createdatabasecommand.cpp

   1 //
   2 //  createdatabasecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 3/28/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "createdatabasecommand.h"
  10 #include "inputdata.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> CreateDatabaseCommand::setParameters(){
  14         try {
  15                 CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  16                 CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
  17                 CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
  18                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  20                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "CreateDatabaseCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string CreateDatabaseCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The create.database command reads a listfile, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
  38                 helpString += "The create.database command parameters are repfasta, list, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required.\n";
  39         helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  40         helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
  41         helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile).\n";
  42         helpString += "The group file is optional and will just give you the abundance breakdown by group.\n";
  43         helpString += "The label parameter allows you to specify a label to be used from your listfile.\n";
  44         helpString += "NOTE: Make SURE the repfasta, repnames and contaxonomy are for the same label as the listfile.\n";
  45         helpString += "The create.database command should be in the following format: \n";
  46                 helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
  47                 helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
  48                 helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string CreateDatabaseCommand::getOutputFileNameTag(string type, string inputName=""){
  58         try {
  59         string outputFileName = "";
  60                 map<string, vector<string> >::iterator it;
  61
  62         //is this a type this command creates
  63         it = outputTypes.find(type);
  64         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  65         else {
  66             if (type == "database") {  outputFileName =  "database"; }
  67             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  68         }
  69         return outputFileName;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "CreateDatabaseCommand", "getOutputFileNameTag");
  73                 exit(1);
  74         }
  75 }
  76
  77 //**********************************************************************************************************************
  78 CreateDatabaseCommand::CreateDatabaseCommand(){
  79         try {
  80                 abort = true; calledHelp = true;
  81                 setParameters();
  82                 vector<string> tempOutNames;
  83                 outputTypes["database"] = tempOutNames;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
  87                 exit(1);
  88         }
  89 }
  90
  91 //**********************************************************************************************************************
  92 CreateDatabaseCommand::CreateDatabaseCommand(string option)  {
  93         try{
  94                 abort = false; calledHelp = false;
  95
  96                 //allow user to run help
  97                 if (option == "help") {
  98                         help(); abort = true; calledHelp = true;
  99                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 100                 else {
 101                         vector<string> myArray = setParameters();
 102
 103                         OptionParser parser(option);
 104                         map<string, string> parameters = parser.getParameters();
 105
 106                         ValidParameters validParameter;
 107                         map<string, string>::iterator it;
 108
 109                         //check to make sure all parameters are valid for command
 110                         for (it = parameters.begin(); it != parameters.end(); it++) {
 111                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 112                         }
 113
 114                         //initialize outputTypes
 115                         vector<string> tempOutNames;
 116                         outputTypes["database"] = tempOutNames;
 117
 118                         //if the user changes the input directory command factory will send this info to us in the output parameter
 119                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 120                         if (inputDir == "not found"){   inputDir = "";          }
 121                         else {
 122                                 string path;
 123                                 it = parameters.find("list");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 129                                 }
 130
 131                                 it = parameters.find("repname");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["repname"] = inputDir + it->second;          }
 137                                 }
 138
 139                                 it = parameters.find("contaxonomy");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 145                                 }
 146
 147                                 it = parameters.find("repfasta");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["repfasta"] = inputDir + it->second;         }
 153                                 }
 154
 155                                 it = parameters.find("group");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 161                                 }
 162                         }
 163
 164
 165                         //if the user changes the output directory command factory will send this info to us in the output parameter
 166                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 167
 168                         //check for required parameters
 169                         listfile = validParameter.validFile(parameters, "list", true);
 170                         if (listfile == "not found") {
 171                                 //if there is a current list file, use it
 172                                 listfile = m->getListFile();
 173                                 if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 174                                 else {  m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 175                         }
 176                         else if (listfile == "not open") { abort = true; }
 177                         else { m->setListFile(listfile); }
 178
 179                         contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 180                         if (contaxonomyfile == "not found") {  //if there is a current list file, use it
 181                contaxonomyfile = "";  m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 182                         }
 183                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 184
 185             repfastafile = validParameter.validFile(parameters, "repfasta", true);
 186                         if (repfastafile == "not found") {  //if there is a current list file, use it
 187                 repfastafile = "";  m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 188                         }
 189                         else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
 190
 191             repnamesfile = validParameter.validFile(parameters, "repname", true);
 192                         if (repnamesfile == "not found") {  //if there is a current list file, use it
 193                 repnamesfile = "";  m->mothurOut("The repnames parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 194                         }
 195                         else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
 196
 197                         groupfile = validParameter.validFile(parameters, "group", true);
 198                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 199                         else if (groupfile == "not found") { groupfile = ""; }
 200                         else { m->setGroupFile(groupfile); }
 201
 202                         //check for optional parameter and set defaults
 203                         // ...at some point should added some additional type checking...
