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;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["shared"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> MergeGroupsCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"design", "shared"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "MergeGroupsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> MergeGroupsCommand::getRequiredFiles(){
  52         try {
  53                 string Array[] =  {};
  54                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "MergeGroupsCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63
  64 MergeGroupsCommand::MergeGroupsCommand(string option) {
  65         try {
  66                 globaldata = GlobalData::getInstance();
  67                 abort = false;
  68                 allLines = 1;
  69                 labels.clear();
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; }
  73
  74                 else {
  75                         //valid paramters for this command
  76                         string AlignArray[] =  {"groups","label","outputdir","shared","design","processors","inputdir"};
  77                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  78
  79                         OptionParser parser(option);
  80                         map<string,string> parameters = parser.getParameters();
  81
  82                         ValidParameters validParameter;
  83
  84                         //check to make sure all parameters are valid for command
  85                         map<string,string>::iterator it;
  86                         for (it = parameters.begin(); it != parameters.end(); it++) {
  87                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  88                         }
  89
  90                         //initialize outputTypes
  91                         vector<string> tempOutNames;
  92                         outputTypes["shared"] = tempOutNames;
  93
  94                         //if the user changes the output directory command factory will send this info to us in the output parameter
  95                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
  96
  97                         //if the user changes the input directory command factory will send this info to us in the output parameter
  98                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  99                         if (inputDir == "not found"){   inputDir = "";          }
 100                         else {
 101                                 string path;
 102                                 it = parameters.find("design");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 108                                 }
 109
 110                                 it = parameters.find("shared");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 116                                 }
 117                         }
 118
 119                         //check for required parameters
 120                         designfile = validParameter.validFile(parameters, "design", true);
 121                         if (designfile == "not open") { abort = true; }
 122                         else if (designfile == "not found") {  designfile = "";  m->mothurOut("You must provide a design file."); m->mothurOutEndLine(); abort = true; }
 123
 124                         //make sure the user has already run the read.otu command
 125                         sharedfile = validParameter.validFile(parameters, "shared", true);
 126                         if (sharedfile == "not open") { abort = true; }
 127                         else if (sharedfile == "not found") {  sharedfile = "";  m->mothurOut("You must provide a shared file."); m->mothurOutEndLine(); abort = true; }
 128
 129                         //check for optional parameter and set defaults
 130                         // ...at some point should added some additional type checking...
 131                         label = validParameter.validFile(parameters, "label", false);
 132                         if (label == "not found") { label = ""; }
 133                         else {
 134                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 135                                 else { allLines = 1;  }
 136                         }
 137
 138                         groups = validParameter.validFile(parameters, "groups", false);
 139                         if (groups == "not found") { groups = "all";  }
 140                         m->splitAtDash(groups, Groups);
 141                         globaldata->Groups = Groups;
 142                 }
 143
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "MergeGroupsCommand", "MergeGroupsCommand");
 147                 exit(1);
 148         }
 149 }
 150
 151 //**********************************************************************************************************************
 152
 153 void MergeGroupsCommand::help(){
 154         try {
 155                 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");
 156                 m->mothurOut("The merge.groups command outputs a .shared file. \n");
 157                 m->mothurOut("The merge.groups command parameters are shared, groups, label and design.  The design and shared parameter are required.\n");
 158                 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");
 159                 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");
 160                 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");
 161                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
 162                 m->mothurOut("The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
 163                 m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
 164                 m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n");
 165                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 166
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "MergeGroupsCommand", "help");
 170                 exit(1);
 171         }
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 MergeGroupsCommand::~MergeGroupsCommand(){}
 177
 178 //**********************************************************************************************************************
 179
 180 int MergeGroupsCommand::execute(){
 181         try {
 182
 183                 if (abort == true) { return 0; }
 184
 185                 if (outputDir == "") {  outputDir += m->hasPath(sharedfile);  }
 186                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" +  m->getExtension(sharedfile);
 187                 outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 188
 189                 ofstream out;
 190                 m->openOutputFile(outputFileName, out);
 191
 192                 designMap = new GroupMap(designfile);
