readotucommand.cpp

   1 /*
   2  *  readotu.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readotucommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 ReadOtuCommand::ReadOtuCommand(){
  15         try {
  16                 abort = true; calledHelp = true;
  17                 setParameters();
  18                 vector<string> tempOutNames;
  19                 outputTypes["rabund"] = tempOutNames;
  20                 outputTypes["shared"] = tempOutNames;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 ReadOtuCommand::ReadOtuCommand(string option)  {
  29         try {
  30                 abort = false; calledHelp = false;
  31                 allLines = 1;
  32
  33                 //allow user to run help
  34                 if(option == "help") { help(); abort = true; calledHelp = true; }
  35
  36                 else {
  37                         /*
  38                         //valid paramters for this command
  39                         string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
  40                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  41
  42                         OptionParser parser(option);
  43                         map<string, string> parameters = parser.getParameters();
  44
  45                         ValidParameters validParameter;
  46                         map<string, string>::iterator it;
  47
  48                         //check to make sure all parameters are valid for command
  49                         for (it = parameters.begin(); it != parameters.end(); it++) {
  50                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  51                         }
  52
  53                         //initialize outputTypes
  54                         vector<string> tempOutNames;
  55                         outputTypes["rabund"] = tempOutNames;
  56                         outputTypes["shared"] = tempOutNames;
  57
  58                         globaldata->newRead();
  59
  60                         //if the user changes the input directory command factory will send this info to us in the output parameter
  61                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  62                         if (inputDir == "not found"){   inputDir = "";          }
  63                         else {
  64                                 string path;
  65                                 it = parameters.find("list");
  66                                 //user has given a template file
  67                                 if(it != parameters.end()){
  68                                         path = m->hasPath(it->second);
  69                                         //if the user has not given a path then, add inputdir. else leave path alone.
  70                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
  71                                 }
  72
  73                                 it = parameters.find("order");
  74                                 //user has given a template file
  75                                 if(it != parameters.end()){
  76                                         path = m->hasPath(it->second);
  77                                         //if the user has not given a path then, add inputdir. else leave path alone.
  78                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
  79                                 }
  80
  81                                 it = parameters.find("shared");
  82                                 //user has given a template file
  83                                 if(it != parameters.end()){
  84                                         path = m->hasPath(it->second);
  85                                         //if the user has not given a path then, add inputdir. else leave path alone.
  86                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
  87                                 }
  88
  89                                 it = parameters.find("group");
  90                                 //user has given a template file
  91                                 if(it != parameters.end()){
  92                                         path = m->hasPath(it->second);
  93                                         //if the user has not given a path then, add inputdir. else leave path alone.
  94                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  95                                 }
  96
  97                                 it = parameters.find("sabund");
  98                                 //user has given a template file
  99                                 if(it != parameters.end()){
 100                                         path = m->hasPath(it->second);
 101                                         //if the user has not given a path then, add inputdir. else leave path alone.
