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