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
  15 MakeGroupCommand::MakeGroupCommand(string option)  {
  16         try {
  17
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24
  25                         //valid paramters for this command
  26                         string AlignArray[] =  {"fasta","groups","outputdir","inputdir"};
  27                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string, string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33                         map<string, string>::iterator it;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  42                         if (inputDir == "not found"){   inputDir = "";          }
  43
  44                         filename = outputDir;
  45
  46                         fastaFileName = validParameter.validFile(parameters, "fasta", false);
  47                         if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
  48                         else {
  49                                 m->splitAtDash(fastaFileName, fastaFileNames);
  50
  51                                 //go through files and make sure they are good, if not, then disregard them
  52                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  53                                         if (inputDir != "") {
  54                                                 string path = m->hasPath(fastaFileNames[i]);
  55                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  56                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  57                                         }
  58
  59                                         ifstream in;
  60                                         int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
  61
  62                                         //if you can't open it, try default location
  63                                         if (ableToOpen == 1) {
  64                                                 if (m->getDefaultPath() != "") { //default path is set
  65                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
  66                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  67                                                         ableToOpen = m->openInputFile(tryPath, in, "noerror");
  68                                                         fastaFileNames[i] = tryPath;
  69                                                 }
  70                                         }
  71                                         in.close();
  72
  73                                         if (ableToOpen == 1) {
  74                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
  75                                                 //erase from file list
  76                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
  77                                                 i--;
  78                                         }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
  79                                 }
  80
  81                                 //prevent giantic file name
  82                                 if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
  83                                 else {  filename += "groups";  }
  84
  85                                 //make sure there is at least one valid file left
  86                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  87                         }
  88
  89                         //if the user changes the output directory command factory will send this info to us in the output parameter
  90                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  91
  92                         groups = validParameter.validFile(parameters, "groups", false);
  93                         if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
  94                         else { m->splitAtDash(groups, groupsNames);     }
  95
  96                         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;  }
  97                 }
  98
  99         }
 100         catch(exception& e) {
 101                 m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
 102                 exit(1);
 103         }
 104 }
 105
 106 //**********************************************************************************************************************
 107
 108 MakeGroupCommand::~MakeGroupCommand(){  }
 109
 110 //**********************************************************************************************************************
 111
 112 void MakeGroupCommand::help(){
 113         try {
 114                 m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
 115                 m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n");
 116                 m->mothurOut("The make.group command should be in the following format: \n");
 117                 m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n");
 118                 m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
 119                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "MakeGroupCommand", "help");
 123                 exit(1);
 124         }
 125 }
 126
 127
 128 //**********************************************************************************************************************
 129
 130 int MakeGroupCommand::execute(){
 131         try {
 132                 if (abort == true) {    return 0;       }
 133
 134                 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
 135
 136                 filename = outputDir + filename;
 137
 138                 ofstream out;
 139                 m->openOutputFile(filename, out);
 140
 141                 for (int i = 0; i < fastaFileNames.size(); i++) {
 142
 143                         if (m->control_pressed) {  out.close(); remove(filename.c_str()); return 0; }
 144
 145                         ifstream in;
 146                         m->openInputFile(fastaFileNames[i], in);
 147
 148                         while (!in.eof()) {
 149
 150                                 Sequence seq(in, "no align"); m->gobble(in);
 151
 152                                 if (m->control_pressed) {  in.close(); out.close(); remove(filename.c_str()); return 0; }
 153
 154                                 if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
 155                         }
 156                         in.close();
 157                 }
 158
 159                 out.close();
 160
 161                 m->mothurOutEndLine();
 162                 m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine();
 163                 m->mothurOutEndLine();
 164
 165                 return 0;
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "MakeGroupCommand", "execute");
 169                 exit(1);
 170         }
 171 }
 172 //**********************************************************************************************************************
 173
 174