790                         ofstream* temp2;
 791                         map<string, ofstream*> filehandles;
 792                         map<string, ofstream*>::iterator it3;
 793
 794                         for (int i=0; i<Groups.size(); i++) {
 795                                 temp = new ofstream;
 796                                 filehandles[Groups[i]+".rare"] = temp;
 797                                 temp2 = new ofstream;
 798                                 filehandles[Groups[i]+".abund"] = temp2;
 799
 800                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"]));
 801                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"]));
 802                         }
 803
 804                         //write rare
 805                         for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
 806                                         string group = groupMap->getGroup(*itRare);
 807
 808                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 809                                                 *(filehandles[group+".rare"]) << *itRare << endl;
 810                                         }
 811                         }
 812
 813                         //write abund
 814                         for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
 815                                         string group = groupMap->getGroup(*itAbund);
 816
 817                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 818                                                 *(filehandles[group+".abund"]) << *itAbund << endl;
 819                                         }
 820                         }
 821
 822                         //close files
 823                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 824                                 (*(filehandles[it3->first])).close();
 825                                 outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));  outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));
 826                                 delete it3->second;
 827                         }
 828                 }
 829
 830                 return 0;
 831
 832         }
 833         catch(exception& e) {
 834                 m->errorOut(e, "SplitAbundCommand", "writeAccnos");
 835                 exit(1);
 836         }
 837 }
 838 /**********************************************************************************************************************/
 839 int SplitAbundCommand::parseGroup(string tag) { //namefile
 840         try {
 841
 842                 map<string, ofstream*> filehandles;
 843
 844                 if (Groups.size() == 0) {
 845                         ofstream aout;
 846                         ofstream rout;
 847
 848                         string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare." + getOutputFileNameTag("group");
 849                         m->openOutputFile(rare, rout);
 850                         outputNames.push_back(rare); outputTypes["group"].push_back(rare);
 851
 852                         string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund." + getOutputFileNameTag("group");
 853 ;
 854                         m->openOutputFile(abund, aout);
 855                         outputNames.push_back(abund); outputTypes["group"].push_back(abund);
 856
 857                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 858                                 vector<string> names;
 859                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 860
 861                                 for (int i = 0; i < names.size(); i++) {
 862
 863                                         string group = groupMap->getGroup(names[i]);
 864
 865                                         if (group == "not found") {
 866                                                 m->mothurOut(names[i] + " is not in your groupfile, ignoring, please correct."); m->mothurOutEndLine();
 867                                         }else {
 868                                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 869                                                         rout << names[i] << '\t' << group << endl;
 870                                                 }else{ //you are a abund name
 871                                                         aout << names[i] << '\t' << group << endl;
 872                                                 }
 873                                         }
 874                                 }
 875                         }
 876
 877                         rout.close();
 878                         aout.close();
 879
 880                 }else{ //parse names by abundance and group
 881                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(groupfile));
 882                         ofstream* temp;
 883                         ofstream* temp2;
 884                         map<string, ofstream*> filehandles;
 885                         map<string, ofstream*>::iterator it3;
 886
 887                         for (int i=0; i<Groups.size(); i++) {
 888                                 temp = new ofstream;
 889                                 filehandles[Groups[i]+".rare"] = temp;
 890                                 temp2 = new ofstream;
 891                                 filehandles[Groups[i]+".abund"] = temp2;
 892
 893                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"]));
 894                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"]));
 895                         }
 896
 897                         for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
 898                                 vector<string> names;
 899                                 m->splitAtComma(itName->second, names);  //parses bin into individual sequence names
 900
 901                                 string rareAbund;
 902                                 if (rareNames.count(itName->first) != 0) { //you are a rare name
 903                                         rareAbund = ".rare";
 904                                 }else{ //you are a abund name
 905                                         rareAbund = ".abund";
 906                                 }
 907
 908                                 for (int i = 0; i < names.size(); i++) {
 909
 910                                         string group = groupMap->getGroup(names[i]);
 911
 912                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 913                                                 *(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
 914                                         }
 915                                 }
 916                         }
 917
 918                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 919                                 (*(filehandles[it3->first])).close();
 920                                 outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));  outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));
