getsharedotucommand.cpp

   1 /*
   2  *  getsharedotucommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/22/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getsharedotucommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> GetSharedOTUCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "sharedFasta", "none", "none","fasta",false,false); parameters.push_back(pfasta);
  17                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "groupList","",false,false,true); parameters.push_back(pgroup);
  18                 CommandParameter plist("list", "InputTypes", "", "", "sharedList", "sharedList", "groupList","sharedseq",false,false,true); parameters.push_back(plist);
  19         CommandParameter pshared("shared", "InputTypes", "", "", "sharedList-sharedFasta", "sharedList", "none","sharedseq",false,false,true); parameters.push_back(pshared);
  20                 CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
  21                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  22                 CommandParameter puniquegroups("uniquegroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(puniquegroups);
  23                 CommandParameter psharedgroups("sharedgroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(psharedgroups);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "GetSharedOTUCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string GetSharedOTUCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The get.sharedseqs command parameters are list, group, shared, label, uniquegroups, sharedgroups, output and fasta.  The list and group or shared parameters are required, unless you have valid current files.\n";
  41                 helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
  42                 helpString += "The uniquegroups and sharedgroups parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
  43                 helpString += "If you enter your groups under the uniquegroups parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
  44                 helpString += "If you enter your groups under the sharedgroups parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
  45                 helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group or shared file.\n";
  46                 helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified. It can only be used with a list and group file not the shared file input.\n";
  47                 helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
  48                 helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
  49                 helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
  50                 helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, uniquegroups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
  51                 helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=amazon.groups, uniquegroups=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
  52                 helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
  53                 helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
  54                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
  55                 return helpString;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 string GetSharedOTUCommand::getOutputPattern(string type) {
  64     try {
  65         string pattern = "";
  66
  67         if (type == "fasta")            {   pattern =  "[filename],[distance],[group],shared.fasta";   }
  68         else if (type == "accnos")      {   pattern =  "[filename],[distance],[group],accnos";         }
  69         else if (type == "sharedseqs")  {   pattern =  "[filename],[distance],[group],shared.seqs";    }
  70         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  71
  72         return pattern;
  73     }
  74     catch(exception& e) {
  75         m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
  76         exit(1);
  77     }
  78 }
  79 //**********************************************************************************************************************
  80 GetSharedOTUCommand::GetSharedOTUCommand(){
  81         try {
  82                 abort = true; calledHelp = true;
  83                 setParameters();
  84                 vector<string> tempOutNames;
  85                 outputTypes["fasta"] = tempOutNames;
  86                 outputTypes["accnos"] = tempOutNames;
  87                 outputTypes["sharedseqs"] = tempOutNames;
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
  91                 exit(1);
  92         }
  93 }
  94 //**********************************************************************************************************************
  95 GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
  96         try {
  97
  98                 abort = false; calledHelp = false;
  99                 unique = true;
 100                 allLines = 1;
 101
 102                 //allow user to run help
 103                 if(option == "help") { help(); abort = true; calledHelp = true; }
 104                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 105
 106                 else {
 107                         vector<string> myArray = setParameters();
 108
 109                         OptionParser parser(option);
 110                         map<string,string> parameters = parser.getParameters();
 111
 112                         ValidParameters validParameter;
 113                         map<string,string>::iterator it;
 114
 115                         //check to make sure all parameters are valid for command
 116                         for (it = parameters.begin(); it != parameters.end(); it++) {
 117                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 118                         }
 119
 120                         //initialize outputTypes
 121                         vector<string> tempOutNames;
 122                         outputTypes["fasta"] = tempOutNames;
