source/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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  36
  37                 else {
  38                         /*
  39                         //valid paramters for this command
  40                         string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
  41                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42
  43                         OptionParser parser(option);
  44                         map<string, string> parameters = parser.getParameters();
  45
  46                         ValidParameters validParameter;
  47                         map<string, string>::iterator it;
  48
  49                         //check to make sure all parameters are valid for command
  50                         for (it = parameters.begin(); it != parameters.end(); it++) {
  51                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  52                         }
  53
  54                         //initialize outputTypes
  55                         vector<string> tempOutNames;
  56                         outputTypes["rabund"] = tempOutNames;
  57                         outputTypes["shared"] = tempOutNames;
  58
  59                         globaldata->newRead();
  60
  61                         //if the user changes the input directory command factory will send this info to us in the output parameter
  62                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  63                         if (inputDir == "not found"){   inputDir = "";          }
  64                         else {
  65                                 string path;
  66                                 it = parameters.find("list");
  67                                 //user has given a template file
  68                                 if(it != parameters.end()){
  69                                         path = m->hasPath(it->second);
  70                                         //if the user has not given a path then, add inputdir. else leave path alone.
  71                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
  72                                 }
  73
  74                                 it = parameters.find("order");
  75                                 //user has given a template file
  76                                 if(it != parameters.end()){
  77                                         path = m->hasPath(it->second);
  78                                         //if the user has not given a path then, add inputdir. else leave path alone.
  79                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
  80                                 }
  81
  82                                 it = parameters.find("shared");
  83                                 //user has given a template file
  84                                 if(it != parameters.end()){
  85                                         path = m->hasPath(it->second);
  86                                         //if the user has not given a path then, add inputdir. else leave path alone.
  87                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
  88                                 }
  89
  90                                 it = parameters.find("group");
  91                                 //user has given a template file
  92                                 if(it != parameters.end()){
  93                                         path = m->hasPath(it->second);
  94                                         //if the user has not given a path then, add inputdir. else leave path alone.
  95                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  96                                 }
  97
  98                                 it = parameters.find("sabund");
  99                                 //user has given a template file
 100                                 if(it != parameters.end()){
 101                                         path = m->hasPath(it->second);
 102                                         //if the user has not given a path then, add inputdir. else leave path alone.
 103                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 104                                 }
 105
 106                                 it = parameters.find("rabund");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 112                                 }
 113
 114                                 it = parameters.find("ordergroup");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 120                                 }
 121
 122                                 it = parameters.find("relabund");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 128                                 }
 129                         }
 130
 131
 132                         //if the user changes the output directory command factory will send this info to us in the output parameter
 133                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 134
 135                         //check for required parameters
 136                         listfile = validParameter.validFile(parameters, "list", true);
 137                         if (listfile == "not open") { abort = true; }
 138                         else if (listfile == "not found") { listfile = ""; }
 139                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
 140
 141                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 142                         if (sabundfile == "not open") { abort = true; }
 143                         else if (sabundfile == "not found") { sabundfile = ""; }
 144                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 145
 146                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 147                         if (rabundfile == "not open") { abort = true; }
 148                         else if (rabundfile == "not found") { rabundfile = ""; }
 149                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
 150
 151                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 152                         if (ordergroupfile == "not open") { abort = true; }
 153                         else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 154                         else {  globaldata->setOrderGroupFile(ordergroupfile);  }
 155
 156                         sharedfile = validParameter.validFile(parameters, "shared", true);
 157                         if (sharedfile == "not open") { abort = true; }
 158                         else if (sharedfile == "not found") { sharedfile = ""; }
 159                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
 160
 161                         relAbundfile = validParameter.validFile(parameters, "relabund", true);
 162                         if (relAbundfile == "not open") { abort = true; }
 163                         else if (relAbundfile == "not found") { relAbundfile = ""; }
 164                         else {  globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund");   }
 165
 166
 167                         groupfile = validParameter.validFile(parameters, "group", true);
 168                         if (groupfile == "not open") { abort = true; }
 169                         else if (groupfile == "not found") { groupfile = ""; }
 170                         else {
 171                                 globaldata->setGroupFile(groupfile);
 172                                 groupMap = new GroupMap(groupfile);
 173
 174                                 int error = groupMap->readMap();
 175                                 if (error == 1) { abort = true; }
 176
 177                                 globaldata->gGroupmap = groupMap;
 178                         }
 179
 180                         groups = validParameter.validFile(parameters, "groups", false);
 181                         if (groups == "not found") { groups = ""; }
 182                         else {
 183                                 m->splitAtDash(groups, Groups);
 184                                 globaldata->Groups = Groups;
 185                         }
 186
 187                         //you are doing a list and group shared
 188                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
 189
 190                         //you have not given a file
 191                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
 192                                 m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
 193                         }
 194
 195                         //check for optional parameter and set defaults
 196                         // ...at some point should added some additional type checking...
 197                         label = validParameter.validFile(parameters, "label", false);
 198                         if (label == "not found") { label = ""; }
 199                         else {
 200                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 201                                 else { allLines = 1;  }
 202                                 globaldata->labels = labels;
 203                         }
 204
 205                         globaldata->allLines = allLines;
 206
 207                         orderfile = validParameter.validFile(parameters, "order", true);
 208                         if (orderfile == "not open") { abort = true; }
 209                         else if (orderfile == "not found") { orderfile = ""; }
 210                         else {  globaldata->setOrderFile(orderfile);    }
 211
 212
 213                         if (abort == false) {
 214                                 //gets whichever one of the above is set
 215                                 filename = globaldata->inputFileName;
 216                         }
 217                          */
 218                 }
 219
 220         }
 221         catch(exception& e) {
 222                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 223                 exit(1);
 224         }
 225 }
 226 ///**********************************************************************************************************************
 227
 228 int ReadOtuCommand::execute(){
 229         try {
 230
 231                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 232                 m->mothurOut(getHelpString()); m->mothurOutEndLine();
 233
 234                 /*
 235                 if (globaldata->getFormat() == "shared") {
 236
 237                         shared = new SharedCommand(outputDir);
 238                         int okay = shared->execute();
 239
 240                         //problem with shared
 241                         if (okay == 1) {
 242                                 globaldata->setListFile("");
 243                                 globaldata->setGroupFile("");
 244                                 globaldata->setSharedFile("");
 245                         }else { //shared command outputs the filenames
 246                                 //m->mothurOutEndLine();
 247                                 //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 248                                 //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
 249                                 //m->mothurOutEndLine();
 250                         }
 251
 252                         outputTypes = shared->getOutputFiles();
 253
 254                         //set rabund file as new current rabundfile
 255                         string current = "";
 256                         itTypes = outputTypes.find("rabund");
 257                         if (itTypes != outputTypes.end()) {
 258                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 259                         }
 260
 261                         itTypes = outputTypes.find("shared");
 262                         if (itTypes != outputTypes.end()) {
 263                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 264                         }
 265
 266                         delete shared;
 267                 }
 268                 */
 269
 270                 return 0;
 271         }
 272         catch(exception& e) {
 273                 m->errorOut(e, "ReadOtuCommand", "execute");
 274                 exit(1);
 275         }
 276 }
 277 //**********************************************************************************************************************