 193                 designMap->readDesignMap();
 194
 195                 InputData input(sharedfile, "sharedfile");
 196                 lookup = input.getSharedRAbundVectors();
 197                 string lastLabel = lookup[0]->getLabel();
 198
 199                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 200                 set<string> processedLabels;
 201                 set<string> userLabels = labels;
 202
 203                 //as long as you are not at the end of the file or done wih the lines you want
 204                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 205
 206                         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; }
 207
 208                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 209
 210                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 211                                 process(lookup, out);
 212
 213                                 processedLabels.insert(lookup[0]->getLabel());
 214                                 userLabels.erase(lookup[0]->getLabel());
 215                         }
 216
 217                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 218                                 string saveLabel = lookup[0]->getLabel();
 219
 220                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 221                                 lookup = input.getSharedRAbundVectors(lastLabel);
 222                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 223
 224                                 process(lookup, out);
 225
 226                                 processedLabels.insert(lookup[0]->getLabel());
 227                                 userLabels.erase(lookup[0]->getLabel());
 228
 229                                 //restore real lastlabel to save below
 230                                 lookup[0]->setLabel(saveLabel);
 231                         }
 232
 233                         lastLabel = lookup[0]->getLabel();
 234                         //prevent memory leak
 235                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 236
 237                         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; }
 238
 239                         //get next line to process
 240                         lookup = input.getSharedRAbundVectors();
 241                 }
 242
 243                 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; }
 244
 245                 //output error messages about any remaining user labels
 246                 set<string>::iterator it;
 247                 bool needToRun = false;
 248                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 249                         m->mothurOut("Your file does not include the label " + *it);
 250                         if (processedLabels.count(lastLabel) != 1) {
 251                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 252                                 needToRun = true;
 253                         }else {
 254                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 255                         }
 256                 }
 257
 258                 //run last label if you need to
 259                 if (needToRun == true)  {
 260                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 261                         lookup = input.getSharedRAbundVectors(lastLabel);
 262
 263                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 264
 265                         process(lookup, out);
 266
 267                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 268                 }
 269
 270                 out.close();
 271                 //reset groups parameter
 272                 globaldata->Groups.clear();
 273                 delete designMap;
 274
 275                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;}
 276
 277                 m->mothurOutEndLine();
 278                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 279                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 280                 m->mothurOutEndLine();
 281
 282                 return 0;
 283         }
 284         catch(exception& e) {
 285                 m->errorOut(e, "MergeGroupsCommand", "execute");
 286                 exit(1);
 287         }
 288 }
 289 //**********************************************************************************************************************
 290
 291 int MergeGroupsCommand::process(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 292         try {
 293
 294                 map<string, SharedRAbundVector> merged;
 295                 map<string, SharedRAbundVector>::iterator it;
 296
 297                 for (int i = 0; i < thisLookUp.size(); i++) {
 298
 299                         if (m->control_pressed) { return 0; }
 300
 301                         //what grouping does this group belong to
 302                         string grouping = designMap->getGroup(thisLookUp[i]->getGroup());
 303                         if (grouping == "not found") { m->mothurOut("[ERROR]: " + thisLookUp[i]->getGroup() + " is not in your design file. Ignoring!"); m->mothurOutEndLine(); grouping = "NOTFOUND"; }
 304
 305                         else {
 306                                 //do we already have a member of this grouping?
 307                                 it = merged.find(grouping);
 308
 309                                 if (it == merged.end()) { //nope, so create it
 310                                         merged[grouping] = *thisLookUp[i];
 311                                         merged[grouping].setGroup(grouping);
 312                                 }else { //yes, merge it
 313
 314                                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 315                                                 int abund = (it->second).getAbundance(j);
 316                                                 abund += thisLookUp[i]->getAbundance(j);
 317
 318                                                 (it->second).set(j, abund, grouping);
 319                                         }
 320                                 }
 321                         }
 322                 }
 323
 324                 //print new file
 325                 for (it = merged.begin(); it != merged.end(); it++) {
 326                         out << (it->second).getLabel() << '\t' << it->first << '\t';
 327                         (it->second).print(out);
 328                 }
 329
 330                 return 0;
 331
 332         }
 333         catch(exception& e) {
 334                 m->errorOut(e, "MergeGroupsCommand", "process");
 335                 exit(1);
 336         }
 337 }
 338 //**********************************************************************************************************************
 339
 340
 341