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";
  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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92
  93                         ValidParameters validParameter;
  94                         map<string,string>::iterator it;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["fasta"] = tempOutNames;
 104                         outputTypes["accnos"] = tempOutNames;
 105                         outputTypes["sharedseqs"] = tempOutNames;
 106
 107                         //if the user changes the output directory command factory will send this info to us in the output parameter
 108                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 112                         if (inputDir == "not found"){   inputDir = "";          }
 113                         else {
 114                                 string path;
 115                                 it = parameters.find("fasta");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 121                                 }
 122
 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("group");
 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["group"] = inputDir + it->second;            }
 137                                 }
 138                         }
 139
 140
 141                         //check for required parameters
 142                         listfile = validParameter.validFile(parameters, "list", true);
 143                         if (listfile == "not open") { abort = true; }
 144                         else if (listfile == "not found") {
 145                                 listfile = m->getListFile();
 146                                 if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 147                                 else {
 148                                         m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
 149                                         abort = true;
 150                                 }
 151                         }else {  format = "list";       }
 152
 153                         groupfile = validParameter.validFile(parameters, "group", true);
 154                         if (groupfile == "not open") { abort = true; }
 155                         else if (groupfile == "not found") {
 156                                 groupfile = m->getGroupFile();
 157                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 158                                 else {
 159                                         m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
 160                                         abort = true;
 161                                 }
 162                         }
 163
 164                         if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
 165
 166                         //check for optional parameter and set defaults
 167                         // ...at some point should added some additional type checking...
 168                         label = validParameter.validFile(parameters, "label", false);
 169                         if (label == "not found") { label = ""; }
 170                         else {
 171                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 172                                 else { allLines = 1;  }
 173                         }
 174
 175                         output = validParameter.validFile(parameters, "output", false);
 176                         if (output == "not found") { output = ""; }
 177                         else if (output == "default") { output = ""; }
 178
 179                         groups = validParameter.validFile(parameters, "unique", false);
 180                         if (groups == "not found") { groups = ""; }
 181                         else {
 182                                 userGroups = "unique." + groups;
 183                                 m->splitAtDash(groups, Groups);
 184                                 m->Groups = Groups;
 185
 186                         }
 187
 188                         groups = validParameter.validFile(parameters, "shared", false);
 189                         if (groups == "not found") { groups = "";  }
 190                         else {
 191                                 userGroups = groups;
 192                                 m->splitAtDash(groups, Groups);
 193                                 m->Groups = Groups;
 194                                 unique = false;
 195                         }
 196
 197                         fastafile = validParameter.validFile(parameters, "fasta", true);
 198                         if (fastafile == "not open") { abort = true; }
 199                         else if (fastafile == "not found") {  fastafile = "";  }
 200
 201                 }
 202
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
 206                 exit(1);
 207         }
 208 }
 209 //**********************************************************************************************************************
 210
 211 int GetSharedOTUCommand::execute(){
 212         try {
 213
 214                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 215
 216                 groupMap = new GroupMap(groupfile);
 217                 int error = groupMap->readMap();
 218                 if (error == 1) { delete groupMap; return 0; }
 219
 220                 if (m->control_pressed) { delete groupMap; return 0; }
 221
 222                 if (Groups.size() == 0) {
 223                         Groups = groupMap->namesOfGroups;
 224
 225                         //make string for outputfile name
 226                         userGroups = "unique.";
 227                         for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 228                         userGroups = userGroups.substr(0, userGroups.length()-1);
 229                 }
 230
 231                 //put groups in map to find easier
 232                 for(int i = 0; i < Groups.size(); i++) {
 233                         groupFinder[Groups[i]] = Groups[i];
 234                 }
 235
 236                 if (fastafile != "") {
 237                         ifstream inFasta;
 238                         m->openInputFile(fastafile, inFasta);
 239
 240                         while(!inFasta.eof()) {
 241                                 if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
 242
 243                                 Sequence seq(inFasta); m->gobble(inFasta);
