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