mergegroupscommand.cpp

   1 /*
   2  *  mergegroupscommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/24/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mergegroupscommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> MergeGroupsCommand::setParameters(){
  15         try {
  16                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
  17                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
  18                 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
  19                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  20                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  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, "MergeGroupsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string MergeGroupsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The merge.groups command reads a shared or group file and a design file and merges the groups that are in the same grouping in the design file.\n";
  38                 helpString += "The merge.groups command outputs a .shared file. \n";
  39                 helpString += "The merge.groups command parameters are shared, group, groups, label and design.  The design parameter is required.\n";
  40                 helpString += "The design parameter allows you to assign your groups to sets. It is required. \n";
  41                 helpString += "The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n";
  42                 helpString += "The groups parameter allows you to specify which of the groups in your shared or group file you would like included. The group names are separated by dashes.\n";
  43                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  44                 helpString += "The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";
  45                 helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";
  46                 helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n";
  47                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  48                 return helpString;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "MergeGroupsCommand", "getHelpString");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 string MergeGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
  57         try {
  58         string outputFileName = "";
  59                 map<string, vector<string> >::iterator it;
  60
  61         //is this a type this command creates
  62         it = outputTypes.find(type);
  63         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  64         else {
  65             if (type == "shared")        {   outputFileName = "merge" +  m->getExtension(inputName);       }
  66             else if (type == "group")    {   outputFileName =   "merge" +  m->getExtension(inputName);     }
  67             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  68         }
  69         return outputFileName;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "MergeGroupsCommand", "getOutputFileNameTag");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77 MergeGroupsCommand::MergeGroupsCommand(){
  78         try {
  79                 abort = true; calledHelp = true;
  80                 setParameters();
  81                 vector<string> tempOutNames;
  82                 outputTypes["shared"] = tempOutNames;
  83                 outputTypes["group"] = tempOutNames;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 MergeGroupsCommand::MergeGroupsCommand(string option) {
  93         try {
  94                 abort = false; calledHelp = false;
  95                 allLines = 1;
  96
  97                 //allow user to run help
  98                 if(option == "help") { help(); abort = true; calledHelp = true; }
  99                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 100
 101                 else {
 102                         vector<string> myArray = setParameters();
 103
 104                         OptionParser parser(option);
 105                         map<string,string> parameters = parser.getParameters();
 106
 107                         ValidParameters validParameter;
 108
 109                         //check to make sure all parameters are valid for command
 110                         map<string,string>::iterator it;
 111                         for (it = parameters.begin(); it != parameters.end(); it++) {
 112                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["shared"] = tempOutNames;
 118                         outputTypes["group"] = tempOutNames;
 119
 120                         //if the user changes the output directory command factory will send this info to us in the output parameter
 121                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 122
 123                         //if the user changes the input directory command factory will send this info to us in the output parameter
 124                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 125                         if (inputDir == "not found"){   inputDir = "";          }
 126                         else {
 127                                 string path;
 128                                 it = parameters.find("design");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 134                                 }
 135
 136                                 it = parameters.find("shared");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 142                                 }
 143
 144                                 it = parameters.find("group");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 150                                 }
 151
 152                         }
 153
 154                         //check for required parameters
 155                         designfile = validParameter.validFile(parameters, "design", true);
 156                         if (designfile == "not open") { abort = true; }
 157                         else if (designfile == "not found") {
 158                                 //if there is a current shared file, use it
 159                                 designfile = m->getDesignFile();
 160                                 if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 161                                 else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
 162                         }else { m->setDesignFile(designfile); }
 163
 164                         sharedfile = validParameter.validFile(parameters, "shared", true);
 165                         if (sharedfile == "not open") { abort = true; sharedfile = ""; }
 166                         else if (sharedfile == "not found") {  sharedfile = ""; }
 167                         else { m->setSharedFile(sharedfile); }
 168
 169                         groupfile = validParameter.validFile(parameters, "group", true);
 170                         if (groupfile == "not open") { abort = true; groupfile = ""; }
 171                         else if (groupfile == "not found") {  groupfile = ""; }
 172                         else { m->setGroupFile(groupfile); }
 173
 174                         //check for optional parameter and set defaults
 175                         // ...at some point should added some additional type checking...
