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
  12 //**********************************************************************************************************************
  13 vector<string> GetSharedOTUCommand::setParameters(){
  14         try {
  15                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  16                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
  17                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
  18                 CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
  19                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  20                 CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
  21                 CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "GetSharedOTUCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string GetSharedOTUCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta.  The list and group parameters are required, unless you have valid current files.\n";
  39                 helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
  40                 helpString += "The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
  41                 helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
  42                 helpString += "If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
  43                 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 file.\n";
  44                 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.\n";
  45                 helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
  46                 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";
  47                 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";
  48                 helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
  49                 helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
  50                 helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
  51                 helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
  52                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
  53                 return helpString;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 GetSharedOTUCommand::GetSharedOTUCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["accnos"] = tempOutNames;
  68                 outputTypes["sharedseqs"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
  77         try {
  78
  79                 abort = false; calledHelp = false;
  80                 unique = true;
  81                 allLines = 1;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85
  86                 else {
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string,string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["fasta"] = tempOutNames;
 103                         outputTypes["accnos"] = tempOutNames;
 104                         outputTypes["sharedseqs"] = tempOutNames;
 105
 106                         //if the user changes the output directory command factory will send this info to us in the output parameter
 107                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 108
 109                         //if the user changes the input directory command factory will send this info to us in the output parameter
 110                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 111                         if (inputDir == "not found"){   inputDir = "";          }
 112                         else {
 113                                 string path;
 114                                 it = parameters.find("fasta");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 120                                 }
 121
 122                                 it = parameters.find("list");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 128                                 }
 129
 130                                 it = parameters.find("group");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 136                                 }
 137                         }
 138
 139
 140                         //check for required parameters
 141                         listfile = validParameter.validFile(parameters, "list", true);
 142                         if (listfile == "not open") { abort = true; }
 143                         else if (listfile == "not found") {
 144                                 listfile = m->getListFile();
 145                                 if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 146                                 else {
 147                                         m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
 148                                         abort = true;
 149                                 }
 150                         }else {  format = "list";       }
 151
 152                         groupfile = validParameter.validFile(parameters, "group", true);
 153                         if (groupfile == "not open") { abort = true; }
 154                         else if (groupfile == "not found") {
 155                                 groupfile = m->getGroupFile();
 156                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 157                                 else {
 158                                         m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
 159                                         abort = true;
 160                                 }
 161                         }
 162
 163                         if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
 164
 165                         //check for optional parameter and set defaults
 166                         // ...at some point should added some additional type checking...
 167                         label = validParameter.validFile(parameters, "label", false);
 168                         if (label == "not found") { label = ""; }
 169                         else {
 170                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 171                                 else { allLines = 1;  }
 172                         }
 173
 174                         output = validParameter.validFile(parameters, "output", false);
 175                         if (output == "not found") { output = ""; }
 176                         else if (output == "default") { output = ""; }
 177
 178                         groups = validParameter.validFile(parameters, "unique", false);
 179                         if (groups == "not found") { groups = ""; }
 180                         else {
 181                                 userGroups = "unique." + groups;
 182                                 m->splitAtDash(groups, Groups);
 183                                 m->Groups = Groups;
 184
 185                         }
 186
 187                         groups = validParameter.validFile(parameters, "shared", false);
 188                         if (groups == "not found") { groups = "";  }
 189                         else {
 190                                 userGroups = groups;
 191                                 m->splitAtDash(groups, Groups);
 192                                 m->Groups = Groups;
 193                                 unique = false;
 194                         }
 195
 196                         fastafile = validParameter.validFile(parameters, "fasta", true);
