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::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqfile);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "MakeFastQCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string MakeFastQCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The make.fastq command read a fasta and quality file and creates a fastq file.\n";
  36                 helpString += "The make.fastq command parameters are fasta and qfile, both are required.\n";
  37                 helpString += "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";
  38                 helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
  39                 helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
  40                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  41                 return helpString;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "MakeFastQCommand", "getHelpString");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string MakeFastQCommand::getOutputFileNameTag(string type, string inputName=""){
  50         try {
  51         string outputFileName = "";
  52                 map<string, vector<string> >::iterator it;
  53
  54         //is this a type this command creates
  55         it = outputTypes.find(type);
  56         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  57         else {
  58             if (type == "fastq")             {   outputFileName =  "fastq";         }
  59             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  60         }
  61         return outputFileName;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "MakeFastQCommand", "getOutputFileNameTag");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 MakeFastQCommand::MakeFastQCommand(){
  70         try {
  71                 abort = true; calledHelp = true;
  72                 setParameters();
  73                 vector<string> tempOutNames;
  74                 outputTypes["fastq"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 MakeFastQCommand::MakeFastQCommand(string option)  {
  83         try {
  84                 abort = false; calledHelp = false;
  85
  86                 //allow user to run help
  87                 if(option == "help") { help(); abort = true; calledHelp = true; }
  88                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  89
  90                 else {
  91                         vector<string> myArray = setParameters();
  92
  93                         OptionParser parser(option);
  94                         map<string,string> parameters = parser.getParameters();
  95
  96                         ValidParameters validParameter;
  97                         map<string,string>::iterator it;
  98
  99                         //check to make sure all parameters are valid for command
 100                         for (it = parameters.begin(); it != parameters.end(); it++) {
 101                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 102                         }
 103
 104                         //initialize outputTypes
 105                         vector<string> tempOutNames;
 106                         outputTypes["fastq"] = tempOutNames;
 107
 108
 109                         //if the user changes the input directory command factory will send this info to us in the output parameter
 110                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 111                         if (inputDir == "not found"){   inputDir = "";          }
 112                         else {
 113                                 string path;
 114                                 it = parameters.find("fasta");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 120                                 }
 121
 122                                 it = parameters.find("qfile");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 128                                 }
 129                         }
 130
 131
 132                         //check for required parameters
 133                         fastafile = validParameter.validFile(parameters, "fasta", true);
 134                         if (fastafile == "not open") { abort = true; fastafile = ""; }
 135                         else if (fastafile == "not found") {
 136                                 fastafile = m->getFastaFile();
 137                                 if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 138                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 139                         }else { m->setFastaFile(fastafile); }
 140
 141                         qualfile = validParameter.validFile(parameters, "qfile", true);
 142                         if (qualfile == "not open") { abort = true; qualfile = ""; }
 143                         else if (qualfile == "not found") {
 144                                 qualfile = m->getQualFile();
 145                                 if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 146                                 else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
 147                         }else { m->setQualFile(qualfile); }
 148
 149                         //if the user changes the output directory command factory will send this info to us in the output parameter
 150                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
 151
 152                 }
 153
 154         }
 155         catch(exception& e) {
 156                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
 157                 exit(1);
 158         }
 159 }
 160 //**********************************************************************************************************************
 161
 162 int MakeFastQCommand::execute(){
 163         try {
 164
 165                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 166
 167
 168                 string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
 169                 outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
 170
 171                 ofstream out;
 172                 m->openOutputFile(outputFile, out);
 173
 174                 ifstream qFile;
 175                 m->openInputFile(qualfile, qFile);
 176
 177                 ifstream fFile;
 178                 m->openInputFile(fastafile, fFile);
 179
 180                 while (!fFile.eof() && !qFile.eof()) {
 181
 182                         if (m->control_pressed) { break; }
 183
 184                         Sequence currSeq(fFile); m->gobble(fFile);
 185                         QualityScores currQual(qFile);  m->gobble(qFile);
 186
 187                         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; }
 188                         else {
 189                                 //print sequence
 190                                 out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
 191
 192                                 string qualityString = convertQual(currQual.getQualityScores());
 193
 194                                 //print quality info
 195                                 out << '+' << currQual.getName() << endl << qualityString << endl;
 196                         }
 197
 198                 }
 199
 200                 fFile.close();
 201                 qFile.close();
 202                 out.close();
 203
 204                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 205
 206                 m->mothurOutEndLine();
 207                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 208                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 209                 m->mothurOutEndLine();
 210
 211                 return 0;
 212
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "MakeFastQCommand", "execute");
 216                 exit(1);
 217         }
 218 }
 219 //**********************************************************************************************************************
 220 string MakeFastQCommand::convertQual(vector<int> qual) {
 221         try {
 222                 string qualScores;
 223
 224                 int controlChar = int('@');
 225
 226                 for (int i = 0; i < qual.size(); i++) {
 227                         int temp = qual[i] + controlChar;
 228                         char qualChar = (char) temp;
 229
 230                         qualScores += qualChar;
 231                 }
 232
 233                 return qualScores;
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "MakeFastQCommand", "convertQual");
 237                 exit(1);
 238         }
 239 }
 240 //**********************************************************************************************************************
 241
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