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 CreateDatabaseCommand::CreateDatabaseCommand(){
  58         try {
  59                 abort = true; calledHelp = true;
  60                 setParameters();
  61                 vector<string> tempOutNames;
  62                 outputTypes["database"] = tempOutNames;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
  66                 exit(1);
  67         }
  68 }
  69
  70 //**********************************************************************************************************************
  71 CreateDatabaseCommand::CreateDatabaseCommand(string option)  {
  72         try{
  73                 abort = false; calledHelp = false;
  74
  75                 //allow user to run help
  76                 if (option == "help") {
  77                         help(); abort = true; calledHelp = true;
  78                 }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  79                 else {
  80                         vector<string> myArray = setParameters();
  81
  82                         OptionParser parser(option);
  83                         map<string, string> parameters = parser.getParameters();
  84
  85                         ValidParameters validParameter;
  86                         map<string, string>::iterator it;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (it = parameters.begin(); it != parameters.end(); it++) {
  90                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["database"] = tempOutNames;
  96
  97                         //if the user changes the input directory command factory will send this info to us in the output parameter
  98                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  99                         if (inputDir == "not found"){   inputDir = "";          }
 100                         else {
 101                                 string path;
 102                                 it = parameters.find("list");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 108                                 }
 109
 110                                 it = parameters.find("repname");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["repname"] = inputDir + it->second;          }
 116                                 }
 117
 118                                 it = parameters.find("contaxonomy");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["contaxonomy"] = inputDir + it->second;              }
 124                                 }
 125
 126                                 it = parameters.find("repfasta");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["repfasta"] = inputDir + it->second;         }
 132                                 }
 133
 134                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 140                                 }
 141                         }
 142
 143
 144                         //if the user changes the output directory command factory will send this info to us in the output parameter
 145                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 146
 147                         //check for required parameters
 148                         listfile = validParameter.validFile(parameters, "list", true);
 149                         if (listfile == "not found") {
 150                                 //if there is a current list file, use it
 151                                 listfile = m->getListFile();
 152                                 if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 153                                 else {  m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 154                         }
 155                         else if (listfile == "not open") { abort = true; }
 156                         else { m->setListFile(listfile); }
 157
 158                         contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
 159                         if (contaxonomyfile == "not found") {  //if there is a current list file, use it
 160                contaxonomyfile = "";  m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 161                         }
 162                         else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
 163
 164             repfastafile = validParameter.validFile(parameters, "repfasta", true);
 165                         if (repfastafile == "not found") {  //if there is a current list file, use it
 166                 repfastafile = "";  m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 167                         }
 168                         else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
 169
 170             repnamesfile = validParameter.validFile(parameters, "repname", true);
 171                         if (repnamesfile == "not found") {  //if there is a current list file, use it
 172                 repnamesfile = "";  m->mothurOut("The repnames parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
 173                         }
 174                         else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
 175
 176                         groupfile = validParameter.validFile(parameters, "group", true);
 177                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 178                         else if (groupfile == "not found") { groupfile = ""; }
 179                         else { m->setGroupFile(groupfile); }
 180
 181                         //check for optional parameter and set defaults
 182                         // ...at some point should added some additional type checking...
 183             label = validParameter.validFile(parameters, "label", false);
 184                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
 185         }
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
 189                 exit(1);
 190         }
 191 }
 192 //**********************************************************************************************************************
 193 int CreateDatabaseCommand::execute(){
 194         try {
 195
 196                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 197
 198         //taxonomies holds the taxonomy info for each Otu
 199         //classifyOtuSizes holds the size info of each Otu to help with error checking
 200         vector<string> taxonomies;
 201         vector<int> classifyOtuSizes = readTax(taxonomies);
 202
 203         if (m->control_pressed) { return 0; }
 204
 205         vector<Sequence> seqs;
 206         vector<int> repOtusSizes = readFasta(seqs);
 207
 208         if (m->control_pressed) { return 0; }
 209
 210         //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.
