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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  69
  70                 else {
  71                         vector<string> myArray = setParameters();
  72
  73                         OptionParser parser(option);
  74                         map<string,string> parameters = parser.getParameters();
  75
  76                         ValidParameters validParameter;
  77                         map<string,string>::iterator it;
  78
  79                         //check to make sure all parameters are valid for command
  80                         for (it = parameters.begin(); it != parameters.end(); it++) {
  81                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  82                         }
  83
  84                         //initialize outputTypes
  85                         vector<string> tempOutNames;
  86                         outputTypes["fastq"] = tempOutNames;
  87
  88
  89                         //if the user changes the input directory command factory will send this info to us in the output parameter
  90                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  91                         if (inputDir == "not found"){   inputDir = "";          }
  92                         else {
  93                                 string path;
  94                                 it = parameters.find("fasta");
  95                                 //user has given a template file
  96                                 if(it != parameters.end()){
  97                                         path = m->hasPath(it->second);
  98                                         //if the user has not given a path then, add inputdir. else leave path alone.
  99                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 100                                 }
 101
 102                                 it = parameters.find("qfile");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 108                                 }
 109                         }
 110
 111
 112                         //check for required parameters
 113                         fastafile = validParameter.validFile(parameters, "fasta", true);
 114                         if (fastafile == "not open") { abort = true; fastafile = ""; }
 115                         else if (fastafile == "not found") {
 116                                 fastafile = m->getFastaFile();
 117                                 if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 118                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 119                         }
 120
 121                         qualfile = validParameter.validFile(parameters, "qfile", true);
 122                         if (qualfile == "not open") { abort = true; qualfile = ""; }
 123                         else if (qualfile == "not found") {
 124                                 qualfile = m->getQualFile();
 125                                 if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 126                                 else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
 127                         }
 128
 129                         //if the user changes the output directory command factory will send this info to us in the output parameter
 130                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);              }
 131
 132                 }
 133
 134         }
 135         catch(exception& e) {
 136                 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
 137                 exit(1);
 138         }
 139 }
 140 //**********************************************************************************************************************
 141
 142 int MakeFastQCommand::execute(){
 143         try {
 144
 145                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 146
 147
 148                 string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
 149                 outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
 150
 151                 ofstream out;
 152                 m->openOutputFile(outputFile, out);
 153
 154                 ifstream qFile;
 155                 m->openInputFile(qualfile, qFile);
 156
 157                 ifstream fFile;
 158                 m->openInputFile(fastafile, fFile);
 159
 160                 while (!fFile.eof() && !qFile.eof()) {
 161
 162                         if (m->control_pressed) { break; }
 163
 164                         Sequence currSeq(fFile); m->gobble(fFile);
 165                         QualityScores currQual(qFile);  m->gobble(qFile);
 166
 167                         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; }
 168                         else {
 169                                 //print sequence
 170                                 out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
 171
 172                                 string qualityString = convertQual(currQual.getQualityScores());
 173
 174                                 //print quality info
 175                                 out << '+' << currQual.getName() << endl << qualityString << endl;
 176                         }
 177
 178                 }
 179
 180                 fFile.close();
 181                 qFile.close();
 182                 out.close();
 183
 184                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 185
 186                 m->mothurOutEndLine();
 187                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 188                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 189                 m->mothurOutEndLine();
 190
 191                 return 0;
 192
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "MakeFastQCommand", "execute");
 196                 exit(1);
 197         }
 198 }
 199 //**********************************************************************************************************************
 200 string MakeFastQCommand::convertQual(vector<int> qual) {
 201         try {
 202                 string qualScores;
 203
 204                 int controlChar = int('!');
 205
 206                 for (int i = 0; i < qual.size(); i++) {
 207                         int temp = qual[i] + controlChar;
 208                         char qualChar = (char) temp;
 209
 210                         qualScores += qualChar;
 211                 }
 212
 213                 return qualScores;
 214         }
 215         catch(exception& e) {
 216                 m->errorOut(e, "MakeFastQCommand", "convertQual");
 217                 exit(1);
 218         }
 219 }
 220 //**********************************************************************************************************************
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