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;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["rabund"] = tempOutNames;
  31                 outputTypes["shared"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> ReadOtuCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"list","shared","relabund","sabund","rabund","or"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> ReadOtuCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "ReadOtuCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 ReadOtuCommand::ReadOtuCommand(string option)  {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65                 abort = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string, string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["rabund"] = tempOutNames;
  90                         outputTypes["shared"] = tempOutNames;
  91
  92                         globaldata->newRead();
  93
  94                         //if the user changes the input directory command factory will send this info to us in the output parameter
  95                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  96                         if (inputDir == "not found"){   inputDir = "";          }
  97                         else {
  98                                 string path;
  99                                 it = parameters.find("list");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 105                                 }
 106
 107                                 it = parameters.find("order");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
 113                                 }
 114
 115                                 it = parameters.find("shared");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 121                                 }
 122
 123                                 it = parameters.find("group");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 129                                 }
 130
 131                                 it = parameters.find("sabund");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 137                                 }
 138
 139                                 it = parameters.find("rabund");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 145                                 }
 146
 147                                 it = parameters.find("ordergroup");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 153                                 }
 154
 155                                 it = parameters.find("relabund");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 161                                 }
 162                         }
 163
 164
 165                         //if the user changes the output directory command factory will send this info to us in the output parameter
 166                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 167
 168                         //check for required parameters
 169                         listfile = validParameter.validFile(parameters, "list", true);
 170                         if (listfile == "not open") { abort = true; }
 171                         else if (listfile == "not found") { listfile = ""; }
 172                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
 173
 174                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 175                         if (sabundfile == "not open") { abort = true; }
 176                         else if (sabundfile == "not found") { sabundfile = ""; }
 177                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 178
 179                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 180                         if (rabundfile == "not open") { abort = true; }
 181                         else if (rabundfile == "not found") { rabundfile = ""; }
 182                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
 183
 184                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 185                         if (ordergroupfile == "not open") { abort = true; }
 186                         else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 187                         else {  globaldata->setOrderGroupFile(ordergroupfile);  }
 188
 189                         sharedfile = validParameter.validFile(parameters, "shared", true);
 190                         if (sharedfile == "not open") { abort = true; }
 191                         else if (sharedfile == "not found") { sharedfile = ""; }
 192                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
 193
 194                         relAbundfile = validParameter.validFile(parameters, "relabund", true);
 195                         if (relAbundfile == "not open") { abort = true; }
 196                         else if (relAbundfile == "not found") { relAbundfile = ""; }
 197                         else {  globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund");   }
 198
 199
 200                         groupfile = validParameter.validFile(parameters, "group", true);
 201                         if (groupfile == "not open") { abort = true; }
 202                         else if (groupfile == "not found") { groupfile = ""; }
 203                         else {
 204                                 globaldata->setGroupFile(groupfile);
 205                                 groupMap = new GroupMap(groupfile);
 206
 207                                 int error = groupMap->readMap();
 208                                 if (error == 1) { abort = true; }
 209
 210                                 globaldata->gGroupmap = groupMap;
 211                         }
 212
 213                         groups = validParameter.validFile(parameters, "groups", false);
 214                         if (groups == "not found") { groups = ""; }
 215                         else {
 216                                 m->splitAtDash(groups, Groups);
 217                                 globaldata->Groups = Groups;
 218                         }
 219
 220                         //you are doing a list and group shared
 221                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
 222
 223                         //you have not given a file
 224                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
 225                                 m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
 226                         }
 227
 228                         //check for optional parameter and set defaults
 229                         // ...at some point should added some additional type checking...
 230                         label = validParameter.validFile(parameters, "label", false);
 231                         if (label == "not found") { label = ""; }
 232                         else {
 233                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 234                                 else { allLines = 1;  }
 235                                 globaldata->labels = labels;
 236                         }
 237
 238                         globaldata->allLines = allLines;
 239
 240                         orderfile = validParameter.validFile(parameters, "order", true);
 241                         if (orderfile == "not open") { abort = true; }
 242                         else if (orderfile == "not found") { orderfile = ""; }
 243                         else {  globaldata->setOrderFile(orderfile);    }
 244
 245
 246                         if (abort == false) {
 247                                 //gets whichever one of the above is set
 248                                 filename = globaldata->inputFileName;
 249                         }
 250                 }
 251
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 255                 exit(1);
 256         }
 257 }
 258 //**********************************************************************************************************************
 259
 260 void ReadOtuCommand::help(){
 261         try {
 262                 m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
 263                 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");
 264                 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");
 265                 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");
 266                 m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
 267                 m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
 268                 m->mothurOut("The label parameter is used to read specific labels in your input.\n");
 269                 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");
 270                 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");
 271                 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");
 272                 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");
 273                 m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
 274                 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");
 275                 m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 276
 277         }
 278         catch(exception& e) {
 279                 m->errorOut(e, "ReadOtuCommand", "help");
 280                 exit(1);
 281         }
 282 }
 283
 284
 285
 286 //**********************************************************************************************************************
 287 ReadOtuCommand::~ReadOtuCommand(){}
 288 //**********************************************************************************************************************
 289
 290 int ReadOtuCommand::execute(){
 291         try {
 292
 293                 if (abort == true) {    return 0;       }
 294
 295                 if (globaldata->getFormat() == "shared") {
 296
 297                         shared = new SharedCommand(outputDir);
 298                         int okay = shared->execute();
 299
 300                         //problem with shared
 301                         if (okay == 1) {
 302                                 globaldata->setListFile("");
 303                                 globaldata->setGroupFile("");
 304                                 globaldata->setSharedFile("");
 305                         }else { //shared command outputs the filenames
 306                                 //m->mothurOutEndLine();
 307                                 //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 308                                 //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
 309                                 //m->mothurOutEndLine();
 310                         }
 311
 312                         outputTypes = shared->getOutputFiles();
 313
 314                         delete shared;
 315                 }
 316                 return 0;
 317         }
 318         catch(exception& e) {
 319                 m->errorOut(e, "ReadOtuCommand", "execute");
 320                 exit(1);
 321         }
 322 }
 323 //**********************************************************************************************************************