makegroupcommand.cpp

   1 /*
   2  *  makegroupcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/7/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "makegroupcommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> MakeGroupCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "output","groups","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "MakeGroupCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 MakeGroupCommand::MakeGroupCommand(){
  27         try {
  28                 abort = true; calledHelp = true;
  29                 vector<string> tempOutNames;
  30                 outputTypes["group"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> MakeGroupCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"fasta","groups"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "MakeGroupCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> MakeGroupCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "MakeGroupCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61
  62 MakeGroupCommand::MakeGroupCommand(string option)  {
  63         try {
  64
  65                 abort = false; calledHelp = false;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; calledHelp = true; }
  69
  70                 else {
  71
  72                         //valid paramters for this command
  73                         string AlignArray[] =  {"fasta","groups","output","outputdir","inputdir"};
  74                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string, string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["group"] = tempOutNames;
  90
  91                         //if the user changes the input directory command factory will send this info to us in the output parameter
  92                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  93                         if (inputDir == "not found"){   inputDir = "";          }
  94
  95                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
  96                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
  97                         else {
  98                                 m->splitAtDash(fastaFileName, fastaFileNames);
  99
 100                                 //go through files and make sure they are good, if not, then disregard them
 101                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 102                                         if (inputDir != "") {
 103                                                 string path = m->hasPath(fastaFileNames[i]);
 104                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 105                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 106                                         }
 107
 108                                         ifstream in;
 109                                         int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 110
 111                                         //if you can't open it, try default location
 112                                         if (ableToOpen == 1) {
 113                                                 if (m->getDefaultPath() != "") { //default path is set
 114                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 115                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 116                                                         ifstream in2;
 117                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 118                                                         in2.close();
 119                                                         fastaFileNames[i] = tryPath;
 120                                                 }
 121                                         }
 122
 123                                         //if you can't open it, try default location
 124                                         if (ableToOpen == 1) {
 125                                                 if (m->getOutputDir() != "") { //default path is set
 126                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 127                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 128                                                         ifstream in2;
 129                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 130                                                         in2.close();
 131                                                         fastaFileNames[i] = tryPath;
 132                                                 }
 133                                         }
 134                                         in.close();
 135
 136                                         if (ableToOpen == 1) {
 137                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 138                                                 //erase from file list
 139                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 140                                                 i--;
 141                                         }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
 142                                 }
 143
 144                                 //prevent giantic file name
 145                                 if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
 146                                 else {  filename += "groups";  }
 147
 148                                 //make sure there is at least one valid file left
 149                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 150                         }
 151
 152                         //if the user changes the output directory command factory will send this info to us in the output parameter
 153                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 154
 155                         output = validParameter.validFile(parameters, "output", false);
 156                         if (output == "not found") { output = "";  }
 157                         else{ filename = output; }
 158
 159                         groups = validParameter.validFile(parameters, "groups", false);
 160                         if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
 161                         else { m->splitAtDash(groups, groupsNames);     }
 162
 163                         if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups.  This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true;  }
 164                 }
 165                 cout << "here" << endl;
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
 169                 exit(1);
 170         }
 171 }
 172
 173 //**********************************************************************************************************************
 174
 175 MakeGroupCommand::~MakeGroupCommand(){  }
 176
 177 //**********************************************************************************************************************
 178
 179 void MakeGroupCommand::help(){
 180         try {
 181                 m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
 182                 m->mothurOut("The make.group command parameters are fasta, groups and output. Fasta and group are required.\n");
 183                 m->mothurOut("The output parameter allows you to specify the name of groupfile created. \n");
 184                 m->mothurOut("The make.group command should be in the following format: \n");
 185                 m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups). \n");
 186                 m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
 187                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
 188         }
 189         catch(exception& e) {
 190                 m->errorOut(e, "MakeGroupCommand", "help");
 191                 exit(1);
 192         }
 193 }
 194
 195
 196 //**********************************************************************************************************************
 197
 198 int MakeGroupCommand::execute(){
 199         try {
 200                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 201
 202                 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
 203
 204                 filename = outputDir + filename;
 205
 206                 ofstream out;
 207                 m->openOutputFile(filename, out);
 208
 209                 for (int i = 0; i < fastaFileNames.size(); i++) {
 210
 211                         if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
 212
 213                         ifstream in;
 214                         m->openInputFile(fastaFileNames[i], in);
 215
 216                         while (!in.eof()) {
 217
 218                                 Sequence seq(in, "no align"); m->gobble(in);
 219
 220                                 if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
 221
 222                                 if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
 223                         }
 224                         in.close();
 225                 }
 226
 227                 out.close();
 228
 229                 m->mothurOutEndLine();
 230                 m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
 231                 m->mothurOutEndLine();
 232
 233                 return 0;
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "MakeGroupCommand", "execute");
 237                 exit(1);
 238         }
 239 }
 240 //**********************************************************************************************************************
 241
 242