getsharedotucommand.cpp

   1 /*
   2  *  getsharedotucommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/22/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getsharedotucommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> GetSharedOTUCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  17                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
  18                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
  19                 CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
  20                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  21                 CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
  22                 CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "GetSharedOTUCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string GetSharedOTUCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 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";
  40                 helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
  41                 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";
  42                 helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
  43                 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";
  44                 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";
  45                 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";
  46                 helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
  47                 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";
  48                 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";
  49                 helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
  50                 helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
  51                 helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
  52                 helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 GetSharedOTUCommand::GetSharedOTUCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["fasta"] = tempOutNames;
  68                 outputTypes["accnos"] = tempOutNames;
  69                 outputTypes["sharedseqs"] = tempOutNames;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77 GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
  78         try {
  79
  80                 abort = false; calledHelp = false;
  81                 unique = true;
  82                 allLines = 1;
  83
  84                 //allow user to run help
  85                 if(option == "help") { help(); abort = true; calledHelp = true; }
  86                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  87
  88                 else {
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string,string> parameters = parser.getParameters();
  93
  94                         ValidParameters validParameter;
  95                         map<string,string>::iterator it;
  96
  97                         //check to make sure all parameters are valid for command
  98                         for (it = parameters.begin(); it != parameters.end(); it++) {
  99                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 100                         }
 101
 102                         //initialize outputTypes
 103                         vector<string> tempOutNames;
 104                         outputTypes["fasta"] = tempOutNames;
 105                         outputTypes["accnos"] = tempOutNames;
 106                         outputTypes["sharedseqs"] = tempOutNames;
 107
 108                         //if the user changes the output directory command factory will send this info to us in the output parameter
 109                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 110
 111                         //if the user changes the input directory command factory will send this info to us in the output parameter
 112                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 113                         if (inputDir == "not found"){   inputDir = "";          }
 114                         else {
 115                                 string path;
 116                                 it = parameters.find("fasta");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 122                                 }
 123
 124                                 it = parameters.find("list");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 130                                 }
 131
 132                                 it = parameters.find("group");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 138                                 }
 139                         }
 140
 141
 142                         //check for required parameters
 143                         listfile = validParameter.validFile(parameters, "list", true);
 144                         if (listfile == "not open") { abort = true; }
 145                         else if (listfile == "not found") {
 146                                 listfile = m->getListFile();
 147                                 if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 148                                 else {
 149                                         m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
 150                                         abort = true;
 151                                 }
 152                         }else {  format = "list";       m->setListFile(listfile); }
 153
 154                         groupfile = validParameter.validFile(parameters, "group", true);
 155                         if (groupfile == "not open") { abort = true; }
 156                         else if (groupfile == "not found") {
 157                                 groupfile = m->getGroupFile();
 158                                 if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 159                                 else {
 160                                         m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
 161                                         abort = true;
 162                                 }
 163                         }else { m->setGroupFile(groupfile); }
 164
 165                         if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
 166
 167                         //check for optional parameter and set defaults
 168                         // ...at some point should added some additional type checking...
 169                         label = validParameter.validFile(parameters, "label", false);
 170                         if (label == "not found") { label = ""; }
 171                         else {
 172                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 173                                 else { allLines = 1;  }
 174                         }
 175
 176                         output = validParameter.validFile(parameters, "output", false);
 177                         if (output == "not found") { output = ""; }
 178                         else if (output == "default") { output = ""; }
 179
 180                         groups = validParameter.validFile(parameters, "unique", false);
 181                         if (groups == "not found") { groups = ""; }
 182                         else {
 183                                 userGroups = "unique." + groups;
 184                                 m->splitAtDash(groups, Groups);
 185                                 m->setGroups(Groups);
 186
 187                         }
 188
 189                         groups = validParameter.validFile(parameters, "shared", false);
 190                         if (groups == "not found") { groups = "";  }
 191                         else {
 192                                 userGroups = groups;
 193                                 m->splitAtDash(groups, Groups);