 921                                 delete it3->second;
 922                         }
 923                 }
 924
 925                 return 0;
 926
 927         }
 928         catch(exception& e) {
 929                 m->errorOut(e, "SplitAbundCommand", "parseGroups");
 930                 exit(1);
 931         }
 932 }
 933 /**********************************************************************************************************************/
 934 int SplitAbundCommand::parseFasta(string tag) { //namefile
 935         try {
 936
 937                 map<string, ofstream*> filehandles;
 938
 939                 if (Groups.size() == 0) {
 940                         ofstream aout;
 941                         ofstream rout;
 942
 943                         string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare." + getOutputFileNameTag("fasta");
 944                         m->openOutputFile(rare, rout);
 945                         outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
 946
 947                         string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund." + getOutputFileNameTag("fasta");
 948                         m->openOutputFile(abund, aout);
 949                         outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
 950
 951                         //open input file
 952                         ifstream in;
 953                         m->openInputFile(fastafile, in);
 954
 955                         while (!in.eof()) {
 956                                 if (m->control_pressed) { break; }
 957
 958                                 Sequence seq(in); m->gobble(in);
 959
 960                                 if (seq.getName() != "") {
 961
 962                                         map<string, string>::iterator itNames;
 963
 964                                         itNames = nameMap.find(seq.getName());
 965
 966                                         if (itNames == nameMap.end()) {
 967                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
 968                                         }else{
 969                                                 if (rareNames.count(seq.getName()) != 0) { //you are a rare name
 970                                                         seq.printSequence(rout);
 971                                                 }else{ //you are a abund name
 972                                                         seq.printSequence(aout);
 973                                                 }
 974                                         }
 975                                 }
 976                         }
 977                         in.close();
 978                         rout.close();
 979                         aout.close();
 980
 981                 }else{ //parse names by abundance and group
 982                         string fileroot =  outputDir + m->getRootName(m->getSimpleName(fastafile));
 983                         ofstream* temp;
 984                         ofstream* temp2;
 985                         map<string, ofstream*> filehandles;
 986                         map<string, ofstream*>::iterator it3;
 987
 988                         for (int i=0; i<Groups.size(); i++) {
 989                                 temp = new ofstream;
 990                                 filehandles[Groups[i]+".rare"] = temp;
 991                                 temp2 = new ofstream;
 992                                 filehandles[Groups[i]+".abund"] = temp2;
 993
 994                                 m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"]));
 995                                 m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"]));
 996                         }
 997
 998                         //open input file
 999                         ifstream in;
1000                         m->openInputFile(fastafile, in);
1001
1002                         while (!in.eof()) {
1003                                 if (m->control_pressed) { break; }
1004
1005                                 Sequence seq(in); m->gobble(in);
1006
1007                                 if (seq.getName() != "") {
1008                                         map<string, string>::iterator itNames = nameMap.find(seq.getName());
1009
1010                                         if (itNames == nameMap.end()) {
1011                                                 m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
1012                                         }else{
1013                                                 vector<string> names;
1014                                                 m->splitAtComma(itNames->second, names);  //parses bin into individual sequence names
1015
1016                                                 string rareAbund;
1017                                                 if (rareNames.count(itNames->first) != 0) { //you are a rare name
1018                                                         rareAbund = ".rare";
1019                                                 }else{ //you are a abund name
1020                                                         rareAbund = ".abund";
1021                                                 }
1022
1023                                                 for (int i = 0; i < names.size(); i++) {
1024
1025                                                         string group = groupMap->getGroup(seq.getName());
1026
1027                                                         if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
1028                                                                 seq.printSequence(*(filehandles[group+rareAbund]));
1029                                                         }else if(group == "not found") {
1030                                                                 m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
1031                                                         }
1032                                                 }
1033                                         }
1034                                 }
1035                         }
1036                         in.close();
1037
1038                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
1039                                 (*(filehandles[it3->first])).close();
1040                                 outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));  outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));
1041                                 delete it3->second;
1042                         }
1043                 }
1044
1045                 return 0;
1046
1047         }
1048         catch(exception& e) {
1049                 m->errorOut(e, "SplitAbundCommand", "parseFasta");
1050                 exit(1);
1051         }
1052 }
1053 /**********************************************************************************************************************/
1054