 197                         if (fastafile == "not open") { abort = true; }
 198                         else if (fastafile == "not found") {  fastafile = "";  }
 199
 200                 }
 201
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 int GetSharedOTUCommand::execute(){
 211         try {
 212
 213                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 214
 215                 groupMap = new GroupMap(groupfile);
 216                 int error = groupMap->readMap();
 217                 if (error == 1) { delete groupMap; return 0; }
 218
 219                 if (m->control_pressed) { delete groupMap; return 0; }
 220
 221                 if (Groups.size() == 0) {
 222                         Groups = groupMap->namesOfGroups;
 223
 224                         //make string for outputfile name
 225                         userGroups = "unique.";
 226                         for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 227                         userGroups = userGroups.substr(0, userGroups.length()-1);
 228                 }
 229
 230                 //put groups in map to find easier
 231                 for(int i = 0; i < Groups.size(); i++) {
 232                         groupFinder[Groups[i]] = Groups[i];
 233                 }
 234
 235                 if (fastafile != "") {
 236                         ifstream inFasta;
 237                         m->openInputFile(fastafile, inFasta);
 238
 239                         while(!inFasta.eof()) {
 240                                 if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
 241
 242                                 Sequence seq(inFasta); m->gobble(inFasta);
 243                                 if (seq.getName() != "") {  seqs.push_back(seq);   }
 244                         }
 245                         inFasta.close();
 246                 }
 247
 248                 ListVector* lastlist = NULL;
 249                 string lastLabel = "";
 250
 251                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 252                 set<string> processedLabels;
 253                 set<string> userLabels = labels;
 254
 255                 ifstream in;
 256                 m->openInputFile(listfile, in);
 257
 258                 //as long as you are not at the end of the file or done wih the lines you want
 259                 while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
 260
 261                         if (m->control_pressed) {
 262                                 if (lastlist != NULL) {         delete lastlist;        }
 263                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  outputTypes.clear();
 264                                 delete groupMap; return 0;
 265                         }
 266
 267                         list = new ListVector(in);
 268
 269                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 270                                 m->mothurOut(list->getLabel());
 271                                 process(list);
 272
 273                                 processedLabels.insert(list->getLabel());
 274                                 userLabels.erase(list->getLabel());
 275                         }
 276
 277                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 278                                         string saveLabel = list->getLabel();
 279
 280                                         m->mothurOut(lastlist->getLabel());
 281                                         process(lastlist);
 282
 283                                         processedLabels.insert(lastlist->getLabel());
 284                                         userLabels.erase(lastlist->getLabel());
 285
 286                                         //restore real lastlabel to save below
 287                                         list->setLabel(saveLabel);
 288                         }
 289
 290                         lastLabel = list->getLabel();
 291
 292                         if (lastlist != NULL) {         delete lastlist;        }
 293                         lastlist = list;
 294                 }
 295
 296                 in.close();
 297
 298                 //output error messages about any remaining user labels
 299                 set<string>::iterator it;
 300                 bool needToRun = false;
 301                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 302                         m->mothurOut("Your file does not include the label " + *it);
 303                         if (processedLabels.count(lastLabel) != 1) {
 304                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 305                                 needToRun = true;
 306                         }else {
 307                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 308                         }
 309                 }
 310
 311                 //run last label if you need to
 312                 if (needToRun == true)  {
 313                                 m->mothurOut(lastlist->getLabel());
 314                                 process(lastlist);
 315
 316                                 processedLabels.insert(lastlist->getLabel());
 317                                 userLabels.erase(lastlist->getLabel());
 318                 }
 319
 320
 321                 //reset groups parameter
 322                 m->Groups.clear();
 323
 324                 if (lastlist != NULL) {         delete lastlist;        }
 325
 326                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); }  delete groupMap; return 0; }
 327
 328                 //set fasta file as new current fastafile
 329                 string current = "";
 330                 itTypes = outputTypes.find("fasta");
 331                 if (itTypes != outputTypes.end()) {
 332                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 333                 }
 334
 335                 if (output == "accnos") {
 336                         itTypes = outputTypes.find("accnos");
 337                         if (itTypes != outputTypes.end()) {
 338                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 339                         }
 340                 }
 341
 342                 m->mothurOutEndLine();
 343                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 344                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 345                 m->mothurOutEndLine();
 346
 347
 348                 return 0;
 349         }
 350
 351         catch(exception& e) {
 352                 m->errorOut(e, "GetSharedOTUCommand", "execute");
 353                 exit(1);
 354         }
 355 }
 356 /***********************************************************/
 357 int GetSharedOTUCommand::process(ListVector* shared) {
 358         try {
 359
 360                 map<string, string> fastaMap;
 361
 362                 ofstream outNames;
 363                 string outputFileNames;
 364
 365                 if (outputDir == "") { outputDir += m->hasPath(listfile); }
 366                 if (output != "accnos") {
 367                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
 368                 }else {
 369                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
 370                 }
 371                 m->openOutputFile(outputFileNames, outNames);
 372