 123                         outputTypes["accnos"] = tempOutNames;
 124                         outputTypes["sharedseqs"] = tempOutNames;
 125
 126                         //if the user changes the output directory command factory will send this info to us in the output parameter
 127                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 128
 129                         //if the user changes the input directory command factory will send this info to us in the output parameter
 130                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 131                         if (inputDir == "not found"){   inputDir = "";          }
 132                         else {
 133                                 string path;
 134                                 it = parameters.find("fasta");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 140                                 }
 141
 142                                 it = parameters.find("list");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 148                                 }
 149
 150                 it = parameters.find("shared");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 156                                 }
 157
 158                                 it = parameters.find("group");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 164                                 }
 165                         }
 166
 167
 168                         //check for required parameters
 169                         listfile = validParameter.validFile(parameters, "list", true);
 170                         if (listfile == "not open") { abort = true; }
 171                         else if (listfile == "not found") { listfile = "";                      }
 172             else {  format = "list";    m->setListFile(listfile); }
 173
 174                         groupfile = validParameter.validFile(parameters, "group", true);
 175                         if (groupfile == "not open") { abort = true; }
 176                         else if (groupfile == "not found") { groupfile = ""; }
 177                         else { m->setGroupFile(groupfile); }
 178
 179             sharedfile = validParameter.validFile(parameters, "shared", true);
 180                         if (sharedfile == "not open") { abort = true; }
 181                         else if (sharedfile == "not found") { sharedfile = ""; }
 182                         else { m->setSharedFile(sharedfile); }
 183
 184             fastafile = validParameter.validFile(parameters, "fasta", true);
 185                         if (fastafile == "not open") { abort = true; }
 186                         else if (fastafile == "not found") {  fastafile = "";  }
 187                         else { m->setFastaFile(fastafile); }
 188
 189
 190             if ((sharedfile == "") && (listfile == "")) { //look for currents
 191                 //is there are current file available for either of these?
 192                                 //give priority to shared, then list
 193                                 sharedfile = m->getSharedFile();
 194                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 195                                 else {
 196                                         listfile = m->getListFile();
 197                                         if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 198                                         else {
 199                                                 m->mothurOut("No valid current files. You must provide a shared or list file."); m->mothurOutEndLine();
 200                                                 abort = true;
 201                                         }
 202                                 }
 203             }else if ((sharedfile != "") && (listfile != "")) {
 204                 m->mothurOut("You may enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true;
 205             }
 206
 207             if (listfile != "") {
 208                                 if (groupfile == ""){
 209                                         groupfile = m->getGroupFile();
 210                                         if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 211                                         else { m->mothurOut("You need to provide a group file if you are going to use the list format."); m->mothurOutEndLine(); abort = true;
 212                                         }
 213                                 }
 214                         }
 215
 216                         if ((sharedfile != "") && (fastafile != "")) { m->mothurOut("You cannot use the fasta file with the shared file."); m->mothurOutEndLine(); abort = true; }
 217
 218                         //check for optional parameter and set defaults
 219                         // ...at some point should added some additional type checking...
 220                         label = validParameter.validFile(parameters, "label", false);
 221                         if (label == "not found") { label = ""; }
 222                         else {
 223                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 224                                 else { allLines = 1;  }
 225                         }
 226
 227                         output = validParameter.validFile(parameters, "output", false);
 228                         if (output == "not found") { output = ""; }
 229                         else if (output == "default") { output = ""; }
 230
 231                         groups = validParameter.validFile(parameters, "uniquegroups", false);
 232                         if (groups == "not found") { groups = ""; }
 233                         else {
 234                                 userGroups = "unique." + groups;
 235                                 m->splitAtDash(groups, Groups);
 236                         }
 237
 238                         groups = validParameter.validFile(parameters, "sharedgroups", false);
