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 GetListCountCommand::GetListCountCommand(string option){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17                 allLines = 1;
  18                 labels.clear();
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string AlignArray[] =  {"list","label"};
  26                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string, string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         string ranRead = globaldata->getListFile();
  39
  40                         //check for required parameters
  41                         listfile = validParameter.validFile(parameters, "list", true);
  42                         if ((listfile == "not found") && (globaldata->getListFile() == ""))  { mothurOut("You must read a listfile before running the get.listcount command.");  mothurOutEndLine(); abort = true; }
  43                         else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); }
  44                         else if (listfile == "not open") { abort = true; }
  45                         else { globaldata->setListFile(listfile); }
  46
  47                         //check for optional parameter and set defaults
  48                         // ...at some point should added some additional type checking...
  49
  50                         label = validParameter.validFile(parameters, "label", false);
  51                         if (label == "not found") { label = ""; }
  52                         else {
  53                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  54                                 else { allLines = 1;  }
  55                         }
  56
  57                         //if the user has not specified any labels use the ones from read.otu
  58                         if ((label == "") && (ranRead != "")) {
  59                                 allLines = globaldata->allLines;
  60                                 labels = globaldata->labels;
  61                         }
  62                 }
  63         }
  64         catch(exception& e) {
  65                 errorOut(e, "GetListCountCommand", "GetListCountCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 void GetListCountCommand::help(){
  72         try {
  73                 mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
  74                 mothurOut("The get.listcount command parameters are list and label.  No parameters are required.\n");
  75                 mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
  76                 mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
  77                 mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
  78                 mothurOut("The default value for label is all lines in your inputfile.\n");
  79                 mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n");
  80                 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
  81         }
  82         catch(exception& e) {
  83                 errorOut(e, "GetListCountCommand", "help");
  84                 exit(1);
  85         }
  86 }
  87
  88 //**********************************************************************************************************************
  89
  90 GetListCountCommand::~GetListCountCommand(){}
  91
  92 //**********************************************************************************************************************
  93
  94 int GetListCountCommand::execute(){
  95         try {
  96                 if (abort == true) {    return 0;       }
  97
  98                 globaldata->setFormat("list");
  99
 100                 //read list file
 101                 read = new ReadOTUFile(listfile);
 102                 read->read(&*globaldata);
 103
 104                 input = globaldata->ginput;
 105                 list = globaldata->gListVector;
 106                 string lastLabel = list->getLabel();
 107
 108                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 109                 set<string> processedLabels;
 110                 set<string> userLabels = labels;
 111
 112                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 113
 114                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 115
 116                                 process(list);
 117
 118                                 processedLabels.insert(list->getLabel());
 119                                 userLabels.erase(list->getLabel());
 120                         }
 121
 122                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 123                                 string saveLabel = list->getLabel();
 124
 125                                 delete list;
 126                                 list = input->getListVector(lastLabel);
 127
 128                                 process(list);
 129
 130                                 processedLabels.insert(list->getLabel());
 131                                 userLabels.erase(list->getLabel());
 132
 133                                 //restore real lastlabel to save below
 134                                 list->setLabel(saveLabel);
 135                         }
 136
 137                         lastLabel = list->getLabel();
 138
 139                         delete list;
 140                         list = input->getListVector();
 141                 }
 142
 143
 144                 //output error messages about any remaining user labels
 145                 set<string>::iterator it;
 146                 bool needToRun = false;
 147                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 148                         mothurOut("Your file does not include the label " + *it);
 149                         if (processedLabels.count(lastLabel) != 1) {
 150                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 151                                 needToRun = true;
 152                         }else {
 153                                 mothurOut(". Please refer to " + lastLabel + ".");  mothurOutEndLine();
 154                         }
 155                 }
 156
 157                 //run last label if you need to
 158                 if (needToRun == true)  {
 159                         if (list != NULL) {             delete list;    }
 160                         list = input->getListVector(lastLabel);
 161
 162                         process(list);
 163                         delete list;
 164                 }
 165
 166                 delete read;
 167                 globaldata->gListVector = NULL;
 168
 169                 return 0;
 170         }
 171         catch(exception& e) {
 172                 errorOut(e, "GetListCountCommand", "execute");
 173                 exit(1);
 174         }
 175 }
 176
 177 //**********************************************************************************************************************
 178 //return 1 if error, 0 otherwise
 179 void GetListCountCommand::process(ListVector* list) {
 180         try {
 181                 string binnames, name, sequence;
 182                 string outputFileName = getRootName(listfile) + list->getLabel() + ".otu";
 183                 openOutputFile(outputFileName, out);
 184
 185                 mothurOut(list->getLabel()); mothurOutEndLine();
 186
 187                 //for each bin in the list vector
 188                 for (int i = 0; i < list->getNumBins(); i++) {
 189                         binnames = list->get(i);
 190                         out << i+1 << '\t' << binnames << endl;
 191                 }
 192
 193                 out.close();
 194         }
 195         catch(exception& e) {
 196                 errorOut(e, "GetListCountCommand", "process");
 197                 exit(1);
 198         }
 199 }
 200 //**********************************************************************************************************************
 201
 202