 176                         label = validParameter.validFile(parameters, "label", false);
 177                         if (label == "not found") { label = ""; }
 178                         else {
 179                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 180                                 else { allLines = 1;  }
 181                         }
 182
 183                         groups = validParameter.validFile(parameters, "groups", false);
 184                         if (groups == "not found") { groups = "all";  }
 185                         m->splitAtDash(groups, Groups);
 186                         m->setGroups(Groups);
 187
 188                         if ((sharedfile == "") && (groupfile == "")) {
 189                                 //give priority to group, then shared
 190                                 groupfile = m->getGroupFile();
 191                                 if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 192                                 else {
 193                                         sharedfile = m->getSharedFile();
 194                                         if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 195                                         else {
 196                                                 m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 197                                         }
 198                                 }
 199                         }
 200                 }
 201
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "MergeGroupsCommand", "MergeGroupsCommand");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 int MergeGroupsCommand::execute(){
 211         try {
 212
 213                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 214
 215                 designMap = new GroupMap(designfile);
 216                 designMap->readDesignMap();
 217
 218                 if (groupfile != "") { processGroupFile(designMap); }
 219                 if (sharedfile != "") { processSharedFile(designMap); }
 220
 221                 //reset groups parameter
 222                 m->clearGroups();
 223                 delete designMap;
 224
 225                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0;}
 226
 227
 228                 //set shared file as new current sharedfile
 229                 string current = "";
 230                 itTypes = outputTypes.find("shared");
 231                 if (itTypes != outputTypes.end()) {
 232                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 233                 }
 234
 235                 itTypes = outputTypes.find("group");
 236                 if (itTypes != outputTypes.end()) {
 237                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 238                 }
 239
 240                 m->mothurOutEndLine();
 241                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 242                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 243                 m->mothurOutEndLine();
 244
 245                 return 0;
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "MergeGroupsCommand", "execute");
 249                 exit(1);
 250         }
 251 }
 252 //**********************************************************************************************************************
 253
 254 int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 255         try {
 256
 257                 map<string, SharedRAbundVector> merged;
 258                 map<string, SharedRAbundVector>::iterator it;
 259
 260                 for (int i = 0; i < thisLookUp.size(); i++) {
 261
 262                         if (m->control_pressed) { return 0; }
 263
 264                         //what grouping does this group belong to
 265                         string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
 266                         if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
 267
 268                         else {
 269                                 //do we already have a member of this grouping?
 270                                 it = merged.find(grouping);
 271
 272                                 if (it == merged.end()) { //nope, so create it
 273                                         merged[grouping] = *thisLookUp[i];
 274                                         merged[grouping].setGroup(grouping);
 275                                 }else { //yes, merge it
 276
 277                                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 278                                                 int abund = (it->second).getAbundance(j);
 279                                                 abund += thisLookUp[i]->getAbundance(j);
 280
 281                                                 (it->second).set(j, abund, grouping);
 282                                         }
 283                                 }
 284                         }
 285                 }
 286
 287                 //print new file
 288                 for (it = merged.begin(); it != merged.end(); it++) {
 289                         out << (it->second).getLabel() << '\t' << it->first << '\t';
 290                         (it->second).print(out);
 291                 }
 292
 293                 return 0;
 294
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "MergeGroupsCommand", "process");
 298                 exit(1);
 299         }
 300 }
 301 //**********************************************************************************************************************
 302
 303 int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
 304         try {
 305
 306                 string thisOutputDir = outputDir;
 307                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 308                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
 309         outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 310
 311                 ofstream out;
 312                 m->openOutputFile(outputFileName, out);
 313
 314                 InputData input(sharedfile, "sharedfile");
 315                 lookup = input.getSharedRAbundVectors();
 316                 string lastLabel = lookup[0]->getLabel();
 317
 318                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 319                 set<string> processedLabels;
