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 vector<string> ReadOtuCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "ReadOtuCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 ReadOtuCommand::ReadOtuCommand(){
  26         try {
  27                 abort = true; calledHelp = true;
  28                 vector<string> tempOutNames;
  29                 outputTypes["rabund"] = tempOutNames;
  30                 outputTypes["shared"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> ReadOtuCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"list","shared","relabund","sabund","rabund","or"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> ReadOtuCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "ReadOtuCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 ReadOtuCommand::ReadOtuCommand(string option)  {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false; calledHelp = false;
  65                 allLines = 1;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; calledHelp = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string, string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79                         map<string, string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["rabund"] = tempOutNames;
  89                         outputTypes["shared"] = tempOutNames;
  90
  91                         globaldata->newRead();
  92
  93                         //if the user changes the input directory command factory will send this info to us in the output parameter
  94                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  95                         if (inputDir == "not found"){   inputDir = "";          }
  96                         else {
  97                                 string path;
  98                                 it = parameters.find("list");
  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["list"] = inputDir + it->second;             }
 104                                 }
 105
 106                                 it = parameters.find("order");
 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["order"] = inputDir + it->second;            }
 112                                 }
 113
 114                                 it = parameters.find("shared");
 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["shared"] = inputDir + it->second;           }
 120                                 }
 121
 122                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 128                                 }
 129
 130                                 it = parameters.find("sabund");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 136                                 }
 137
 138                                 it = parameters.find("rabund");
 139                                 //user has given a template file
 140                                 if(it != parameters.end()){
 141                                         path = m->hasPath(it->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 144                                 }
 145
 146                                 it = parameters.find("ordergroup");
 147                                 //user has given a template file
 148                                 if(it != parameters.end()){
 149                                         path = m->hasPath(it->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 152                                 }
 153
 154                                 it = parameters.find("relabund");
 155                                 //user has given a template file
 156                                 if(it != parameters.end()){
 157                                         path = m->hasPath(it->second);
 158                                         //if the user has not given a path then, add inputdir. else leave path alone.
 159                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 160                                 }
 161                         }
 162
 163
 164                         //if the user changes the output directory command factory will send this info to us in the output parameter
 165                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 166
 167                         //check for required parameters
 168                         listfile = validParameter.validFile(parameters, "list", true);
 169                         if (listfile == "not open") { abort = true; }
 170                         else if (listfile == "not found") { listfile = ""; }
 171                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
 172
 173                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 174                         if (sabundfile == "not open") { abort = true; }
 175                         else if (sabundfile == "not found") { sabundfile = ""; }
 176                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 177
 178                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 179                         if (rabundfile == "not open") { abort = true; }
 180                         else if (rabundfile == "not found") { rabundfile = ""; }
 181                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
 182
 183                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 184                         if (ordergroupfile == "not open") { abort = true; }
 185                         else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 186                         else {  globaldata->setOrderGroupFile(ordergroupfile);  }
 187
 188                         sharedfile = validParameter.validFile(parameters, "shared", true);
 189                         if (sharedfile == "not open") { abort = true; }
 190                         else if (sharedfile == "not found") { sharedfile = ""; }
 191                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
 192
 193                         relAbundfile = validParameter.validFile(parameters, "relabund", true);
 194                         if (relAbundfile == "not open") { abort = true; }
 195                         else if (relAbundfile == "not found") { relAbundfile = ""; }
 196                         else {  globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund");   }
 197
 198
 199                         groupfile = validParameter.validFile(parameters, "group", true);
 200                         if (groupfile == "not open") { abort = true; }
 201                         else if (groupfile == "not found") { groupfile = ""; }
 202                         else {
 203                                 globaldata->setGroupFile(groupfile);
 204                                 groupMap = new GroupMap(groupfile);
 205
 206                                 int error = groupMap->readMap();
 207                                 if (error == 1) { abort = true; }
 208
 209                                 globaldata->gGroupmap = groupMap;
 210                         }
 211
 212                         groups = validParameter.validFile(parameters, "groups", false);
 213                         if (groups == "not found") { groups = ""; }
 214                         else {
 215                                 m->splitAtDash(groups, Groups);
 216                                 globaldata->Groups = Groups;
 217                         }
 218
 219                         //you are doing a list and group shared
 220                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
 221
 222                         //you have not given a file
 223                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
 224                                 m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
 225                         }
 226
 227                         //check for optional parameter and set defaults
 228                         // ...at some point should added some additional type checking...
 229                         label = validParameter.validFile(parameters, "label", false);
 230                         if (label == "not found") { label = ""; }
 231                         else {
 232                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 233                                 else { allLines = 1;  }
 234                                 globaldata->labels = labels;
 235                         }
 236
 237                         globaldata->allLines = allLines;
 238
 239                         orderfile = validParameter.validFile(parameters, "order", true);
 240                         if (orderfile == "not open") { abort = true; }
 241                         else if (orderfile == "not found") { orderfile = ""; }
 242                         else {  globaldata->setOrderFile(orderfile);    }
 243
 244
 245                         if (abort == false) {
 246                                 //gets whichever one of the above is set
 247                                 filename = globaldata->inputFileName;
 248                         }
 249                 }
 250
 251         }
 252         catch(exception& e) {
 253                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 254                 exit(1);
 255         }
 256 }
 257 //**********************************************************************************************************************
 258
 259 void ReadOtuCommand::help(){
 260         try {
 261                 m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
 262                 m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
 263                 m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, relabund, group, order, ordergroup, label and groups.\n");
 264                 m->mothurOut("The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
 265                 m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
 266                 m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
 267                 m->mothurOut("The label parameter is used to read specific labels in your input.\n");
 268                 m->mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n");
 269                 m->mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile).  \n");
 270                 m->mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
 271                 m->mothurOut("and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n");
 272                 m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
 273                 m->mothurOut("You can use the ordergroup parameter to provide a file containing a list of group names in the order you would like them to appear in your shared file. \n");
 274                 m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 275
 276         }
 277         catch(exception& e) {
 278                 m->errorOut(e, "ReadOtuCommand", "help");
 279                 exit(1);
 280         }
 281 }
 282
 283
 284
 285 //**********************************************************************************************************************
 286 ReadOtuCommand::~ReadOtuCommand(){}
 287 //**********************************************************************************************************************
 288
 289 int ReadOtuCommand::execute(){
 290         try {
 291
 292                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 293
 294                 if (globaldata->getFormat() == "shared") {
 295
 296                         shared = new SharedCommand(outputDir);
 297                         int okay = shared->execute();
 298
 299                         //problem with shared
 300                         if (okay == 1) {
 301                                 globaldata->setListFile("");
 302                                 globaldata->setGroupFile("");
 303                                 globaldata->setSharedFile("");
 304                         }else { //shared command outputs the filenames
 305                                 //m->mothurOutEndLine();
 306                                 //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 307                                 //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
 308                                 //m->mothurOutEndLine();
 309                         }
 310
 311                         outputTypes = shared->getOutputFiles();
 312
 313                         delete shared;
 314                 }
 315                 return 0;
 316         }
 317         catch(exception& e) {
 318                 m->errorOut(e, "ReadOtuCommand", "execute");
 319                 exit(1);
 320         }
 321 }
 322 //**********************************************************************************************************************