getlistcountcommand.cpp

   1 /*
   2  *  getlistcountcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/12/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlistcountcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetListCountCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  16                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  17                 CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort);
  18                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  19                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  20
  21                 vector<string> myArray;
  22                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "GetListCountCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string GetListCountCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The get.otulist command parameters are list, sort and label.  list is required, unless you have a valid current list file.\n";
  35                 helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
  36                 helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n";
  37                 helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n";
  38                 helpString += "If name is selected the output will be a sequence name followed by its otu number.\n";
  39                 helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n";
  40                 helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
  41                 helpString += "The default value for label is all lines in your inputfile.\n";
  42                 helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n";
  43                 helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
  44                 return helpString;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "GetListCountCommand", "getHelpString");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string GetListCountCommand::getOutputFileNameTag(string type, string inputName=""){
  53         try {
  54         string outputFileName = "";
  55                 map<string, vector<string> >::iterator it;
  56
  57         //is this a type this command creates
  58         it = outputTypes.find(type);
  59         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  60         else {
  61             if (type == "otu") {  outputFileName =  "otu"; }
  62             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  63         }
  64         return outputFileName;
  65         }
  66         catch(exception& e) {
  67                 m->errorOut(e, "GetListCountCommand", "getOutputFileNameTag");
  68                 exit(1);
  69         }
  70 }
  71 //**********************************************************************************************************************
  72 GetListCountCommand::GetListCountCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76                 vector<string> tempOutNames;
  77                 outputTypes["otu"] = tempOutNames;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
  81                 exit(1);
  82         }
  83 }
  84 //**********************************************************************************************************************
  85 GetListCountCommand::GetListCountCommand(string option)  {
  86         try {
  87                 abort = false; calledHelp = false;
  88                 allLines = 1;
  89
  90                 //allow user to run help
  91                 if(option == "help") { help(); abort = true; calledHelp = true; }
  92                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  93
  94                 else {
  95                         vector<string> myArray = setParameters();
  96
  97                         OptionParser parser(option);
  98                         map<string, string> parameters = parser.getParameters();
  99
 100                         ValidParameters validParameter;
 101                         map<string, string>::iterator it;
 102
 103                         //check to make sure all parameters are valid for command
 104                         for (it = parameters.begin(); it != parameters.end(); it++) {
 105                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 106                         }
 107
 108                         //initialize outputTypes
 109                         vector<string> tempOutNames;
 110                         outputTypes["otu"] = tempOutNames;
 111
 112                         //if the user changes the input directory command factory will send this info to us in the output parameter
 113                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 114                         if (inputDir == "not found"){   inputDir = "";          }
 115                         else {
 116                                 string path;
 117                                 it = parameters.find("list");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 123                                 }
 124                         }
 125
 126                         //if the user changes the output directory command factory will send this info to us in the output parameter
 127                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 128
 129                         //check for required parameters
 130                         listfile = validParameter.validFile(parameters, "list", true);
 131                         if (listfile == "not found")  {
 132                                 listfile = m->getListFile();
 133                                 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 134                                 else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 135                         }
 136                         else if (listfile == "not open") { abort = true; }
 137                         else { m->setListFile(listfile); }
 138
 139
 140                         //check for optional parameter and set defaults
 141                         // ...at some point should added some additional type checking...
 142                         sort = validParameter.validFile(parameters, "sort", false);       if (sort == "not found") { sort = "otu"; }
 143                         if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; }
 144
 145                         label = validParameter.validFile(parameters, "label", false);
 146                         if (label == "not found") { label = ""; }
 147                         else {
 148                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 149                                 else { allLines = 1;  }
 150                         }
 151                 }
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159
 160 int GetListCountCommand::execute(){
 161         try {
 162                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 163
 164                 input = new InputData(listfile, "list");
 165                 list = input->getListVector();
 166                 string lastLabel = list->getLabel();
 167
 168                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 169                 set<string> processedLabels;
 170                 set<string> userLabels = labels;
 171
 172                 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 173
 174                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 175
 176                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 177
 178                                 process(list);
 179
 180                                 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 181
 182                                 processedLabels.insert(list->getLabel());
 183                                 userLabels.erase(list->getLabel());
 184                         }
 185
 186                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 187                                 string saveLabel = list->getLabel();
 188
 189                                 delete list;
 190                                 list = input->getListVector(lastLabel);
 191
 192                                 process(list);
 193
 194                                 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 195
 196
 197                                 processedLabels.insert(list->getLabel());
 198                                 userLabels.erase(list->getLabel());
 199
 200                                 //restore real lastlabel to save below
 201                                 list->setLabel(saveLabel);
 202                         }
 203
 204                         lastLabel = list->getLabel();
 205
 206                         delete list;
 207                         list = input->getListVector();
 208                 }
 209
 210
 211                 //output error messages about any remaining user labels
 212                 set<string>::iterator it;
 213                 bool needToRun = false;
 214                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 215                         m->mothurOut("Your file does not include the label " + *it);
 216                         if (processedLabels.count(lastLabel) != 1) {
 217                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 218                                 needToRun = true;
 219                         }else {
 220                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 221                         }
 222                 }
 223
 224                 //run last label if you need to
 225                 if (needToRun == true)  {
 226                         if (list != NULL) {             delete list;    }
 227                         list = input->getListVector(lastLabel);
 228
 229                         process(list);
 230
 231                         if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 232
 233                         delete list;
 234                 }
 235
 236                 delete input;
 237
 238                 m->mothurOutEndLine();
 239                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 240                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 241                 m->mothurOutEndLine();
 242
 243                 return 0;
 244         }
 245         catch(exception& e) {
 246                 m->errorOut(e, "GetListCountCommand", "execute");
 247                 exit(1);
 248         }
 249 }
 250
 251 //**********************************************************************************************************************
 252 //return 1 if error, 0 otherwise
 253 void GetListCountCommand::process(ListVector* list) {
 254         try {
 255                 string binnames;
 256                 if (outputDir == "") { outputDir += m->hasPath(listfile); }
 257                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." +getOutputFileNameTag("otu");
 258                 m->openOutputFile(outputFileName, out);
 259                 outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
 260
 261                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 262
 263                 //for each bin in the list vector
 264                 for (int i = 0; i < list->getNumBins(); i++) {
 265                         if (m->control_pressed) { break; }
 266
 267                         binnames = list->get(i);
 268
 269                         if (sort == "otu") {
 270                                 out << i+1 << '\t' << binnames << endl;
 271                         }else{ //sort = name
 272                                 vector<string> names;
 273                                 m->splitAtComma(binnames, names);
 274
 275                                 for (int j = 0; j < names.size(); j++) {
 276                                         out << names[j] << '\t' << i+1 << endl;
 277                                 }
 278                         }
 279                 }
 280
 281                 out.close();
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "GetListCountCommand", "process");
 285                 exit(1);
 286         }
 287 }
 288 //**********************************************************************************************************************
 289
 290