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"};
  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
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         globaldata->newRead();
  38
  39                         //check for required parameters
  40                         listfile = validParameter.validFile(parameters, "list", true);
  41                         if (listfile == "not open") { abort = true; }
  42                         else if (listfile == "not found") { listfile = ""; }
  43                         else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
  44
  45                         sabundfile = validParameter.validFile(parameters, "sabund", true);
  46                         if (sabundfile == "not open") { abort = true; }
  47                         else if (sabundfile == "not found") { sabundfile = ""; }
  48                         else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
  49
  50                         rabundfile = validParameter.validFile(parameters, "rabund", true);
  51                         if (rabundfile == "not open") { abort = true; }
  52                         else if (rabundfile == "not found") { rabundfile = ""; }
  53                         else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
  54
  55                         sharedfile = validParameter.validFile(parameters, "shared", true);
  56                         if (sharedfile == "not open") { abort = true; }
  57                         else if (sharedfile == "not found") { sharedfile = ""; }
  58                         else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
  59
  60                         groupfile = validParameter.validFile(parameters, "group", true);
  61                         if (groupfile == "not open") { abort = true; }
  62                         else if (groupfile == "not found") { groupfile = ""; }
  63                         else {
  64                                 globaldata->setGroupFile(groupfile);
  65                                 groupMap = new GroupMap(groupfile);
  66                                 groupMap->readMap();
  67                                 globaldata->gGroupmap = groupMap;
  68                         }
  69
  70                         groups = validParameter.validFile(parameters, "groups", false);
  71                         if (groups == "not found") { groups = ""; }
  72                         else {
  73                                 splitAtDash(groups, Groups);
  74                                 globaldata->Groups = Groups;
  75                         }
  76
  77                         //you are doing a list and group shared
  78                         if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
  79
  80                         //you have not given a file
  81                         if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
  82                                 mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
  83                         }
  84
  85                         //check for optional parameter and set defaults
  86                         // ...at some point should added some additional type checking...
  87                         label = validParameter.validFile(parameters, "label", false);
  88                         if (label == "not found") { label = ""; }
  89                         else {
  90                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  91                                 else { allLines = 1;  }
  92                                 globaldata->labels = labels;
  93                         }
  94
  95                         globaldata->allLines = allLines;
  96
  97                         orderfile = validParameter.validFile(parameters, "order", true);
  98                         if (orderfile == "not open") { abort = true; }
  99                         else if (orderfile == "not found") { orderfile = ""; }
 100                         else {  globaldata->setOrderFile(orderfile);    }
 101
 102
 103                         if (abort == false) {
 104                                 //gets whichever one of the above is set
 105                                 filename = globaldata->inputFileName;
 106                         }
 107
 108                 }
 109
 110         }
 111         catch(exception& e) {
 112                 errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 113                 exit(1);
 114         }
 115 }
 116 //**********************************************************************************************************************
 117
 118 void ReadOtuCommand::help(){
 119         try {
 120                 mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
 121                 mothurOut("collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
 122                 mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order and label.\n");
 123                 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");
 124                 mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
 125                 mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
 126                 mothurOut("The label parameter is used to read specific labels in your input.\n");
 127                 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");
 128                 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");
 129                 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");
 130                 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");
 131                 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 132
 133         }
 134         catch(exception& e) {
 135                 errorOut(e, "ReadOtuCommand", "help");
 136                 exit(1);
 137         }
 138 }
 139
 140
 141
 142 //**********************************************************************************************************************
 143
 144 ReadOtuCommand::~ReadOtuCommand(){
 145         }
 146
 147 //**********************************************************************************************************************
 148
 149 int ReadOtuCommand::execute(){
 150         try {
 151
 152                 if (abort == true) {    return 0;       }
 153
 154                 if (globaldata->getFormat() == "shared") {
 155
 156                         shared = new SharedCommand();
 157                         int okay = shared->execute();
 158                         delete shared;
 159
 160                         //problem with shared
 161                         if (okay == 1) {
 162                                 globaldata->setListFile("");
 163                                 globaldata->setGroupFile("");
 164                                 globaldata->setSharedFile("");
 165                         }else{
 166
 167                                 //change format to shared  to speed up commands
 168                                 globaldata->setFormat("sharedfile");
 169                                 globaldata->setListFile("");
 170                                 globaldata->setGroupFile("");
 171                                 globaldata->setSharedFile(getRootName(filename) + "shared");
 172                         }
 173                 }
 174                 return 0;
 175         }
 176         catch(exception& e) {
 177                 errorOut(e, "ReadOtuCommand", "execute");
 178                 exit(1);
 179         }
 180 }
 181 //**********************************************************************************************************************