 239                         if (groups == "not found") { groups = "";  }
 240                         else {
 241                                 userGroups = groups;
 242                                 m->splitAtDash(groups, Groups);
 243                                 unique = false;
 244                         }
 245
 246         }
 247
 248         }
 249         catch(exception& e) {
 250                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
 251                 exit(1);
 252         }
 253 }
 254 //**********************************************************************************************************************
 255
 256 int GetSharedOTUCommand::execute(){
 257         try {
 258
 259                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 260
 261         if ( sharedfile != "") { runShared(); }
 262         else {
 263             m->setGroups(Groups);
 264             groupMap = new GroupMap(groupfile);
 265             int error = groupMap->readMap();
 266             if (error == 1) { delete groupMap; return 0; }
 267
 268             if (m->control_pressed) { delete groupMap; return 0; }
 269
 270             if (Groups.size() == 0) {
 271                 Groups = groupMap->getNamesOfGroups();
 272
 273                 //make string for outputfile name
 274                 userGroups = "unique.";
 275                 for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 276                 userGroups = userGroups.substr(0, userGroups.length()-1);
 277             }else{
 278                 //sanity check for group names
 279                 SharedUtil util;
 280                 vector<string> namesOfGroups = groupMap->getNamesOfGroups();
 281                 util.setGroups(Groups, namesOfGroups);
 282                 groupMap->setNamesOfGroups(namesOfGroups);
 283             }
 284
 285             //put groups in map to find easier
 286             for(int i = 0; i < Groups.size(); i++) {
 287                 groupFinder[Groups[i]] = Groups[i];
 288             }
 289
 290             if (fastafile != "") {
 291                 ifstream inFasta;
 292                 m->openInputFile(fastafile, inFasta);
 293
 294                 while(!inFasta.eof()) {
 295                     if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
 296
 297                     Sequence seq(inFasta); m->gobble(inFasta);
 298                     if (seq.getName() != "") {  seqs.push_back(seq);   }
 299                 }
 300                 inFasta.close();
 301             }
 302
 303             ListVector* lastlist = NULL;
 304             string lastLabel = "";
 305
 306             //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 307             set<string> processedLabels;
 308             set<string> userLabels = labels;
 309
 310             ifstream in;
 311             m->openInputFile(listfile, in);
 312
 313             //as long as you are not at the end of the file or done wih the lines you want
 314             while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
 315
 316                 if (m->control_pressed) {
 317                     if (lastlist != NULL) {             delete lastlist;        }
 318                     for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]); }  outputTypes.clear();
 319                     delete groupMap; return 0;
 320                 }
 321
 322                 list = new ListVector(in);
 323
 324                 if(allLines == 1 || labels.count(list->getLabel()) == 1){
 325                     m->mothurOut(list->getLabel());
 326                     process(list);
 327
 328                     processedLabels.insert(list->getLabel());
 329                     userLabels.erase(list->getLabel());
 330                 }
 331
 332                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 333                         string saveLabel = list->getLabel();
 334
 335                         m->mothurOut(lastlist->getLabel());
 336                         process(lastlist);
 337
 338                         processedLabels.insert(lastlist->getLabel());
 339                         userLabels.erase(lastlist->getLabel());
 340
 341                         //restore real lastlabel to save below
 342                         list->setLabel(saveLabel);
 343                 }
 344
 345                 lastLabel = list->getLabel();
 346
 347                 if (lastlist != NULL) {         delete lastlist;        }
 348                 lastlist = list;
 349             }
 350
 351             in.close();
 352
 353             //output error messages about any remaining user labels
 354             set<string>::iterator it;
 355             bool needToRun = false;
 356             for (it = userLabels.begin(); it != userLabels.end(); it++) {
 357                 m->mothurOut("Your file does not include the label " + *it);
 358                 if (processedLabels.count(lastLabel) != 1) {
 359                     m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 360                     needToRun = true;
 361                 }else {
 362                     m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 363                 }
 364             }
 365
 366             //run last label if you need to
 367             if (needToRun == true)  {
 368                     m->mothurOut(lastlist->getLabel());
 369                     process(lastlist);
 370
 371                     processedLabels.insert(lastlist->getLabel());
 372                     userLabels.erase(lastlist->getLabel());
 373             }
 374
 375
 376             //reset groups parameter
 377             m->clearGroups();
 378
 379             if (lastlist != NULL) {             delete lastlist;        }
 380
 381             if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); }  delete groupMap; return 0; }
 382                 }
 383                 //set fasta file as new current fastafile