 194                                 m->setGroups(Groups);
 195                                 unique = false;
 196                         }
 197
 198                         fastafile = validParameter.validFile(parameters, "fasta", true);
 199                         if (fastafile == "not open") { abort = true; }
 200                         else if (fastafile == "not found") {  fastafile = "";  }
 201                         else { m->setFastaFile(fastafile); }
 202                 }
 203
 204         }
 205         catch(exception& e) {
 206                 m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
 207                 exit(1);
 208         }
 209 }
 210 //**********************************************************************************************************************
 211
 212 int GetSharedOTUCommand::execute(){
 213         try {
 214
 215                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 216
 217                 groupMap = new GroupMap(groupfile);
 218                 int error = groupMap->readMap();
 219                 if (error == 1) { delete groupMap; return 0; }
 220
 221                 if (m->control_pressed) { delete groupMap; return 0; }
 222
 223                 if (Groups.size() == 0) {
 224                         Groups = groupMap->getNamesOfGroups();
 225
 226                         //make string for outputfile name
 227                         userGroups = "unique.";
 228                         for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 229                         userGroups = userGroups.substr(0, userGroups.length()-1);
 230                 }else{
 231                         //sanity check for group names
 232                         SharedUtil util;
 233                         vector<string> namesOfGroups = groupMap->getNamesOfGroups();
 234                         util.setGroups(Groups, namesOfGroups);
 235                         groupMap->setNamesOfGroups(namesOfGroups);
 236                 }
 237
 238                 //put groups in map to find easier
 239                 for(int i = 0; i < Groups.size(); i++) {
 240                         groupFinder[Groups[i]] = Groups[i];
 241                 }
 242
 243                 if (fastafile != "") {
 244                         ifstream inFasta;
 245                         m->openInputFile(fastafile, inFasta);
 246
 247                         while(!inFasta.eof()) {
 248                                 if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
 249
 250                                 Sequence seq(inFasta); m->gobble(inFasta);
 251                                 if (seq.getName() != "") {  seqs.push_back(seq);   }
 252                         }
 253                         inFasta.close();
 254                 }
 255
 256                 ListVector* lastlist = NULL;
 257                 string lastLabel = "";
 258
 259                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 260                 set<string> processedLabels;
 261                 set<string> userLabels = labels;
 262
 263                 ifstream in;
 264                 m->openInputFile(listfile, in);
 265
 266                 //as long as you are not at the end of the file or done wih the lines you want
 267                 while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
 268
 269                         if (m->control_pressed) {
 270                                 if (lastlist != NULL) {         delete lastlist;        }
 271                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); }  outputTypes.clear();
 272                                 delete groupMap; return 0;
 273                         }
 274
 275                         list = new ListVector(in);
 276
 277                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 278                                 m->mothurOut(list->getLabel());
 279                                 process(list);
 280
 281                                 processedLabels.insert(list->getLabel());
 282                                 userLabels.erase(list->getLabel());
 283                         }
 284
 285                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 286                                         string saveLabel = list->getLabel();
 287
 288                                         m->mothurOut(lastlist->getLabel());
 289                                         process(lastlist);
 290
 291                                         processedLabels.insert(lastlist->getLabel());
 292                                         userLabels.erase(lastlist->getLabel());
 293
 294                                         //restore real lastlabel to save below
 295                                         list->setLabel(saveLabel);
 296                         }
 297
 298                         lastLabel = list->getLabel();
 299
 300                         if (lastlist != NULL) {         delete lastlist;        }
 301                         lastlist = list;
 302                 }
 303
 304                 in.close();
 305
 306                 //output error messages about any remaining user labels
 307                 set<string>::iterator it;
 308                 bool needToRun = false;
 309                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 310                         m->mothurOut("Your file does not include the label " + *it);
 311                         if (processedLabels.count(lastLabel) != 1) {
 312                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 313                                 needToRun = true;
 314                         }else {
 315                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 316                         }
 317                 }
 318
 319                 //run last label if you need to
 320                 if (needToRun == true)  {
 321                                 m->mothurOut(lastlist->getLabel());
 322                                 process(lastlist);
 323
 324                                 processedLabels.insert(lastlist->getLabel());
 325                                 userLabels.erase(lastlist->getLabel());
 326                 }
 327
 328
 329                 //reset groups parameter
 330                 m->clearGroups();
 331
 332                 if (lastlist != NULL) {         delete lastlist;        }
 333
 334                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); }  delete groupMap; return 0; }
 335
 336                 //set fasta file as new current fastafile
 337                 string current = "";
 338                 itTypes = outputTypes.find("fasta");
 339                 if (itTypes != outputTypes.end()) {
 340                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 341                 }
 342
 343                 if (output == "accnos") {
 344                         itTypes = outputTypes.find("accnos");
 345                         if (itTypes != outputTypes.end()) {
 346                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 347                         }
 348                 }
 349
 350                 m->mothurOutEndLine();
 351                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 352                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 353                 m->mothurOutEndLine();
 354
 355
 356                 return 0;
 357         }
 358
 359         catch(exception& e) {
 360                 m->errorOut(e, "GetSharedOTUCommand", "execute");
 361                 exit(1);
 362         }
 363 }
 364 /***********************************************************/
 365 int GetSharedOTUCommand::process(ListVector* shared) {
 366         try {
 367
 368                 map<string, string> fastaMap;
 369
 370                 ofstream outNames;
