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;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["group"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> MakeGroupCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta","groups"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "MakeGroupCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> MakeGroupCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "MakeGroupCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62
  63 MakeGroupCommand::MakeGroupCommand(string option)  {
  64         try {
  65
  66                 abort = false;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72
  73                         //valid paramters for this command
  74                         string AlignArray[] =  {"fasta","groups","output","outputdir","inputdir"};
  75                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["group"] = tempOutNames;
  91
  92                         //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                         if (inputDir == "not found"){   inputDir = "";          }
  95
  96                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
  97                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
  98                         else {
  99                                 m->splitAtDash(fastaFileName, fastaFileNames);
 100
 101                                 //go through files and make sure they are good, if not, then disregard them
 102                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 103                                         if (inputDir != "") {
 104                                                 string path = m->hasPath(fastaFileNames[i]);
 105                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 106                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 107                                         }
 108
 109                                         ifstream in;
 110                                         int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 111
 112                                         //if you can't open it, try default location
 113                                         if (ableToOpen == 1) {
 114                                                 if (m->getDefaultPath() != "") { //default path is set
 115                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 116                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 117                                                         ifstream in2;
 118                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 119                                                         in2.close();
 120                                                         fastaFileNames[i] = tryPath;
 121                                                 }
 122                                         }
 123
 124                                         //if you can't open it, try default location
 125                                         if (ableToOpen == 1) {
 126                                                 if (m->getOutputDir() != "") { //default path is set
 127                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 128                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 129                                                         ifstream in2;
 130                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 131                                                         in2.close();
 132                                                         fastaFileNames[i] = tryPath;
 133                                                 }
 134                                         }
 135                                         in.close();
 136
 137                                         if (ableToOpen == 1) {
 138                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 139                                                 //erase from file list
 140                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 141                                                 i--;
 142                                         }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
 143                                 }
 144
 145                                 //prevent giantic file name
 146                                 if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
 147                                 else {  filename += "groups";  }
 148
 149                                 //make sure there is at least one valid file left
 150                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 151                         }
 152
 153                         //if the user changes the output directory command factory will send this info to us in the output parameter
 154                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 155
 156                         output = validParameter.validFile(parameters, "output", false);
 157                         if (output == "not found") { output = "";  }
 158                         else{ filename = output; }
 159
 160                         groups = validParameter.validFile(parameters, "groups", false);
 161                         if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
 162                         else { m->splitAtDash(groups, groupsNames);     }
 163
 164                         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;  }
 165                 }
 166                 cout << "here" << endl;
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
 170                 exit(1);
 171         }
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 MakeGroupCommand::~MakeGroupCommand(){  }
 177
 178 //**********************************************************************************************************************
 179
 180 void MakeGroupCommand::help(){
 181         try {
 182                 m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
 183                 m->mothurOut("The make.group command parameters are fasta, groups and output. Fasta and group are required.\n");
 184                 m->mothurOut("The output parameter allows you to specify the name of groupfile created. \n");
 185                 m->mothurOut("The make.group command should be in the following format: \n");
 186                 m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups). \n");
 187                 m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
 188                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
 189         }
 190         catch(exception& e) {
 191                 m->errorOut(e, "MakeGroupCommand", "help");
 192                 exit(1);
 193         }
 194 }
 195
 196
 197 //**********************************************************************************************************************
 198
 199 int MakeGroupCommand::execute(){
 200         try {
 201                 if (abort == true) { return 0;  }
 202
 203                 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
 204
 205                 filename = outputDir + filename;
 206
 207                 ofstream out;
 208                 m->openOutputFile(filename, out);
 209
 210                 for (int i = 0; i < fastaFileNames.size(); i++) {
 211
 212                         if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
 213
 214                         ifstream in;
 215                         m->openInputFile(fastaFileNames[i], in);
 216
 217                         while (!in.eof()) {
 218
 219                                 Sequence seq(in, "no align"); m->gobble(in);
 220
 221                                 if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
 222
 223                                 if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
 224                         }
 225                         in.close();
 226                 }
 227
 228                 out.close();
 229
 230                 m->mothurOutEndLine();
 231                 m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
 232                 m->mothurOutEndLine();
 233
 234                 return 0;
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "MakeGroupCommand", "execute");
 238                 exit(1);
 239         }
 240 }
 241 //**********************************************************************************************************************
 242
 243