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