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 MakeFastQCommand::MakeFastQCommand(){
  50         try {
  51                 abort = true; calledHelp = true;
  52                 setParameters();
  53                 vector<string> tempOutNames;
  54                 outputTypes["fastq"] = tempOutNames;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
  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                         vector<string> myArray = setParameters();
  71
  72                         OptionParser parser(option);
  73                         map<string,string> parameters = parser.getParameters();
  74
  75                         ValidParameters validParameter;
  76                         map<string,string>::iterator it;
  77
  78                         //check to make sure all parameters are valid for command
  79                         for (it = parameters.begin(); it != parameters.end(); it++) {
  80                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  81                         }
  82
  83                         //initialize outputTypes
  84                         vector<string> tempOutNames;
  85                         outputTypes["fastq"] = tempOutNames;
  86
  87
  88                         //if the user changes the input directory command factory will send this info to us in the output parameter
  89                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  90                         if (inputDir == "not found"){   inputDir = "";          }
  91                         else {
  92                                 string path;
  93                                 it = parameters.find("fasta");
  94                                 //user has given a template file
  95                                 if(it != parameters.end()){
  96                                         path = m->hasPath(it->second);
  97                                         //if the user has not given a path then, add inputdir. else leave path alone.
  98                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  99                                 }
 100
 101                                 it = parameters.find("qfile");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 107                                 }
 108                         }
 109
 110
 111                         //check for required parameters
 112                         fastafile = validParameter.validFile(parameters, "fasta", true);
 113                         if (fastafile == "not open") { abort = true; fastafile = ""; }
 114                         else if (fastafile == "not found") {
 115                                 fastafile = m->getFastaFile();
 116                                 if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 117                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 118                         }
 119
 120                         qualfile = validParameter.validFile(parameters, "qfile", true);
 121                         if (qualfile == "not open") { abort = true; qualfile = ""; }
 122                         else if (qualfile == "not found") {
 123                                 qualfile = m->getQualFile();
 124                                 if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 125                                 else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
 126                         }
 127
 128                         //if the user changes the output directory command factory will send this info to us in the output parameter
 129                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
 130
 131                 }
 132
 133         }
 134         catch(exception& e) {
 135                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
 136                 exit(1);
 137         }
 138 }
 139 //**********************************************************************************************************************
 140
 141 int MakeFastQCommand::execute(){
 142         try {
 143
 144                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 145
 146
 147                 string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
 148                 outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
 149
 150                 ofstream out;
 151                 m->openOutputFile(outputFile, out);
 152
 153                 ifstream qFile;
 154                 m->openInputFile(qualfile, qFile);
 155
 156                 ifstream fFile;
 157                 m->openInputFile(fastafile, fFile);
 158
 159                 while (!fFile.eof() && !qFile.eof()) {
 160
 161                         if (m->control_pressed) { break; }
 162
 163                         Sequence currSeq(fFile); m->gobble(fFile);
 164                         QualityScores currQual(qFile);  m->gobble(qFile);
 165
 166                         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; }
 167                         else {
 168                                 //print sequence
 169                                 out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
 170
 171                                 string qualityString = convertQual(currQual.getQualityScores());
 172
 173                                 //print quality info
 174                                 out << '+' << currQual.getName() << endl << qualityString << endl;
 175                         }
 176
 177                 }
 178
 179                 fFile.close();
 180                 qFile.close();
 181                 out.close();
 182
 183                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 184
 185                 m->mothurOutEndLine();
 186                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 187                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 188                 m->mothurOutEndLine();
 189
 190                 return 0;
 191
 192         }
 193         catch(exception& e) {
 194                 m->errorOut(e, "MakeFastQCommand", "execute");
 195                 exit(1);
 196         }
 197 }
 198 //**********************************************************************************************************************
 199 string MakeFastQCommand::convertQual(vector<int> qual) {
 200         try {
 201                 string qualScores;
 202
 203                 int controlChar = int('!');
 204
 205                 for (int i = 0; i < qual.size(); i++) {
 206                         int temp = qual[i] + controlChar;
 207                         char qualChar = (char) temp;
 208
 209                         qualScores += qualChar;
 210                 }
 211
 212                 return qualScores;
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "MakeFastQCommand", "convertQual");
 216                 exit(1);
 217         }
 218 }
 219 //**********************************************************************************************************************
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