 102                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 103                                 }
 104
 105                                 it = parameters.find("rabund");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 111                                 }
 112
 113                                 it = parameters.find("ordergroup");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 119                                 }
 120
 121                                 it = parameters.find("relabund");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 127                                 }
 128                         }
 129
 130
 131                         //if the user changes the output directory command factory will send this info to us in the output parameter
 132                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 133
 134                         //check for required parameters
 135                         listfile = validParameter.validFile(parameters, "list", true);
 136                         if (listfile == "not open") { abort = true; }
 137                         else if (listfile == "not found") { listfile = ""; }
 138                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
 139
 140                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 141                         if (sabundfile == "not open") { abort = true; }
 142                         else if (sabundfile == "not found") { sabundfile = ""; }
 143                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 144
 145                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 146                         if (rabundfile == "not open") { abort = true; }
 147                         else if (rabundfile == "not found") { rabundfile = ""; }
 148                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
 149
 150                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 151                         if (ordergroupfile == "not open") { abort = true; }
 152                         else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 153                         else {  globaldata->setOrderGroupFile(ordergroupfile);  }
 154
 155                         sharedfile = validParameter.validFile(parameters, "shared", true);
 156                         if (sharedfile == "not open") { abort = true; }
 157                         else if (sharedfile == "not found") { sharedfile = ""; }
 158                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
 159
 160                         relAbundfile = validParameter.validFile(parameters, "relabund", true);
 161                         if (relAbundfile == "not open") { abort = true; }
 162                         else if (relAbundfile == "not found") { relAbundfile = ""; }
 163                         else {  globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund");   }
 164
 165
 166                         groupfile = validParameter.validFile(parameters, "group", true);
 167                         if (groupfile == "not open") { abort = true; }
 168                         else if (groupfile == "not found") { groupfile = ""; }
 169                         else {
 170                                 globaldata->setGroupFile(groupfile);
 171                                 groupMap = new GroupMap(groupfile);
 172
 173                                 int error = groupMap->readMap();
 174                                 if (error == 1) { abort = true; }
 175
 176                                 globaldata->gGroupmap = groupMap;
 177                         }
 178
 179                         groups = validParameter.validFile(parameters, "groups", false);
 180                         if (groups == "not found") { groups = ""; }
 181                         else {
 182                                 m->splitAtDash(groups, Groups);
 183                                 globaldata->Groups = Groups;
 184                         }
 185
 186                         //you are doing a list and group shared
 187                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
 188
 189                         //you have not given a file
 190                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
 191                                 m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
 192                         }
 193
 194                         //check for optional parameter and set defaults
 195                         // ...at some point should added some additional type checking...
 196                         label = validParameter.validFile(parameters, "label", false);
 197                         if (label == "not found") { label = ""; }
 198                         else {
 199                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 200                                 else { allLines = 1;  }
 201                                 globaldata->labels = labels;
 202                         }
 203
 204                         globaldata->allLines = allLines;
 205
 206                         orderfile = validParameter.validFile(parameters, "order", true);
 207                         if (orderfile == "not open") { abort = true; }
 208                         else if (orderfile == "not found") { orderfile = ""; }
 209                         else {  globaldata->setOrderFile(orderfile);    }
 210
 211
 212                         if (abort == false) {
 213                                 //gets whichever one of the above is set
 214                                 filename = globaldata->inputFileName;
 215                         }
 216                          */
 217                 }
 218
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 222                 exit(1);
 223         }
 224 }
 225 ///**********************************************************************************************************************
 226
 227 int ReadOtuCommand::execute(){
 228         try {
 229
 230                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 231                 m->mothurOut(getHelpString()); m->mothurOutEndLine();
 232
 233                 /*
 234                 if (globaldata->getFormat() == "shared") {
 235
 236                         shared = new SharedCommand(outputDir);
 237                         int okay = shared->execute();
 238
 239                         //problem with shared
 240                         if (okay == 1) {
 241                                 globaldata->setListFile("");
 242                                 globaldata->setGroupFile("");
 243                                 globaldata->setSharedFile("");
 244                         }else { //shared command outputs the filenames
 245                                 //m->mothurOutEndLine();
 246                                 //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 247                                 //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
 248                                 //m->mothurOutEndLine();
 249                         }
 250
 251                         outputTypes = shared->getOutputFiles();
 252
 253                         //set rabund file as new current rabundfile
 254                         string current = "";
 255                         itTypes = outputTypes.find("rabund");
 256                         if (itTypes != outputTypes.end()) {
 257                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 258                         }
 259
 260                         itTypes = outputTypes.find("shared");
 261                         if (itTypes != outputTypes.end()) {
 262                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 263                         }
 264
 265                         delete shared;
 266                 }
 267                 */
 268
 269                 return 0;
 270         }
 271         catch(exception& e) {
 272                 m->errorOut(e, "ReadOtuCommand", "execute");
 273                 exit(1);
 274         }
 275 }
 276 //**********************************************************************************************************************