 371                 string outputFileNames;
 372
 373                 if (outputDir == "") { outputDir += m->hasPath(listfile); }
 374                 if (output != "accnos") {
 375                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
 376                 }else {
 377                         outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
 378                 }
 379                 m->openOutputFile(outputFileNames, outNames);
 380
 381                 bool wroteSomething = false;
 382                 int num = 0;
 383
 384                 //go through each bin, find out if shared
 385                 for (int i = 0; i < shared->getNumBins(); i++) {
 386                         if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
 387
 388                         bool uniqueOTU = true;
 389
 390                         map<string, int> atLeastOne;
 391                         for (int f = 0; f < Groups.size(); f++) {
 392                                 atLeastOne[Groups[f]] = 0;
 393                         }
 394
 395                         vector<string> namesOfSeqsInThisBin;
 396
 397                         string names = shared->get(i);
 398                         while ((names.find_first_of(',') != -1)) {
 399                                 string name = names.substr(0,names.find_first_of(','));
 400                                 names = names.substr(names.find_first_of(',')+1, names.length());
 401
 402                                 //find group
 403                                 string seqGroup = groupMap->getGroup(name);
 404                                 if (output != "accnos") {
 405                                         namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
 406                                 }else {  namesOfSeqsInThisBin.push_back(name);  }
 407
 408                                 if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 409
 410                                 //is this seq in one of hte groups we care about
 411                                 it = groupFinder.find(seqGroup);
 412                                 if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 413                                 else {  atLeastOne[seqGroup]++;  }
 414                         }
 415
 416                         //get last name
 417                         string seqGroup = groupMap->getGroup(names);
 418                         if (output != "accnos") {
 419                                 namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
 420                         }else {  namesOfSeqsInThisBin.push_back(names); }
 421
 422                         if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
 423
 424                         //is this seq in one of hte groups we care about
 425                         it = groupFinder.find(seqGroup);
 426                         if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
 427                         else {  atLeastOne[seqGroup]++;  }
 428
 429
 430                         //make sure you have at least one seq from each group you want
 431                         bool sharedByAll = true;
 432                         map<string, int>::iterator it2;
 433                         for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
 434                                 if (it2->second == 0) {  sharedByAll = false;   }
 435                         }
 436
 437                         //if the user wants unique bins and this is unique then print
 438                         //or this the user wants shared bins and this bin is shared then print
 439                         if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
 440
 441                                 wroteSomething = true;
 442                                 num++;
 443
 444                                 //output list of names
 445                                 for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
 446                                         outNames << namesOfSeqsInThisBin[j] << endl;
 447
 448                                         if (fastafile != "") {
 449                                                 if (output != "accnos") {
 450                                                         string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
 451                                                         seqName = seqName.substr(0,seqName.find_last_of('|'));
 452                                                         fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
 453                                                 }else {
 454                                                         fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
 455                                                 }
 456                                         }
 457                                 }
 458                         }
 459                 }
 460
 461                 outNames.close();
 462
 463                 if (!wroteSomething) {
 464                         m->mothurRemove(outputFileNames);
 465                         string outputString = "\t" + toString(num) + " - No otus shared by groups";
 466
 467                         string groupString = "";
 468                         for (int h = 0; h < Groups.size(); h++) {
 469                                 groupString += "  " + Groups[h];
 470                         }
 471
 472                         outputString += groupString + ".";
 473                         m->mothurOut(outputString); m->mothurOutEndLine();
 474                 }else {
 475                         m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
 476                         outputNames.push_back(outputFileNames);
 477                         if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
 478                         else { outputTypes["accnos"].push_back(outputFileNames); }
 479                 }
 480
 481                 //if fasta file provided output new fasta file
 482                 if ((fastafile != "") && wroteSomething) {
 483                         if (outputDir == "") { outputDir += m->hasPath(fastafile); }
 484                         string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
 485                         ofstream outFasta;
 486                         m->openOutputFile(outputFileFasta, outFasta);
 487                         outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
 488
 489                         for (int k = 0; k < seqs.size(); k++) {
 490                                 if (m->control_pressed) { outFasta.close(); return 0; }
 491
 492                                 //if this is a sequence we want, output it
 493                                 it = fastaMap.find(seqs[k].getName());
 494                                 if (it != fastaMap.end()) {
 495
 496                                         if (output != "accnos") {
 497                                                 outFasta << ">" << it->second << endl;
 498                                         }else {
 499                                                 outFasta << ">" << it->first << endl;
 500                                         }
 501
 502                                         outFasta << seqs[k].getAligned() << endl;
 503                                 }
 504                         }
 505
 506                         outFasta.close();
 507                 }
 508
 509                 return 0;
 510
 511         }
 512         catch(exception& e) {
 513                 m->errorOut(e, "GetSharedOTUCommand", "process");
 514                 exit(1);
 515         }
 516 }
 517
 518 //**********************************************************************************************************************