 211         map<string, string> repNames;
 212         int numUniqueNamesFile = readNames(repNames);
 213
 214         //are there the same number of otus in the fasta and name files
 215         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; }
 216
 217         if (m->control_pressed) { return 0; }
 218
 219         //are there the same number of OTUs in the tax and fasta file
 220         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; }
 221
 222         if (m->control_pressed) { return 0; }
 223
 224         //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
 225         for (int i = 0; i < classifyOtuSizes.size(); i++) {
 226             if (classifyOtuSizes[i] != repOtusSizes[i]) {
 227                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;
 228             }
 229         }
 230
 231         if (m->control_pressed) { return 0; }
 232
 233         //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
 234         ListVector* list = getList();
 235
 236         if (m->control_pressed) { delete list; return 0; }
 237
 238         GroupMap* groupmap = NULL;
 239         if (groupfile != "") {
 240                         groupmap = new GroupMap(groupfile);
 241                         groupmap->readMap();
 242                 }
 243
 244         if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
 245
 246         if (outputDir == "") { outputDir += m->hasPath(listfile); }
 247         string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + "database";
 248         outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
 249
 250         ofstream out;
 251         m->openOutputFile(outputFileName, out);
 252
 253         string header = "OTUNumber\tAbundance\t";
 254         if (groupfile != "") {
 255             header = "OTUNumber\t";
 256             for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
 257         }
 258         header += "repSeqName\trepSeq\tOTUConTaxonomy";
 259         out << header << endl;
 260
 261         for (int i = 0; i < list->getNumBins(); i++) {
 262
 263             if (m->control_pressed) { break; }
 264
 265             out << (i+1) << '\t';
 266
 267             vector<string> binNames;
 268             string bin = list->get(i);
 269
 270             map<string, string>::iterator it = repNames.find(bin);
 271             if (it == repNames.end()) {
 272                 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;
 273             }
 274
 275             m->splitAtComma(bin, binNames);
 276
 277             //sanity check
 278             if (binNames.size() != classifyOtuSizes[i]) {
 279                  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;
 280             }
 281
 282             //output abundances
 283             if (groupfile != "") {
 284                 string groupAbunds = "";
 285                 map<string, int> counts;
 286                 //initialize counts to 0
 287                 for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
 288
 289                 //find abundances by group
 290                 bool error = false;
 291                 for (int j = 0; j < binNames.size(); j++) {
 292                     string group = groupmap->getGroup(binNames[j]);
 293                     if (group == "not found") {
 294                         m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
 295                         error = true;
 296                     }else { counts[group]++; }
 297                 }
 298
 299                 //output counts
 300                 for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t';  }
 301
 302                 if (error) { m->control_pressed = true; }
 303             }else { out << binNames.size() << '\t'; }
 304
 305             //output repSeq
 306             out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
 307         }
 308         out.close();
 309
 310         delete list;
 311         if (groupfile != "") { delete groupmap; }
 312
 313         if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 314
 315         m->mothurOutEndLine();
 316                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 317                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 318                 m->mothurOutEndLine();
 319
 320         return 0;
 321
 322     }
 323         catch(exception& e) {
 324                 m->errorOut(e, "CreateDatabaseCommand", "execute");
 325                 exit(1);
 326         }
 327 }
 328 //**********************************************************************************************************************
 329 vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies){
 330         try {
 331
 332         vector<int> sizes;
 333
 334         ifstream in;
 335         m->openInputFile(contaxonomyfile, in);
 336
 337         //read headers
 338         m->getline(in);
 339
 340         while (!in.eof()) {
 341
 342             if (m->control_pressed) { break; }
 343
 344             string otu = ""; string tax = "unknown";
 345             int size = 0;
 346
 347             in >> otu >> size >> tax; m->gobble(in);
 348
 349             sizes.push_back(size);
 350             taxonomies.push_back(tax);
 351         }
 352         in.close();
 353
 354         return sizes;
 355     }
 356         catch(exception& e) {
 357                 m->errorOut(e, "CreateDatabaseCommand", "readTax");
 358                 exit(1);
 359         }
 360 }
 361 //**********************************************************************************************************************
