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", "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                 //initialize outputTypes
  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;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71
  72                         //valid paramters for this command
  73                         string AlignArray[] =  {"fasta","groups","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                         filename = outputDir;
  96
  97                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
  98                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
  99                         else {
 100                                 m->splitAtDash(fastaFileName, fastaFileNames);
 101
 102                                 //go through files and make sure they are good, if not, then disregard them
 103                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 104                                         if (inputDir != "") {
 105                                                 string path = m->hasPath(fastaFileNames[i]);
 106                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 107                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 108                                         }
 109
 110                                         ifstream in;
 111                                         int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 112
 113                                         //if you can't open it, try default location
 114                                         if (ableToOpen == 1) {
 115                                                 if (m->getDefaultPath() != "") { //default path is set
 116                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 117                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 118                                                         ifstream in2;
 119                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 120                                                         in2.close();
 121                                                         fastaFileNames[i] = tryPath;
 122                                                 }
 123                                         }
 124
 125                                         //if you can't open it, try default location
 126                                         if (ableToOpen == 1) {
 127                                                 if (m->getOutputDir() != "") { //default path is set
 128                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 129                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 130                                                         ifstream in2;
 131                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 132                                                         in2.close();
 133                                                         fastaFileNames[i] = tryPath;
 134                                                 }
 135                                         }
 136                                         in.close();
 137
 138                                         if (ableToOpen == 1) {
 139                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 140                                                 //erase from file list
 141                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 142                                                 i--;
 143                                         }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
 144                                 }
 145
 146                                 //prevent giantic file name
 147                                 if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
 148                                 else {  filename += "groups";  }
 149
 150                                 //make sure there is at least one valid file left
 151                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 152                         }
 153
 154                         //if the user changes the output directory command factory will send this info to us in the output parameter
 155                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 156
 157                         groups = validParameter.validFile(parameters, "groups", false);
 158                         if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
 159                         else { m->splitAtDash(groups, groupsNames);     }
 160
 161                         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;  }
 162                 }
 163
 164         }
 165         catch(exception& e) {
 166                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
 167                 exit(1);
 168         }
 169 }
 170
 171 //**********************************************************************************************************************
 172
 173 MakeGroupCommand::~MakeGroupCommand(){  }
 174
 175 //**********************************************************************************************************************
 176
 177 void MakeGroupCommand::help(){
 178         try {
 179                 m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
 180                 m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n");
 181                 m->mothurOut("The make.group command should be in the following format: \n");
 182                 m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n");
 183                 m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
 184                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
 185         }
 186         catch(exception& e) {
 187                 m->errorOut(e, "MakeGroupCommand", "help");
 188                 exit(1);
 189         }
 190 }
 191
 192
 193 //**********************************************************************************************************************
 194
 195 int MakeGroupCommand::execute(){
 196         try {
 197                 if (abort == true) {    return 0;       }
 198
 199                 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
 200
 201                 filename = outputDir + filename;
 202
 203                 ofstream out;
 204                 m->openOutputFile(filename, out);
 205
 206                 for (int i = 0; i < fastaFileNames.size(); i++) {
 207
 208                         if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
 209
 210                         ifstream in;
 211                         m->openInputFile(fastaFileNames[i], in);
 212
 213                         while (!in.eof()) {
 214
 215                                 Sequence seq(in, "no align"); m->gobble(in);
 216
 217                                 if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
 218
 219                                 if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
 220                         }
 221                         in.close();
 222                 }
 223
 224                 out.close();
 225
 226                 m->mothurOutEndLine();
 227                 m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
 228                 m->mothurOutEndLine();
 229
 230                 return 0;
 231         }
 232         catch(exception& e) {
 233                 m->errorOut(e, "MakeGroupCommand", "execute");
 234                 exit(1);
 235         }
 236 }
 237 //**********************************************************************************************************************
 238
 239