makefastqcommand.cpp

   1 /*
   2  *  makefastqcommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 2/14/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "makefastqcommand.h"
  11 #include "sequence.hpp"
  12 #include "qualityscores.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> MakeFastQCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta","qfile","outputdir","inputdir" };
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "MakeFastQCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 MakeFastQCommand::MakeFastQCommand(){
  28         try {
  29                 abort = true; calledHelp = true;
  30                 vector<string> tempOutNames;
  31                 outputTypes["fastq"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> MakeFastQCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta","qfile"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "MakeFastQCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> MakeFastQCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "MakeFastQCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 MakeFastQCommand::MakeFastQCommand(string option)  {
  63         try {
  64                 abort = false; calledHelp = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; calledHelp = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"fasta","qfile", "outputdir","inputdir" };
  72                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  73
  74                         OptionParser parser(option);
  75                         map<string,string> parameters = parser.getParameters();
  76
  77                         ValidParameters validParameter;
  78                         map<string,string>::iterator it;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["fastq"] = tempOutNames;
  88
  89
  90                         //if the user changes the input directory command factory will send this info to us in the output parameter
  91                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  92                         if (inputDir == "not found"){   inputDir = "";          }
  93                         else {
  94                                 string path;
  95                                 it = parameters.find("fasta");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 101                                 }
 102
 103                                 it = parameters.find("qfile");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 109                                 }
 110
 111                                 it = parameters.find("list");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 117                                 }
 118                         }
 119
 120
 121                         //check for required parameters
 122                         fastafile = validParameter.validFile(parameters, "fasta", true);
 123                         if (fastafile == "not open") { abort = true; fastafile = ""; }
 124                         else if (fastafile == "not found") {  fastafile = "";  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
 125
 126                         qualfile = validParameter.validFile(parameters, "qfile", true);
 127                         if (qualfile == "not open") { abort = true; qualfile = ""; }
 128                         else if (qualfile == "not found") {  qualfile = "";  m->mothurOut("You must provide a quality file."); m->mothurOutEndLine(); abort = true; }
 129
 130                         //if the user changes the output directory command factory will send this info to us in the output parameter
 131                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
 132
 133                 }
 134
 135         }
 136         catch(exception& e) {
 137                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
 138                 exit(1);
 139         }
 140 }
 141 //**********************************************************************************************************************
 142
 143 void MakeFastQCommand::help(){
 144         try {
 145                 /*m->mothurOut("The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
 146                 m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
 147                 m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
 148                 m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
 149                 m->mothurOut("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");
 150                 m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
 151                 m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
 152                 m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
 153                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");*/
 154         }
 155         catch(exception& e) {
 156                 m->errorOut(e, "MakeFastQCommand", "help");
 157                 exit(1);
 158         }
 159 }
 160
 161 //**********************************************************************************************************************
 162
 163 int MakeFastQCommand::execute(){
 164         try {
 165
 166                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 167
 168
 169                 string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
 170                 outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
 171
 172                 ofstream out;
 173                 m->openOutputFile(outputFile, out);
 174
 175                 ifstream qFile;
 176                 m->openInputFile(qualfile, qFile);
 177
 178                 ifstream fFile;
 179                 m->openInputFile(fastafile, fFile);
 180
 181                 while (!fFile.eof() && !qFile.eof()) {
 182
 183                         if (m->control_pressed) { break; }
 184
 185                         Sequence currSeq(fFile); m->gobble(fFile);
 186                         QualityScores currQual(qFile);  m->gobble(qFile);
 187
 188                         if (currSeq.getName() != currQual.getName()) { m->mothurOut("[ERROR]: mismatch between fasta and quality files. Found " + currSeq.getName() + " in fasta file and " + currQual.getName() + " in quality file."); m->mothurOutEndLine(); m->control_pressed = true; }
 189                         else {
 190                                 //print sequence
 191                                 out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
 192
 193                                 string qualityString = convertQual(currQual.getQualityScores());
 194
 195                                 //print quality info
 196                                 out << '+' << currQual.getName() << endl << qualityString << endl;
 197                         }
 198
 199                 }
 200
 201                 fFile.close();
 202                 qFile.close();
 203                 out.close();
 204
 205                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 206
 207                 m->mothurOutEndLine();
 208                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 209                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 210                 m->mothurOutEndLine();
 211
 212                 return 0;
 213
 214         }
 215         catch(exception& e) {
 216                 m->errorOut(e, "MakeFastQCommand", "execute");
 217                 exit(1);
 218         }
 219 }
 220 //**********************************************************************************************************************
 221 string MakeFastQCommand::convertQual(vector<int> qual) {
 222         try {
 223                 string qualScores;
 224
 225                 int controlChar = int('!');
 226
 227                 for (int i = 0; i < qual.size(); i++) {
 228                         int temp = qual[i] + controlChar;
 229                         char qualChar = (char) temp;
 230
 231                         qualScores += qualChar;
 232                 }
 233
 234                 return qualScores;
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "MakeFastQCommand", "convertQual");
 238                 exit(1);
 239         }
 240 }
 241 //**********************************************************************************************************************
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