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","shared",false,false,true); parameters.push_back(pshared);
  17                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
  18                 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,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 //**********************************************************************************************************************
  57 string MergeGroupsCommand::getOutputPattern(string type) {
  58     try {
  59         string pattern = "";
  60
  61         if (type == "shared") {  pattern = "[filename],merge,[extension]"; }
  62         else if (type == "group") {  pattern = "[filename],merge,[extension]"; }
  63         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  64
  65         return pattern;
  66     }
  67     catch(exception& e) {
  68         m->errorOut(e, "MergeGroupsCommand", "getOutputPattern");
  69         exit(1);
  70     }
  71 }
  72 //**********************************************************************************************************************
  73 MergeGroupsCommand::MergeGroupsCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["shared"] = tempOutNames;
  79                 outputTypes["group"] = tempOutNames;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87
  88 MergeGroupsCommand::MergeGroupsCommand(string option) {
  89         try {
  90                 abort = false; calledHelp = false;
  91                 allLines = 1;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  96
  97                 else {
  98                         vector<string> myArray = setParameters();
  99
 100                         OptionParser parser(option);
 101                         map<string,string> parameters = parser.getParameters();
 102
 103                         ValidParameters validParameter;
 104
 105                         //check to make sure all parameters are valid for command
 106                         map<string,string>::iterator it;
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111                         //initialize outputTypes
 112                         vector<string> tempOutNames;
 113                         outputTypes["shared"] = tempOutNames;
 114                         outputTypes["group"] = tempOutNames;
 115
 116                         //if the user changes the output directory command factory will send this info to us in the output parameter
 117                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 118
 119                         //if the user changes the input directory command factory will send this info to us in the output parameter
 120                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 121                         if (inputDir == "not found"){   inputDir = "";          }
 122                         else {
 123                                 string path;
 124                                 it = parameters.find("design");
 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["design"] = inputDir + it->second;           }
 130                                 }
 131
 132                                 it = parameters.find("shared");
 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["shared"] = inputDir + it->second;           }
 138                                 }
 139
 140                                 it = parameters.find("group");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 146                                 }
 147
 148                         }
 149
 150                         //check for required parameters
 151                         designfile = validParameter.validFile(parameters, "design", true);
 152                         if (designfile == "not open") { abort = true; }
 153                         else if (designfile == "not found") {
 154                                 //if there is a current shared file, use it
 155                                 designfile = m->getDesignFile();
 156                                 if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 157                                 else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
 158                         }else { m->setDesignFile(designfile); }
 159
 160                         sharedfile = validParameter.validFile(parameters, "shared", true);
 161                         if (sharedfile == "not open") { abort = true; sharedfile = ""; }
 162                         else if (sharedfile == "not found") {  sharedfile = ""; }
 163                         else { m->setSharedFile(sharedfile); }
 164
 165                         groupfile = validParameter.validFile(parameters, "group", true);
 166                         if (groupfile == "not open") { abort = true; groupfile = ""; }
 167                         else if (groupfile == "not found") {  groupfile = ""; }
 168                         else { m->setGroupFile(groupfile); }
 169
 170                         //check for optional parameter and set defaults
 171                         // ...at some point should added some additional type checking...
 172                         label = validParameter.validFile(parameters, "label", false);
 173                         if (label == "not found") { label = ""; }
 174                         else {
 175                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 176                                 else { allLines = 1;  }
 177                         }
 178
 179                         groups = validParameter.validFile(parameters, "groups", false);
 180                         if (groups == "not found") { groups = "all";  }
 181                         m->splitAtDash(groups, Groups);
 182                         m->setGroups(Groups);
 183
 184                         if ((sharedfile == "") && (groupfile == "")) {
 185                                 //give priority to group, then shared
 186                                 groupfile = m->getGroupFile();
 187                                 if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 188                                 else {
 189                                         sharedfile = m->getSharedFile();
 190                                         if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 191                                         else {
 192                                                 m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 193                                         }
 194                                 }
 195                         }
 196                 }
 197
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "MergeGroupsCommand", "MergeGroupsCommand");
 201                 exit(1);
 202         }
 203 }
 204 //**********************************************************************************************************************
 205
 206 int MergeGroupsCommand::execute(){
 207         try {
 208
 209                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 210
 211                 designMap = new GroupMap(designfile);
 212                 designMap->readDesignMap();
 213
 214                 if (groupfile != "") { processGroupFile(designMap); }
 215                 if (sharedfile != "") { processSharedFile(designMap); }
 216
 217                 //reset groups parameter
 218                 m->clearGroups();
 219                 delete designMap;
 220
 221                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0;}
 222
 223
 224                 //set shared file as new current sharedfile
 225                 string current = "";
 226                 itTypes = outputTypes.find("shared");
 227                 if (itTypes != outputTypes.end()) {
 228                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 229                 }
 230
 231                 itTypes = outputTypes.find("group");
 232                 if (itTypes != outputTypes.end()) {
 233                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 234                 }
 235
 236                 m->mothurOutEndLine();
 237                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 238                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 239                 m->mothurOutEndLine();
 240
 241                 return 0;
 242         }
 243         catch(exception& e) {
 244                 m->errorOut(e, "MergeGroupsCommand", "execute");
 245                 exit(1);
 246         }
 247 }
 248 //**********************************************************************************************************************
 249
 250 int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 251         try {
 252
 253                 map<string, SharedRAbundVector> merged;
 254                 map<string, SharedRAbundVector>::iterator it;
 255
 256                 for (int i = 0; i < thisLookUp.size(); i++) {
 257
 258                         if (m->control_pressed) { return 0; }
 259
 260                         //what grouping does this group belong to
 261                         string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
 262                         if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
 263
 264                         else {
 265                                 //do we already have a member of this grouping?
