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::getValidParameters(){
  15         try {
  16                 string Array[] =  {"shared","label","outputdir","design","groups","processors","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "MergeGroupsCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 MergeGroupsCommand::MergeGroupsCommand(){
  27         try {
  28                 abort = true; calledHelp = true;
  29                 vector<string> tempOutNames;
  30                 outputTypes["shared"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> MergeGroupsCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"design", "shared"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "MergeGroupsCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> MergeGroupsCommand::getRequiredFiles(){
  51         try {
  52                 string Array[] =  {};
  53                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "MergeGroupsCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62
  63 MergeGroupsCommand::MergeGroupsCommand(string option) {
  64         try {
  65                 globaldata = GlobalData::getInstance();
  66                 abort = false; calledHelp = false;
  67                 allLines = 1;
  68                 labels.clear();
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; calledHelp = true; }
  72
  73                 else {
  74                         //valid paramters for this command
  75                         string AlignArray[] =  {"groups","label","outputdir","shared","design","processors","inputdir"};
  76                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  77
  78                         OptionParser parser(option);
  79                         map<string,string> parameters = parser.getParameters();
  80
  81                         ValidParameters validParameter;
  82
  83                         //check to make sure all parameters are valid for command
  84                         map<string,string>::iterator it;
  85                         for (it = parameters.begin(); it != parameters.end(); it++) {
  86                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  87                         }
  88
  89                         //initialize outputTypes
  90                         vector<string> tempOutNames;
  91                         outputTypes["shared"] = tempOutNames;
  92
  93                         //if the user changes the output directory command factory will send this info to us in the output parameter
  94                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
  95
  96                         //if the user changes the input directory command factory will send this info to us in the output parameter
  97                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  98                         if (inputDir == "not found"){   inputDir = "";          }
  99                         else {
 100                                 string path;
 101                                 it = parameters.find("design");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 107                                 }
 108
 109                                 it = parameters.find("shared");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 115                                 }
 116                         }
 117
 118                         //check for required parameters
 119                         designfile = validParameter.validFile(parameters, "design", true);
 120                         if (designfile == "not open") { abort = true; }
 121                         else if (designfile == "not found") {  designfile = "";  m->mothurOut("You must provide a design file."); m->mothurOutEndLine(); abort = true; }
 122
 123                         //make sure the user has already run the read.otu command
 124                         sharedfile = validParameter.validFile(parameters, "shared", true);
 125                         if (sharedfile == "not open") { abort = true; }
 126                         else if (sharedfile == "not found") {  sharedfile = "";  m->mothurOut("You must provide a shared file."); m->mothurOutEndLine(); abort = true; }
 127
 128                         //check for optional parameter and set defaults
 129                         // ...at some point should added some additional type checking...
 130                         label = validParameter.validFile(parameters, "label", false);
 131                         if (label == "not found") { label = ""; }
 132                         else {
 133                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 134                                 else { allLines = 1;  }
 135                         }
 136
 137                         groups = validParameter.validFile(parameters, "groups", false);
 138                         if (groups == "not found") { groups = "all";  }
 139                         m->splitAtDash(groups, Groups);
 140                         globaldata->Groups = Groups;
 141                 }
 142
 143         }
 144         catch(exception& e) {
 145                 m->errorOut(e, "MergeGroupsCommand", "MergeGroupsCommand");
 146                 exit(1);
 147         }
 148 }
 149
 150 //**********************************************************************************************************************
 151
 152 void MergeGroupsCommand::help(){
 153         try {
 154                 m->mothurOut("The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n");
 155                 m->mothurOut("The merge.groups command outputs a .shared file. \n");
 156                 m->mothurOut("The merge.groups command parameters are shared, groups, label and design.  The design and shared parameter are required.\n");
 157                 m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
 158                 m->mothurOut("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");
 159                 m->mothurOut("The groups parameter allows you to specify which of the groups in your shared you would like included. The group names are separated by dashes.\n");
 160                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
 161                 m->mothurOut("The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
 162                 m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
 163                 m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n");
 164                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 165
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "MergeGroupsCommand", "help");
 169                 exit(1);
 170         }
 171 }
 172
 173 //**********************************************************************************************************************
 174
 175 MergeGroupsCommand::~MergeGroupsCommand(){}
 176
 177 //**********************************************************************************************************************
 178
 179 int MergeGroupsCommand::execute(){
 180         try {
 181
 182                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 183