 204             label = validParameter.validFile(parameters, "label", false);
 205                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
 206         }
 207         }
 208         catch(exception& e) {
 209                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
 210                 exit(1);
 211         }
 212 }
 213 //**********************************************************************************************************************
 214 int CreateDatabaseCommand::execute(){
 215         try {
 216
 217                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 218
 219         //taxonomies holds the taxonomy info for each Otu
 220         //classifyOtuSizes holds the size info of each Otu to help with error checking
 221         vector<string> taxonomies;
 222         vector<int> classifyOtuSizes = readTax(taxonomies);
 223
 224         if (m->control_pressed) { return 0; }
 225
 226         vector<Sequence> seqs;
 227         vector<int> repOtusSizes = readFasta(seqs);
 228
 229         if (m->control_pressed) { return 0; }
 230
 231         //names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
 232         map<string, string> repNames;
 233         int numUniqueNamesFile = m->readNames(repnamesfile, repNames);
 234
 235         //are there the same number of otus in the fasta and name files
 236         if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file.  These should match.\n"); m->control_pressed = true; }
 237
 238         if (m->control_pressed) { return 0; }
 239
 240         //are there the same number of OTUs in the tax and fasta file
 241         if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file.  These should match.\n"); m->control_pressed = true; }
 242
 243         if (m->control_pressed) { return 0; }
 244
 245         //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
 246         for (int i = 0; i < classifyOtuSizes.size(); i++) {
 247             if (classifyOtuSizes[i] != repOtusSizes[i]) {
 248                m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ".  These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;
 249             }
 250         }
 251
 252         if (m->control_pressed) { return 0; }
 253
 254         //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
 255         ListVector* list = getList();
 256
 257         if (m->control_pressed) { delete list; return 0; }
 258
 259         GroupMap* groupmap = NULL;
 260         if (groupfile != "") {
 261                         groupmap = new GroupMap(groupfile);
 262                         groupmap->readMap();
 263                 }
 264
 265         if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
 266
 267         if (outputDir == "") { outputDir += m->hasPath(listfile); }
 268         string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database");
 269         outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
 270
 271         ofstream out;
 272         m->openOutputFile(outputFileName, out);
 273
 274         string header = "OTUNumber\tAbundance\t";
 275         if (groupfile != "") {
 276             header = "OTUNumber\t";
 277             for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
 278         }
 279         header += "repSeqName\trepSeq\tOTUConTaxonomy";
 280         out << header << endl;
 281
 282         for (int i = 0; i < list->getNumBins(); i++) {
 283
 284             if (m->control_pressed) { break; }
 285
 286             out << (i+1) << '\t';
 287
 288             vector<string> binNames;
 289             string bin = list->get(i);
 290
 291             map<string, string>::iterator it = repNames.find(bin);
 292             if (it == repNames.end()) {
 293                 m->mothurOut("[ERROR: OTU " + toString(i+1) + " is not in the repnames file. Make sure you are using files for the same distance.\n"); m->control_pressed = true;   break;
 294             }
 295
 296             m->splitAtComma(bin, binNames);
 297
 298             //sanity check
 299             if (binNames.size() != classifyOtuSizes[i]) {
 300                  m->mothurOut("[ERROR: OTU " + toString(i+1) + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[i]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true;   break;
 301             }
 302
 303             //output abundances
 304             if (groupfile != "") {
 305                 string groupAbunds = "";
 306                 map<string, int> counts;
 307                 //initialize counts to 0
 308                 for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
 309
 310                 //find abundances by group
 311                 bool error = false;
 312                 for (int j = 0; j < binNames.size(); j++) {
 313                     string group = groupmap->getGroup(binNames[j]);
 314                     if (group == "not found") {
 315                         m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
 316                         error = true;
 317                     }else { counts[group]++; }
 318                 }
 319
 320                 //output counts
 321                 for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t';  }
 322
 323                 if (error) { m->control_pressed = true; }
 324             }else { out << binNames.size() << '\t'; }
 325
 326             //output repSeq
 327             out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
 328         }
 329         out.close();
 330
 331         delete list;
 332         if (groupfile != "") { delete groupmap; }
 333
 334         if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 335
 336         m->mothurOutEndLine();
 337                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 338                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 339                 m->mothurOutEndLine();
 340
 341         return 0;
 342
 343     }
 344         catch(exception& e) {
 345                 m->errorOut(e, "CreateDatabaseCommand", "execute");
 346                 exit(1);
 347         }
 348 }
 349 //**********************************************************************************************************************