 320                 set<string> userLabels = labels;
 321
 322                 //as long as you are not at the end of the file or done wih the lines you want
 323                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 324
 325                         if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } return 0; }
 326
 327                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 328
 329                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 330
 331                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 332                                 process(lookup, out);
 333
 334                                 processedLabels.insert(lookup[0]->getLabel());
 335                                 userLabels.erase(lookup[0]->getLabel());
 336                         }
 337
 338                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 339                                 string saveLabel = lookup[0]->getLabel();
 340
 341                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 342                                 lookup = input.getSharedRAbundVectors(lastLabel);
 343                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 344
 345                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 346                                 process(lookup, out);
 347
 348                                 processedLabels.insert(lookup[0]->getLabel());
 349                                 userLabels.erase(lookup[0]->getLabel());
 350
 351                                 //restore real lastlabel to save below
 352                                 lookup[0]->setLabel(saveLabel);
 353                         }
 354
 355                         lastLabel = lookup[0]->getLabel();
 356                         //prevent memory leak
 357                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 358
 359                         if (m->control_pressed) {  out.close(); m->clearGroups();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0; }
 360
 361                         //get next line to process
 362                         lookup = input.getSharedRAbundVectors();
 363                 }
 364
 365                 if (m->control_pressed) { out.close(); m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); }  return 0; }
 366
 367                 //output error messages about any remaining user labels
 368                 set<string>::iterator it;
 369                 bool needToRun = false;
 370                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 371                         m->mothurOut("Your file does not include the label " + *it);
 372                         if (processedLabels.count(lastLabel) != 1) {
 373                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 374                                 needToRun = true;
 375                         }else {
 376                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 377                         }
 378                 }
 379
 380                 //run last label if you need to
 381                 if (needToRun == true)  {
 382                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 383                         lookup = input.getSharedRAbundVectors(lastLabel);
 384
 385                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 386
 387                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 388                         process(lookup, out);
 389
 390                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 391                 }
 392
 393                 out.close();
 394
 395
 396                 return 0;
 397
 398         }
 399         catch(exception& e) {
 400                 m->errorOut(e, "MergeGroupsCommand", "processSharedFile");
 401                 exit(1);
 402         }
 403 }
 404 //**********************************************************************************************************************
 405
 406 int MergeGroupsCommand::processGroupFile(GroupMap*& designMap){
 407         try {
 408
 409                 string thisOutputDir = outputDir;
 410                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 411                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 412                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 413
 414                 ofstream out;
 415                 m->openOutputFile(outputFileName, out);
 416
 417                 //read groupfile
 418                 GroupMap groupMap(groupfile);
 419                 groupMap.readMap();
 420
 421                 //fill Groups - checks for "all" and for any typo groups
 422                 SharedUtil* util = new SharedUtil();
 423                 vector<string> nameGroups = groupMap.getNamesOfGroups();
 424                 util->setGroups(Groups, nameGroups);
 425                 delete util;
 426
 427                 vector<string> namesOfSeqs = groupMap.getNamesSeqs();
 428                 bool error = false;
 429
 430                 for (int i = 0; i < namesOfSeqs.size(); i++) {
 431
 432                         if (m->control_pressed) { break; }
 433
 434                         string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
 435
 436                         //are you in a group the user wants
 437                         if (m->inUsersGroups(thisGroup, Groups)) {
 438                                 string thisGrouping = designMap->getGroup(thisGroup);
 439
 440                                 if (thisGrouping == "not found") { m->mothurOut("[ERROR]: " + namesOfSeqs[i] + " is from group " + thisGroup + " which is not in your design file, please correct."); m->mothurOutEndLine();  error = true; }
 441                                 else {
 442                                         out << namesOfSeqs[i] << '\t' << thisGrouping << endl;
 443                                 }
 444                         }
 445                 }
 446
 447                 if (error) { m->control_pressed = true; }
 448
 449                 out.close();
 450
 451                 return 0;
 452
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
 456                 exit(1);
 457         }
 458 }
 459 //**********************************************************************************************************************
 460
 461
 462