 362 vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 363         try {
 364
 365         vector<int> sizes;
 366
 367         ifstream in;
 368         m->openInputFile(repfastafile, in);
 369
 370         while (!in.eof()) {
 371
 372             if (m->control_pressed) { break; }
 373
 374             string binInfo;
 375             Sequence seq(in, binInfo, true);  m->gobble(in);
 376
 377             //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
 378             vector<string> info;
 379             m->splitAtChar(binInfo, info, '|');
 380             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;}
 381
 382             int size = 0;
 383             m->mothurConvert(info[1], size);
 384
 385             sizes.push_back(size);
 386             seqs.push_back(seq);
 387         }
 388         in.close();
 389
 390         return sizes;
 391     }
 392         catch(exception& e) {
 393                 m->errorOut(e, "CreateDatabaseCommand", "readFasta");
 394                 exit(1);
 395         }
 396 }
 397 /**********************************************************************************************************************/
 398 int CreateDatabaseCommand::readNames(map<string, string>& nameMap) {
 399         try {
 400
 401                 //open input file
 402                 ifstream in;
 403                 m->openInputFile(repnamesfile, in);
 404
 405                 while (!in.eof()) {
 406                         if (m->control_pressed) { break; }
 407
 408                         string firstCol, secondCol;
 409                         in >> firstCol >> secondCol; m->gobble(in);
 410
 411                         nameMap[secondCol] = firstCol;
 412                 }
 413                 in.close();
 414
 415                 return nameMap.size();
 416
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "CreateDatabaseCommand", "readNames");
 420                 exit(1);
 421         }
 422 }
 423 //**********************************************************************************************************************
 424 ListVector* CreateDatabaseCommand::getList(){
 425         try {
 426                 InputData* input = new InputData(listfile, "list");
 427                 ListVector* list = input->getListVector();
 428                 string lastLabel = list->getLabel();
 429
 430                 if (label == "") { label = lastLabel; delete input; return list; }
 431
 432                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 433                 set<string> labels; labels.insert(label);
 434                 set<string> processedLabels;
 435                 set<string> userLabels = labels;
 436
 437                 //as long as you are not at the end of the file or done wih the lines you want
 438                 while((list != NULL) && (userLabels.size() != 0)) {
 439                         if (m->control_pressed) {  delete input; return list;  }
 440
 441                         if(labels.count(list->getLabel()) == 1){
 442                                 processedLabels.insert(list->getLabel());
 443                                 userLabels.erase(list->getLabel());
 444                                 break;
 445                         }
 446
 447                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 448                                 string saveLabel = list->getLabel();
 449
 450                                 delete list;
 451                                 list = input->getListVector(lastLabel);
 452
 453                                 processedLabels.insert(list->getLabel());
 454                                 userLabels.erase(list->getLabel());
 455
 456                                 //restore real lastlabel to save below
 457                                 list->setLabel(saveLabel);
 458                                 break;
 459                         }
 460
 461                         lastLabel = list->getLabel();
 462
 463                         //get next line to process
 464                         //prevent memory leak
 465                         delete list;
 466                         list = input->getListVector();
 467                 }
 468
 469
 470                 if (m->control_pressed) { delete input; return list;  }
 471
 472                 //output error messages about any remaining user labels
 473                 set<string>::iterator it;
 474                 bool needToRun = false;
 475                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 476                         m->mothurOut("Your file does not include the label " + *it);
 477                         if (processedLabels.count(lastLabel) != 1) {
 478                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 479                                 needToRun = true;
 480                         }else {
 481                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 482                         }
 483                 }
 484
 485                 //run last label if you need to
 486                 if (needToRun == true)  {
 487                         delete list;
 488                         list = input->getListVector(lastLabel);
 489                 }
 490
 491                 delete input;
 492
 493         return list;
 494     }
 495         catch(exception& e) {
 496                 m->errorOut(e, "CreateDatabaseCommand", "getList");
 497                 exit(1);
 498         }
 499 }
 500 //**********************************************************************************************************************
 501
 502