countgroupscommand.cpp

   1 /*
   2  *  countgroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 8/9/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "countgroupscommand.h"
  11 #include "sharedutilities.h"
  12 #include "inputdata.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> CountGroupsCommand::setParameters(){
  16         try {
  17                 CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  20                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "CountGroupsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string CountGroupsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n";
  38                 helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n";
  39                 helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n";
  40                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n";
  41                 helpString += "The count.groups command should be in the following format: count.groups(accnos=yourAccnos, group=yourGroupFile).\n";
  42                 helpString += "Example count.groups(accnos=amazon.accnos, group=amazon.groups).\n";
  43                 helpString += "or count.groups(groups=pasture, group=amazon.groups).\n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. group), '=' and parameters (i.e.yourGroupFile).\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "CountGroupsCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 CountGroupsCommand::CountGroupsCommand(){
  54         try {
  55                 abort = true; calledHelp = true;
  56                 setParameters();
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64 CountGroupsCommand::CountGroupsCommand(string option)  {
  65         try {
  66                 abort = false; calledHelp = false;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  71
  72                 else {
  73                         vector<string> myArray = setParameters();
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //if the user changes the output directory command factory will send this info to us in the output parameter
  87                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  88
  89                         //if the user changes the input directory command factory will send this info to us in the output parameter
  90                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  91                         if (inputDir == "not found"){   inputDir = "";          }
  92                         else {
  93                                 string path;
  94                                 it = parameters.find("accnos");
  95                                 //user has given a template file
  96                                 if(it != parameters.end()){
  97                                         path = m->hasPath(it->second);
  98                                         //if the user has not given a path then, add inputdir. else leave path alone.
  99                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 100                                 }
 101
 102                                 it = parameters.find("group");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 108                                 }
 109
 110                                 it = parameters.find("shared");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 116                                 }
 117                         }
 118
 119
 120                         //check for required parameters
 121                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 122                         if (accnosfile == "not open") { abort = true; }
 123                         else if (accnosfile == "not found") {  accnosfile = ""; }
 124                         else { m->setAccnosFile(accnosfile); }
 125
 126                         groups = validParameter.validFile(parameters, "groups", false);
 127                         if (groups == "not found") { groups = ""; }
 128                         else {
 129                                 m->splitAtDash(groups, Groups);
 130                                 m->setGroups(Groups);
 131                         }
 132
 133                         sharedfile = validParameter.validFile(parameters, "shared", true);
 134                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 135                         else if (sharedfile == "not found") {  sharedfile = "";  }
 136                         else { m->setSharedFile(sharedfile); }
 137
 138                         groupfile = validParameter.validFile(parameters, "group", true);
 139                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 140                         else if (groupfile == "not found") {    groupfile = ""; }
 141                         else { m->setGroupFile(groupfile); }
 142
 143                         if ((sharedfile == "") && (groupfile == "")) {
 144                                 //give priority to shared, then group
 145                                 sharedfile = m->getSharedFile();
 146                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 147                                 else {
 148                                         groupfile = m->getGroupFile();
 149                                         if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 150                                         else {
 151                                                 m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
 152                                         }
 153                                 }
 154                         }
 155
 156                         if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->setGroups(Groups); }
 157                 }
 158
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166
 167 int CountGroupsCommand::execute(){
 168         try {
 169
 170                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 171
 172                 //get groups you want to remove
 173                 if (accnosfile != "") { readAccnos(); }
 174
 175                 if (groupfile != "") {
 176                         GroupMap groupMap(groupfile);
 177                         groupMap.readMap();
 178
 179                         //make sure groups are valid
 180                         //takes care of user setting groupNames that are invalid or setting groups=all
 181                         SharedUtil util;
 182                         vector<string> nameGroups = groupMap.getNamesOfGroups();
 183                         util.setGroups(Groups, nameGroups);
 184
 185                         for (int i = 0; i < Groups.size(); i++) {
 186                                 m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
 187                         }
 188                 }
 189
 190                 if (m->control_pressed) { return 0; }
 191
 192                 if (sharedfile != "")           {
 193                         InputData input(sharedfile, "sharedfile");
 194                         vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 195
 196                         for (int i = 0; i < lookup.size(); i++) {
 197                                 m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + "."); m->mothurOutEndLine();
 198                                 delete lookup[i];
 199                         }
 200                 }
 201
 202                 return 0;
 203         }
 204
 205         catch(exception& e) {
 206                 m->errorOut(e, "CountGroupsCommand", "execute");
 207                 exit(1);
 208         }
 209 }
 210 //**********************************************************************************************************************
 211 void CountGroupsCommand::readAccnos(){
 212         try {
 213                 Groups.clear();
 214
 215                 ifstream in;
 216                 m->openInputFile(accnosfile, in);
 217                 string name;
 218
 219                 while(!in.eof()){
 220                         in >> name;
 221
 222                         Groups.push_back(name);
 223
 224                         m->gobble(in);
 225                 }
 226                 in.close();
 227
 228                 m->setGroups(Groups);
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "CountGroupsCommand", "readAccnos");
 233                 exit(1);
 234         }
 235 }
 236 //**********************************************************************************************************************
 237
 238