 373                 bool wroteSomething = false;
 374                 int num = 0;
 375
 376                 //go through each bin, find out if shared
 377                 for (int i = 0; i < shared->getNumBins(); i++) {
 378                         if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
 379
 380                         bool uniqueOTU = true;
 381
 382                         map<string, int> atLeastOne;
 383                         for (int f = 0; f < Groups.size(); f++) {
 384                                 atLeastOne[Groups[f]] = 0;
 385                         }
 386
 387                         vector<string> namesOfSeqsInThisBin;
 388
 389                         string names = shared->get(i);
 390                         while ((names.find_first_of(',') != -1)) {
 391                                 string name = names.substr(0,names.find_first_of(','));
 392                                 names = names.substr(names.find_first_of(',')+1, names.length());
 393
 394                                 //find group
 395                                 string seqGroup = groupMap->getGroup(name);
 396                                 if (output != "accnos") {
 397                                         namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
 398                                 }else {  namesOfSeqsInThisBin.push_back(name);  }
 399
 400                                 if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 401
 402                                 //is this seq in one of hte groups we care about
 403                                 it = groupFinder.find(seqGroup);
 404                                 if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 405                                 else {  atLeastOne[seqGroup]++;  }
 406                         }
 407
 408                         //get last name
 409                         string seqGroup = groupMap->getGroup(names);
 410                         if (output != "accnos") {
 411                                 namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
 412                         }else {  namesOfSeqsInThisBin.push_back(names); }
 413
 414                         if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 415
 416                         //is this seq in one of hte groups we care about
 417                         it = groupFinder.find(seqGroup);
 418                         if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 419                         else {  atLeastOne[seqGroup]++;  }
 420
 421
 422                         //make sure you have at least one seq from each group you want
 423                         bool sharedByAll = true;
 424                         map<string, int>::iterator it2;
 425                         for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
 426                                 if (it2->second == 0) {  sharedByAll = false;   }
 427                         }
 428
 429                         //if the user wants unique bins and this is unique then print
 430                         //or this the user wants shared bins and this bin is shared then print
 431                         if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
 432
 433                                 wroteSomething = true;
 434                                 num++;
 435
 436                                 //output list of names
 437                                 for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
 438                                         outNames << namesOfSeqsInThisBin[j] << endl;
 439
 440                                         if (fastafile != "") {
 441                                                 if (output != "accnos") {
 442                                                         string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
 443                                                         seqName = seqName.substr(0,seqName.find_last_of('|'));
 444                                                         fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
 445                                                 }else {
 446                                                         fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
 447                                                 }
 448                                         }
 449                                 }
 450                         }
 451                 }
 452
 453                 outNames.close();
 454
 455                 if (!wroteSomething) {
 456                         remove(outputFileNames.c_str());
 457                         string outputString = "\t" + toString(num) + " - No otus shared by groups";
 458
 459                         string groupString = "";
 460                         for (int h = 0; h < Groups.size(); h++) {
 461                                 groupString += "  " + Groups[h];
 462                         }
 463
 464                         outputString += groupString + ".";
 465                         m->mothurOut(outputString); m->mothurOutEndLine();
 466                 }else {
 467                         m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
 468                         outputNames.push_back(outputFileNames);
 469                         if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
 470                         else { outputTypes["accnos"].push_back(outputFileNames); }
 471                 }
 472
 473                 //if fasta file provided output new fasta file
 474                 if ((fastafile != "") && wroteSomething) {
 475                         if (outputDir == "") { outputDir += m->hasPath(fastafile); }
 476                         string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
 477                         ofstream outFasta;
 478                         m->openOutputFile(outputFileFasta, outFasta);
 479                         outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
 480
 481                         for (int k = 0; k < seqs.size(); k++) {
 482                                 if (m->control_pressed) { outFasta.close(); return 0; }
 483
 484                                 //if this is a sequence we want, output it
 485                                 it = fastaMap.find(seqs[k].getName());
 486                                 if (it != fastaMap.end()) {
 487
 488                                         if (output != "accnos") {
 489                                                 outFasta << ">" << it->second << endl;
 490                                         }else {
 491                                                 outFasta << ">" << it->first << endl;
 492                                         }
 493
 494                                         outFasta << seqs[k].getAligned() << endl;
 495                                 }
 496                         }
 497
 498                         outFasta.close();
 499                 }
 500
 501                 return 0;
 502
 503         }
 504         catch(exception& e) {
 505                 m->errorOut(e, "GetSharedOTUCommand", "process");
 506                 exit(1);
 507         }
 508 }
 509
 510 //**********************************************************************************************************************