 384                 string current = "";
 385                 itTypes = outputTypes.find("fasta");
 386                 if (itTypes != outputTypes.end()) {
 387                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 388                 }
 389
 390                 if (output == "accnos") {
 391                         itTypes = outputTypes.find("accnos");
 392                         if (itTypes != outputTypes.end()) {
 393                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 394                         }
 395                 }
 396
 397                 m->mothurOutEndLine();
 398                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 399                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 400                 m->mothurOutEndLine();
 401
 402
 403                 return 0;
 404         }
 405
 406         catch(exception& e) {
 407                 m->errorOut(e, "GetSharedOTUCommand", "execute");
 408                 exit(1);
 409         }
 410 }
 411 /***********************************************************/
 412 int GetSharedOTUCommand::process(ListVector* shared) {
 413         try {
 414
 415                 map<string, string> fastaMap;
 416
 417                 ofstream outNames;
 418                 string outputFileNames;
 419
 420                 if (outputDir == "") { outputDir += m->hasPath(listfile); }
 421         map<string, string> variables;
 422         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
 423         variables["[distance]"] = shared->getLabel();
 424         variables["[group]"] = userGroups;
 425                 if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
 426                 else { outputFileNames = getOutputFileName("accnos", variables); }
 427
 428                 m->openOutputFile(outputFileNames, outNames);
 429
 430                 bool wroteSomething = false;
 431                 int num = 0;
 432
 433                 //go through each bin, find out if shared
 434                 for (int i = 0; i < shared->getNumBins(); i++) {
 435                         if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
 436
 437                         bool uniqueOTU = true;
 438
 439                         map<string, int> atLeastOne;
 440                         for (int f = 0; f < Groups.size(); f++) {
 441                                 atLeastOne[Groups[f]] = 0;
 442                         }
 443
 444                         vector<string> namesOfSeqsInThisBin;
 445
 446                         string names = shared->get(i);
 447             vector<string> binNames;
 448             m->splitAtComma(names, binNames);
 449                         for(int j = 0; j < binNames.size(); j++) {
 450                                 string name = binNames[j];
 451
 452                                 //find group
 453                                 string seqGroup = groupMap->getGroup(name);
 454                                 if (output != "accnos") {
 455                                         namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
 456                                 }else {  namesOfSeqsInThisBin.push_back(name);  }
 457
 458                                 if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 459
 460                                 //is this seq in one of hte groups we care about
 461                                 it = groupFinder.find(seqGroup);
 462                                 if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 463                                 else {  atLeastOne[seqGroup]++;  }
 464                         }
 465
 466                         //make sure you have at least one seq from each group you want
 467                         bool sharedByAll = true;
 468                         map<string, int>::iterator it2;
 469                         for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
 470                                 if (it2->second == 0) {  sharedByAll = false;   }
 471                         }
 472
 473                         //if the user wants unique bins and this is unique then print
 474                         //or this the user wants shared bins and this bin is shared then print
 475                         if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
 476
 477                                 wroteSomething = true;
 478                                 num++;
 479
 480                                 //output list of names
 481                                 for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
 482                                         outNames << namesOfSeqsInThisBin[j] << endl;
 483
 484                                         if (fastafile != "") {
 485                                                 if (output != "accnos") {
 486                                                         string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
 487                                                         seqName = seqName.substr(0,seqName.find_last_of('|'));
 488                                                         fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
 489                                                 }else {
 490                                                         fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
 491                                                 }
 492                                         }
 493                                 }
 494                         }
 495                 }
 496
 497                 outNames.close();
 498
 499                 if (!wroteSomething) {
 500                         m->mothurRemove(outputFileNames);
 501                         string outputString = "\t" + toString(num) + " - No otus shared by groups";
 502
 503                         string groupString = "";
 504                         for (int h = 0; h < Groups.size(); h++) {
 505                                 groupString += "  " + Groups[h];