 266                                 it = merged.find(grouping);
 267
 268                                 if (it == merged.end()) { //nope, so create it
 269                                         merged[grouping] = *thisLookUp[i];
 270                                         merged[grouping].setGroup(grouping);
 271                                 }else { //yes, merge it
 272
 273                                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 274                                                 int abund = (it->second).getAbundance(j);
 275                                                 abund += thisLookUp[i]->getAbundance(j);
 276
 277                                                 (it->second).set(j, abund, grouping);
 278                                         }
 279                                 }
 280                         }
 281                 }
 282
 283                 //print new file
 284                 for (it = merged.begin(); it != merged.end(); it++) {
 285                         out << (it->second).getLabel() << '\t' << it->first << '\t';
 286                         (it->second).print(out);
 287                 }
 288
 289                 return 0;
 290
 291         }
 292         catch(exception& e) {
 293                 m->errorOut(e, "MergeGroupsCommand", "process");
 294                 exit(1);
 295         }
 296 }
 297 //**********************************************************************************************************************
 298
 299 int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
 300         try {
 301
 302                 string thisOutputDir = outputDir;
 303                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 304         map<string, string> variables;
 305         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 306         variables["[extension]"] = m->getExtension(sharedfile);
 307                 string outputFileName = getOutputFileName("shared", variables);
 308         outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 309
 310                 ofstream out;
 311                 m->openOutputFile(outputFileName, out);
 312
 313                 InputData input(sharedfile, "sharedfile");
 314                 lookup = input.getSharedRAbundVectors();
 315                 string lastLabel = lookup[0]->getLabel();
 316
 317                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 318                 set<string> processedLabels;
 319                 set<string> userLabels = labels;
 320
 321                 //as long as you are not at the end of the file or done wih the lines you want
 322                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 323
 324                         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; }
 325
 326                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 327
 328                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 329
 330                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 331                                 process(lookup, out);
 332
 333                                 processedLabels.insert(lookup[0]->getLabel());
 334                                 userLabels.erase(lookup[0]->getLabel());
 335                         }
 336
 337                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 338                                 string saveLabel = lookup[0]->getLabel();
 339
 340                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 341                                 lookup = input.getSharedRAbundVectors(lastLabel);
 342                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 343
 344                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 345                                 process(lookup, out);
 346
 347                                 processedLabels.insert(lookup[0]->getLabel());
 348                                 userLabels.erase(lookup[0]->getLabel());
 349
 350                                 //restore real lastlabel to save below
 351                                 lookup[0]->setLabel(saveLabel);
 352                         }
 353
 354                         lastLabel = lookup[0]->getLabel();
 355                         //prevent memory leak
 356                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 357
 358                         if (m->control_pressed) {  out.close(); m->clearGroups();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0; }
 359
 360                         //get next line to process
 361                         lookup = input.getSharedRAbundVectors();
 362                 }
 363
 364                 if (m->control_pressed) { out.close(); m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); }  return 0; }
 365
 366                 //output error messages about any remaining user labels
 367                 set<string>::iterator it;
 368                 bool needToRun = false;
 369                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 370                         m->mothurOut("Your file does not include the label " + *it);
 371                         if (processedLabels.count(lastLabel) != 1) {
 372                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 373                                 needToRun = true;
 374                         }else {
 375                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 376                         }
 377                 }
 378
 379                 //run last label if you need to
 380                 if (needToRun == true)  {
 381                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 382                         lookup = input.getSharedRAbundVectors(lastLabel);
 383
 384                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 385
 386                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 387                         process(lookup, out);
 388
 389                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 390                 }
 391
 392                 out.close();
 393
 394
 395                 return 0;
 396
 397         }
 398         catch(exception& e) {
 399                 m->errorOut(e, "MergeGroupsCommand", "processSharedFile");
 400                 exit(1);
 401         }
 402 }
 403 //**********************************************************************************************************************
 404
 405 int MergeGroupsCommand::processGroupFile(GroupMap*& designMap){
 406         try {
 407
 408                 string thisOutputDir = outputDir;
 409                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 410         map<string, string> variables;
 411         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 412         variables["[extension]"] = m->getExtension(groupfile);
 413                 string outputFileName = getOutputFileName("group", variables);
 414                 outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
 415
 416                 ofstream out;
 417                 m->openOutputFile(outputFileName, out);
 418
 419                 //read groupfile
 420                 GroupMap groupMap(groupfile);
 421                 groupMap.readMap();
 422
 423                 //fill Groups - checks for "all" and for any typo groups
 424                 SharedUtil* util = new SharedUtil();
 425                 vector<string> nameGroups = groupMap.getNamesOfGroups();
 426                 util->setGroups(Groups, nameGroups);
 427                 delete util;
 428
 429                 vector<string> namesOfSeqs = groupMap.getNamesSeqs();
 430                 bool error = false;
 431
 432                 for (int i = 0; i < namesOfSeqs.size(); i++) {
 433
 434                         if (m->control_pressed) { break; }
 435
 436                         string thisGroup = groupMap.getGroup(namesOfSeqs[i]);
 437
 438                         //are you in a group the user wants
 439                         if (m->inUsersGroups(thisGroup, Groups)) {
 440                                 string thisGrouping = designMap->getGroup(thisGroup);
 441
 442                                 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; }
 443                                 else {
 444                                         out << namesOfSeqs[i] << '\t' << thisGrouping << endl;
 445                                 }
 446                         }
 447                 }
 448
 449                 if (error) { m->control_pressed = true; }
 450
 451                 out.close();
 452
 453                 return 0;
 454
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "MergeGroupsCommand", "processGroupFile");
 458                 exit(1);
 459         }
 460 }
 461 //**********************************************************************************************************************
 462
 463
 464