 244                                 if (seq.getName() != "") {  seqs.push_back(seq);   }
 245                         }
 246                         inFasta.close();
 247                 }
 248
 249                 ListVector* lastlist = NULL;
 250                 string lastLabel = "";
 251
 252                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 253                 set<string> processedLabels;
 254                 set<string> userLabels = labels;
 255
 256                 ifstream in;
 257                 m->openInputFile(listfile, in);
 258
 259                 //as long as you are not at the end of the file or done wih the lines you want
 260                 while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
 261
 262                         if (m->control_pressed) {
 263                                 if (lastlist != NULL) {         delete lastlist;        }
 264                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  outputTypes.clear();
 265                                 delete groupMap; return 0;
 266                         }
 267
 268                         list = new ListVector(in);
 269
 270                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 271                                 m->mothurOut(list->getLabel());
 272                                 process(list);
 273
 274                                 processedLabels.insert(list->getLabel());
 275                                 userLabels.erase(list->getLabel());
 276                         }
 277
 278                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 279                                         string saveLabel = list->getLabel();
 280
 281                                         m->mothurOut(lastlist->getLabel());
 282                                         process(lastlist);
 283
 284                                         processedLabels.insert(lastlist->getLabel());
 285                                         userLabels.erase(lastlist->getLabel());
 286
 287                                         //restore real lastlabel to save below
 288                                         list->setLabel(saveLabel);
 289                         }
 290
 291                         lastLabel = list->getLabel();
 292
 293                         if (lastlist != NULL) {         delete lastlist;        }
 294                         lastlist = list;
 295                 }
 296
 297                 in.close();
 298
 299                 //output error messages about any remaining user labels
 300                 set<string>::iterator it;
 301                 bool needToRun = false;
 302                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 303                         m->mothurOut("Your file does not include the label " + *it);
 304                         if (processedLabels.count(lastLabel) != 1) {
 305                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 306                                 needToRun = true;
 307                         }else {
 308                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 309                         }
 310                 }
 311
 312                 //run last label if you need to
 313                 if (needToRun == true)  {
 314                                 m->mothurOut(lastlist->getLabel());
 315                                 process(lastlist);
 316
 317                                 processedLabels.insert(lastlist->getLabel());
 318                                 userLabels.erase(lastlist->getLabel());
 319                 }
 320
 321
 322                 //reset groups parameter
 323                 m->Groups.clear();
 324
 325                 if (lastlist != NULL) {         delete lastlist;        }
 326
 327                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); }  delete groupMap; return 0; }
 328
 329                 //set fasta file as new current fastafile
 330                 string current = "";
 331                 itTypes = outputTypes.find("fasta");
 332                 if (itTypes != outputTypes.end()) {
 333                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 334                 }
 335
 336                 if (output == "accnos") {
 337                         itTypes = outputTypes.find("accnos");
 338                         if (itTypes != outputTypes.end()) {
 339                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 340                         }
 341                 }
 342
 343                 m->mothurOutEndLine();
 344                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 345                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 346                 m->mothurOutEndLine();
 347
 348
 349                 return 0;
 350         }
 351
 352         catch(exception& e) {
 353                 m->errorOut(e, "GetSharedOTUCommand", "execute");
 354                 exit(1);
 355         }
 356 }
 357 /***********************************************************/
 358 int GetSharedOTUCommand::process(ListVector* shared) {
 359         try {
 360
 361                 map<string, string> fastaMap;
 362
 363                 ofstream outNames;
 364                 string outputFileNames;
 365
 366                 if (outputDir == "") { outputDir += m->hasPath(listfile); }
 367                 if (output != "accnos") {
 368                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
 369                 }else {
 370                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
 371                 }
 372                 m->openOutputFile(outputFileNames, outNames);
 373
 374                 bool wroteSomething = false;
 375                 int num = 0;
 376
 377                 //go through each bin, find out if shared
 378                 for (int i = 0; i < shared->getNumBins(); i++) {
 379                         if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
 380
 381                         bool uniqueOTU = true;
 382
 383                         map<string, int> atLeastOne;
 384                         for (int f = 0; f < Groups.size(); f++) {
 385                                 atLeastOne[Groups[f]] = 0;
 386                         }
 387
 388                         vector<string> namesOfSeqsInThisBin;
 389
 390                         string names = shared->get(i);
 391                         while ((names.find_first_of(',') != -1)) {