 506                         }
 507
 508                         outputString += groupString + ".";
 509                         m->mothurOut(outputString); m->mothurOutEndLine();
 510                 }else {
 511                         m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
 512                         outputNames.push_back(outputFileNames);
 513                         if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
 514                         else { outputTypes["accnos"].push_back(outputFileNames); }
 515                 }
 516
 517                 //if fasta file provided output new fasta file
 518                 if ((fastafile != "") && wroteSomething) {
 519                         if (outputDir == "") { outputDir += m->hasPath(fastafile); }
 520             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
 521                         string outputFileFasta = getOutputFileName("fasta", variables);
 522                         ofstream outFasta;
 523                         m->openOutputFile(outputFileFasta, outFasta);
 524                         outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
 525
 526                         for (int k = 0; k < seqs.size(); k++) {
 527                                 if (m->control_pressed) { outFasta.close(); return 0; }
 528
 529                                 //if this is a sequence we want, output it
 530                                 it = fastaMap.find(seqs[k].getName());
 531                                 if (it != fastaMap.end()) {
 532
 533                                         if (output != "accnos") {
 534                                                 outFasta << ">" << it->second << endl;
 535                                         }else {
 536                                                 outFasta << ">" << it->first << endl;
 537                                         }
 538
 539                                         outFasta << seqs[k].getAligned() << endl;
 540                                 }
 541                         }
 542
 543                         outFasta.close();
 544                 }
 545
 546                 return 0;
 547
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "GetSharedOTUCommand", "process");
 551                 exit(1);
 552         }
 553 }
 554 /***********************************************************/
 555 int GetSharedOTUCommand::runShared() {
 556         try {
 557         InputData input(sharedfile, "sharedfile");
 558                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 559                 string lastLabel = lookup[0]->getLabel();
 560
 561         if (Groups.size() == 0) {
 562             Groups = m->getGroups();
 563
 564             //make string for outputfile name
 565             userGroups = "unique.";
 566             for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 567             userGroups = userGroups.substr(0, userGroups.length()-1);
 568         }else {
 569             //sanity check for group names
 570             SharedUtil util;
 571             vector<string> allGroups = m->getAllGroups();
 572             util.setGroups(Groups, allGroups);
 573         }
 574
 575         //put groups in map to find easier
 576         for(int i = 0; i < Groups.size(); i++) {
 577             groupFinder[Groups[i]] = Groups[i];
 578         }
 579
 580                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 581                 set<string> processedLabels;
 582                 set<string> userLabels = labels;
 583
 584                 //as long as you are not at the end of the file or done wih the lines you want
 585                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 586                         if (m->control_pressed) {
 587                 outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); }
 588                 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0;
 589                         }
 590
 591
 592                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 593                                 m->mothurOut(lookup[0]->getLabel());
 594                                 process(lookup);
 595
 596                                 processedLabels.insert(lookup[0]->getLabel());
 597                                 userLabels.erase(lookup[0]->getLabel());
 598                         }
 599
 600                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 601                 string saveLabel = lookup[0]->getLabel();
 602
 603                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 604                 lookup = input.getSharedRAbundVectors(lastLabel);
 605
 606                 m->mothurOut(lookup[0]->getLabel());
 607                 process(lookup);
 608
 609                 processedLabels.insert(lookup[0]->getLabel());
 610                 userLabels.erase(lookup[0]->getLabel());
 611
 612                 //restore real lastlabel to save below
 613                 lookup[0]->setLabel(saveLabel);
 614                         }
 615
 616                         lastLabel = lookup[0]->getLabel();
 617
 618                         //get next line to process
 619                         //prevent memory leak
 620                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 621                         lookup = input.getSharedRAbundVectors();
 622                 }
 623
 624                 if (m->control_pressed) {
 625             outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
 626             for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0;
 627         }
 628
 629                 //output error messages about any remaining user labels
 630                 set<string>::iterator it;
 631                 bool needToRun = false;
 632                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 633                         m->mothurOut("Your file does not include the label " + *it);