 184                 if (outputDir == "") {  outputDir += m->hasPath(sharedfile);  }
 185                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" +  m->getExtension(sharedfile);
 186                 outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 187
 188                 ofstream out;
 189                 m->openOutputFile(outputFileName, out);
 190
 191                 designMap = new GroupMap(designfile);
 192                 designMap->readDesignMap();
 193
 194                 InputData input(sharedfile, "sharedfile");
 195                 lookup = input.getSharedRAbundVectors();
 196                 string lastLabel = lookup[0]->getLabel();
 197
 198                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 199                 set<string> processedLabels;
 200                 set<string> userLabels = labels;
 201
 202                 //as long as you are not at the end of the file or done wih the lines you want
 203                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 204
 205                         if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
 206
 207                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 208
 209                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 210                                 process(lookup, out);
 211
 212                                 processedLabels.insert(lookup[0]->getLabel());
 213                                 userLabels.erase(lookup[0]->getLabel());
 214                         }
 215
 216                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 217                                 string saveLabel = lookup[0]->getLabel();
 218
 219                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 220                                 lookup = input.getSharedRAbundVectors(lastLabel);
 221                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 222
 223                                 process(lookup, out);
 224
 225                                 processedLabels.insert(lookup[0]->getLabel());
 226                                 userLabels.erase(lookup[0]->getLabel());
 227
 228                                 //restore real lastlabel to save below
 229                                 lookup[0]->setLabel(saveLabel);
 230                         }
 231
 232                         lastLabel = lookup[0]->getLabel();
 233                         //prevent memory leak
 234                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 235
 236                         if (m->control_pressed) {  out.close(); globaldata->Groups.clear();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 237
 238                         //get next line to process
 239                         lookup = input.getSharedRAbundVectors();
 240                 }
 241
 242                 if (m->control_pressed) { out.close(); globaldata->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); }  return 0; }
 243
 244                 //output error messages about any remaining user labels
 245                 set<string>::iterator it;
 246                 bool needToRun = false;
 247                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 248                         m->mothurOut("Your file does not include the label " + *it);
 249                         if (processedLabels.count(lastLabel) != 1) {
 250                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 251                                 needToRun = true;
 252                         }else {
 253                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 254                         }
 255                 }
 256
 257                 //run last label if you need to
 258                 if (needToRun == true)  {
 259                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 260                         lookup = input.getSharedRAbundVectors(lastLabel);
 261
 262                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 263
 264                         process(lookup, out);
 265
 266                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 267                 }
 268
 269                 out.close();
 270                 //reset groups parameter
 271                 globaldata->Groups.clear();
 272                 delete designMap;
 273
 274                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;}
 275
 276                 m->mothurOutEndLine();
 277                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 278                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 279                 m->mothurOutEndLine();
 280
 281                 return 0;
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "MergeGroupsCommand", "execute");
 285                 exit(1);
 286         }
 287 }
 288 //**********************************************************************************************************************
 289
 290 int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 291         try {
 292
 293                 map<string, SharedRAbundVector> merged;
 294                 map<string, SharedRAbundVector>::iterator it;
 295
 296                 for (int i = 0; i < thisLookUp.size(); i++) {
 297
 298                         if (m->control_pressed) { return 0; }
 299
 300                         //what grouping does this group belong to
 301                         string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
 302                         if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
 303
 304                         else {
 305                                 //do we already have a member of this grouping?
 306                                 it = merged.find(grouping);
 307
 308                                 if (it == merged.end()) { //nope, so create it
 309                                         merged[grouping] = *thisLookUp[i];
 310                                         merged[grouping].setGroup(grouping);
 311                                 }else { //yes, merge it
 312
 313                                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 314                                                 int abund = (it->second).getAbundance(j);
 315                                                 abund += thisLookUp[i]->getAbundance(j);
 316
 317                                                 (it->second).set(j, abund, grouping);
 318                                         }
 319                                 }
 320                         }
 321                 }
 322
 323                 //print new file
 324                 for (it = merged.begin(); it != merged.end(); it++) {
 325                         out << (it->second).getLabel() << '\t' << it->first << '\t';
 326                         (it->second).print(out);
 327                 }
 328
 329                 return 0;
 330
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "MergeGroupsCommand", "process");
 334                 exit(1);
 335         }
 336 }
 337 //**********************************************************************************************************************
 338
 339
 340