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", "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 = 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 = 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 = 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 = 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 = 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 = 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 = 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                         }
 102
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 106
 107                         //check for required parameters
 108                         listfile = validParameter.validFile(parameters, "list", true);
 109                         if (listfile == "not open") { abort = true; }
 110                         else if (listfile == "not found") { listfile = ""; }
 111                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
 112
 113                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 114                         if (sabundfile == "not open") { abort = true; }
 115                         else if (sabundfile == "not found") { sabundfile = ""; }
 116                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 117
 118                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 119                         if (rabundfile == "not open") { abort = true; }
 120                         else if (rabundfile == "not found") { rabundfile = ""; }
 121                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
 122
 123                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 124                         if (ordergroupfile == "not open") { abort = true; }
 125                         else if (ordergroupfile == "not found") { ordergroupfile = ""; }
 126                         else {  globaldata->setOrderGroupFile(ordergroupfile);  }
 127
 128                         sharedfile = validParameter.validFile(parameters, "shared", true);
 129                         if (sharedfile == "not open") { abort = true; }
 130                         else if (sharedfile == "not found") { sharedfile = ""; }
 131                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
 132
 133                         groupfile = validParameter.validFile(parameters, "group", true);
 134                         if (groupfile == "not open") { abort = true; }
 135                         else if (groupfile == "not found") { groupfile = ""; }
 136                         else {
 137                                 globaldata->setGroupFile(groupfile);
 138                                 groupMap = new GroupMap(groupfile);
 139
 140                                 int error = groupMap->readMap();
 141                                 if (error == 1) { abort = true; }
 142
 143                                 globaldata->gGroupmap = groupMap;
 144                         }
 145
 146                         groups = validParameter.validFile(parameters, "groups", false);
 147                         if (groups == "not found") { groups = ""; }
 148                         else {
 149                                 splitAtDash(groups, Groups);
 150                                 globaldata->Groups = Groups;
 151                         }
 152
 153                         //you are doing a list and group shared
 154                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
 155
 156                         //you have not given a file
 157                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
 158                                 m->mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
 159                         }
 160
 161                         //check for optional parameter and set defaults
 162                         // ...at some point should added some additional type checking...
 163                         label = validParameter.validFile(parameters, "label", false);
 164                         if (label == "not found") { label = ""; }
 165                         else {
 166                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
 167                                 else { allLines = 1;  }
 168                                 globaldata->labels = labels;
 169                         }
 170
 171                         globaldata->allLines = allLines;
 172
 173                         orderfile = validParameter.validFile(parameters, "order", true);
 174                         if (orderfile == "not open") { abort = true; }
 175                         else if (orderfile == "not found") { orderfile = ""; }
 176                         else {  globaldata->setOrderFile(orderfile);    }
 177
 178
 179                         if (abort == false) {
 180                                 //gets whichever one of the above is set
 181                                 filename = globaldata->inputFileName;
 182                         }
 183                 }
 184
 185         }
 186         catch(exception& e) {
 187                 m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 188                 exit(1);
 189         }
 190 }
 191 //**********************************************************************************************************************
 192
 193 void ReadOtuCommand::help(){
 194         try {
 195                 m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
 196                 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");
 197                 m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, ordergroup, label and groups.\n");
 198                 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");
 199                 m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
 200                 m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
 201                 m->mothurOut("The label parameter is used to read specific labels in your input.\n");
 202                 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");
 203                 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");
 204                 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");
 205                 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");
 206                 m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
 207                 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");
 208                 m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 209
 210         }
 211         catch(exception& e) {
 212                 m->errorOut(e, "ReadOtuCommand", "help");
 213                 exit(1);
 214         }
 215 }
 216
 217
 218
 219 //**********************************************************************************************************************
 220 ReadOtuCommand::~ReadOtuCommand(){}
 221 //**********************************************************************************************************************
 222
 223 int ReadOtuCommand::execute(){
 224         try {
 225
 226                 if (abort == true) {    return 0;       }
 227
 228                 if (globaldata->getFormat() == "shared") {
 229
 230                         shared = new SharedCommand(outputDir);
 231                         int okay = shared->execute();
 232
 233                         //problem with shared
 234                         if (okay == 1) {
 235                                 globaldata->setListFile("");
 236                                 globaldata->setGroupFile("");
 237                                 globaldata->setSharedFile("");
 238                         }else { //shared command outputs the filenames
 239                                 //m->mothurOutEndLine();
 240                                 //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 241                                 //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
 242                                 //m->mothurOutEndLine();
 243                         }
 244
 245                         delete shared;
 246                 }
 247                 return 0;
 248         }
 249         catch(exception& e) {
 250                 m->errorOut(e, "ReadOtuCommand", "execute");
 251                 exit(1);
 252         }
 253 }
 254 //**********************************************************************************************************************