 634                         if (processedLabels.count(lastLabel) != 1) {
 635                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 636                                 needToRun = true;
 637                         }else {
 638                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 639                         }
 640                 }
 641
 642                 //run last label if you need to
 643                 if (needToRun == true)  {
 644             for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) { delete lookup[i];       } }
 645             lookup = input.getSharedRAbundVectors(lastLabel);
 646
 647             m->mothurOut(lookup[0]->getLabel());
 648             process(lookup);
 649             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 650                 }
 651
 652                 //reset groups parameter
 653                 m->clearGroups();
 654
 655                 return 0;
 656
 657     }
 658         catch(exception& e) {
 659                 m->errorOut(e, "GetSharedOTUCommand", "runShared");
 660                 exit(1);
 661         }
 662 }
 663 /***********************************************************/
 664 int GetSharedOTUCommand::process(vector<SharedRAbundVector*>& lookup) {
 665         try {
 666
 667                 string outputFileNames;
 668                 if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
 669         map<string, string> variables;
 670         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 671         variables["[distance]"] = lookup[0]->getLabel();
 672         variables["[group]"] = userGroups;
 673                 if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
 674                 else { outputFileNames = getOutputFileName("accnos", variables); }
 675
 676         ofstream outNames;
 677                 m->openOutputFile(outputFileNames, outNames);
 678
 679                 bool wroteSomething = false;
 680                 int num = 0;
 681
 682                 //go through each bin, find out if shared
 683                 for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 684                         if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
 685
 686                         bool uniqueOTU = true;
 687                         map<string, int> atLeastOne;
 688                         for (int f = 0; f < Groups.size(); f++) {  atLeastOne[Groups[f]] = 0;  }
 689
 690                         set<string> namesOfGroupsInThisBin;
 691
 692                         for(int j = 0; j < lookup.size(); j++) {
 693                                 string seqGroup = lookup[j]->getGroup();
 694                 string name = m->currentBinLabels[i];
 695
 696                 if (lookup[j]->getAbundance(i) != 0) {
 697                     if (output != "accnos") {
 698                         namesOfGroupsInThisBin.insert(name + "|" + seqGroup + "|" + toString(lookup[j]->getAbundance(i)));
 699                     }else {  namesOfGroupsInThisBin.insert(name);       }
 700
 701                     //is this seq in one of the groups we care about
 702                     it = groupFinder.find(seqGroup);
 703                     if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have sequences from a group you don't want
 704                     else {  atLeastOne[seqGroup]++;  }
 705                                 }
 706                         }
 707
 708                         //make sure you have at least one seq from each group you want
 709                         bool sharedByAll = true;
 710                         map<string, int>::iterator it2;
 711                         for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
 712                                 if (it2->second == 0) {  sharedByAll = false;   }
 713                         }
 714
 715                         //if the user wants unique bins and this is unique then print
 716                         //or this the user wants shared bins and this bin is shared then print
 717                         if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
 718
 719                                 wroteSomething = true;
 720                                 num++;
 721
 722                                 //output list of names
 723                                 for (set<string>::iterator itNames = namesOfGroupsInThisBin.begin(); itNames != namesOfGroupsInThisBin.end(); itNames++) {
 724                                         outNames << (*itNames) << endl;
 725                                 }
 726                         }
 727                 }
 728                 outNames.close();
 729
 730                 if (!wroteSomething) {
 731                         m->mothurRemove(outputFileNames);
 732                         string outputString = "\t" + toString(num) + " - No otus shared by groups";
 733
 734                         string groupString = "";
 735                         for (int h = 0; h < Groups.size(); h++) {
 736                                 groupString += "  " + Groups[h];
 737                         }
 738
 739                         outputString += groupString + ".";
 740                         m->mothurOut(outputString); m->mothurOutEndLine();
 741                 }else {
 742                         m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
 743                         outputNames.push_back(outputFileNames);
 744                         if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
 745                         else { outputTypes["accnos"].push_back(outputFileNames); }
 746                 }
 747
 748                 return 0;
 749         }
 750         catch(exception& e) {
 751                 m->errorOut(e, "GetSharedOTUCommand", "process");
 752                 exit(1);
 753         }
 754 }
 755
 756 //**********************************************************************************************************************