 392                                 string name = names.substr(0,names.find_first_of(','));
 393                                 names = names.substr(names.find_first_of(',')+1, names.length());
 394
 395                                 //find group
 396                                 string seqGroup = groupMap->getGroup(name);
 397                                 if (output != "accnos") {
 398                                         namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
 399                                 }else {  namesOfSeqsInThisBin.push_back(name);  }
 400
 401                                 if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 402
 403                                 //is this seq in one of hte groups we care about
 404                                 it = groupFinder.find(seqGroup);
 405                                 if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 406                                 else {  atLeastOne[seqGroup]++;  }
 407                         }
 408
 409                         //get last name
 410                         string seqGroup = groupMap->getGroup(names);
 411                         if (output != "accnos") {
 412                                 namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
 413                         }else {  namesOfSeqsInThisBin.push_back(names); }
 414
 415                         if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 416
 417                         //is this seq in one of hte groups we care about
 418                         it = groupFinder.find(seqGroup);
 419                         if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 420                         else {  atLeastOne[seqGroup]++;  }
 421
 422
 423                         //make sure you have at least one seq from each group you want
 424                         bool sharedByAll = true;
 425                         map<string, int>::iterator it2;
 426                         for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
 427                                 if (it2->second == 0) {  sharedByAll = false;   }
 428                         }
 429
 430                         //if the user wants unique bins and this is unique then print
 431                         //or this the user wants shared bins and this bin is shared then print
 432                         if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
 433
 434                                 wroteSomething = true;
 435                                 num++;
 436
 437                                 //output list of names
 438                                 for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
 439                                         outNames << namesOfSeqsInThisBin[j] << endl;
 440
 441                                         if (fastafile != "") {
 442                                                 if (output != "accnos") {
 443                                                         string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
 444                                                         seqName = seqName.substr(0,seqName.find_last_of('|'));
 445                                                         fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
 446                                                 }else {
 447                                                         fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
 448                                                 }
 449                                         }
 450                                 }
 451                         }
 452                 }
 453
 454                 outNames.close();
 455
 456                 if (!wroteSomething) {
 457                         remove(outputFileNames.c_str());
 458                         string outputString = "\t" + toString(num) + " - No otus shared by groups";
 459
 460                         string groupString = "";
 461                         for (int h = 0; h < Groups.size(); h++) {
 462                                 groupString += "  " + Groups[h];
 463                         }
 464
 465                         outputString += groupString + ".";
 466                         m->mothurOut(outputString); m->mothurOutEndLine();
 467                 }else {
 468                         m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
 469                         outputNames.push_back(outputFileNames);
 470                         if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
 471                         else { outputTypes["accnos"].push_back(outputFileNames); }
 472                 }
 473
 474                 //if fasta file provided output new fasta file
 475                 if ((fastafile != "") && wroteSomething) {
 476                         if (outputDir == "") { outputDir += m->hasPath(fastafile); }
 477                         string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
 478                         ofstream outFasta;
 479                         m->openOutputFile(outputFileFasta, outFasta);
 480                         outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
 481
 482                         for (int k = 0; k < seqs.size(); k++) {
 483                                 if (m->control_pressed) { outFasta.close(); return 0; }
 484
 485                                 //if this is a sequence we want, output it
 486                                 it = fastaMap.find(seqs[k].getName());
 487                                 if (it != fastaMap.end()) {
 488
 489                                         if (output != "accnos") {
 490                                                 outFasta << ">" << it->second << endl;
 491                                         }else {
 492                                                 outFasta << ">" << it->first << endl;
 493                                         }
 494
 495                                         outFasta << seqs[k].getAligned() << endl;
 496                                 }
 497                         }
 498
 499                         outFasta.close();
 500                 }
 501
 502                 return 0;
 503
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "GetSharedOTUCommand", "process");
 507                 exit(1);
 508         }
 509 }
 510
 511 //**********************************************************************************************************************