 350 vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies){
 351         try {
 352
 353         vector<int> sizes;
 354
 355         ifstream in;
 356         m->openInputFile(contaxonomyfile, in);
 357
 358         //read headers
 359         m->getline(in);
 360
 361         while (!in.eof()) {
 362
 363             if (m->control_pressed) { break; }
 364
 365             string otu = ""; string tax = "unknown";
 366             int size = 0;
 367
 368             in >> otu >> size >> tax; m->gobble(in);
 369
 370             sizes.push_back(size);
 371             taxonomies.push_back(tax);
 372         }
 373         in.close();
 374
 375         return sizes;
 376     }
 377         catch(exception& e) {
 378                 m->errorOut(e, "CreateDatabaseCommand", "readTax");
 379                 exit(1);
 380         }
 381 }
 382 //**********************************************************************************************************************
 383 vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 384         try {
 385
 386         vector<int> sizes;
 387
 388         ifstream in;
 389         m->openInputFile(repfastafile, in);
 390
 391         while (!in.eof()) {
 392
 393             if (m->control_pressed) { break; }
 394
 395             string binInfo;
 396             Sequence seq(in, binInfo, true);  m->gobble(in);
 397
 398             //the binInfo should look like - binNumber|size ie. 1|200 if it is binNumber|size|group then the user gave us the wrong repfasta file
 399             vector<string> info;
 400             m->splitAtChar(binInfo, info, '|');
 401             if (info.size() != 2) { m->mothurOut("[ERROR]: your repfasta file is not the right format.  The create database command is designed to be used with the output from get.oturep.  When running get.oturep you can not use a group file, because mothur is only expecting one representative sequence per OTU and when you use a group file with get.oturep a representative is found for each group.\n");  m->control_pressed = true; break;}
 402
 403             int size = 0;
 404             m->mothurConvert(info[1], size);
 405
 406             sizes.push_back(size);
 407             seqs.push_back(seq);
 408         }
 409         in.close();
 410
 411         return sizes;
 412     }
 413         catch(exception& e) {
 414                 m->errorOut(e, "CreateDatabaseCommand", "readFasta");
 415                 exit(1);
 416         }
 417 }
 418 //**********************************************************************************************************************
 419 ListVector* CreateDatabaseCommand::getList(){
 420         try {
 421                 InputData* input = new InputData(listfile, "list");
 422                 ListVector* list = input->getListVector();
 423                 string lastLabel = list->getLabel();
 424
 425                 if (label == "") { label = lastLabel; delete input; return list; }
 426
 427                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 428                 set<string> labels; labels.insert(label);
 429                 set<string> processedLabels;
 430                 set<string> userLabels = labels;
 431
 432                 //as long as you are not at the end of the file or done wih the lines you want
 433                 while((list != NULL) && (userLabels.size() != 0)) {
 434                         if (m->control_pressed) {  delete input; return list;  }
 435
 436                         if(labels.count(list->getLabel()) == 1){
 437                                 processedLabels.insert(list->getLabel());
 438                                 userLabels.erase(list->getLabel());
 439                                 break;
 440                         }
 441
 442                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 443                                 string saveLabel = list->getLabel();
 444
 445                                 delete list;
 446                                 list = input->getListVector(lastLabel);
 447
 448                                 processedLabels.insert(list->getLabel());
 449                                 userLabels.erase(list->getLabel());
 450
 451                                 //restore real lastlabel to save below
 452                                 list->setLabel(saveLabel);
 453                                 break;
 454                         }
 455
 456                         lastLabel = list->getLabel();
 457
 458                         //get next line to process
 459                         //prevent memory leak
 460                         delete list;
 461                         list = input->getListVector();
 462                 }
 463
 464
 465                 if (m->control_pressed) { delete input; return list;  }
 466
 467                 //output error messages about any remaining user labels
 468                 set<string>::iterator it;
 469                 bool needToRun = false;
 470                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 471                         m->mothurOut("Your file does not include the label " + *it);
 472                         if (processedLabels.count(lastLabel) != 1) {
 473                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 474                                 needToRun = true;
 475                         }else {
 476                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 477                         }
 478                 }
 479
 480                 //run last label if you need to
 481                 if (needToRun == true)  {
 482                         delete list;
 483                         list = input->getListVector(lastLabel);
 484                 }
 485
 486                 delete input;
 487
 488         return list;
 489     }
 490         catch(exception& e) {
 491                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 492                 exit(1);
 493         }
 494 }
 495 //**********************************************************************************************************************
 496
 497