//**********************************************************************************************************************
vector<string> MakeFastQCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pqfile);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-illumina1.8+", "sanger", "", "", "","",false,false); parameters.push_back(pformat);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string MakeFastQCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The make.fastq command read a fasta and quality file and creates a fastq file.\n";
- helpString += "The make.fastq command parameters are fasta and qfile, both are required.\n";
- 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";
+ helpString += "The make.fastq command reads a fasta and quality file and creates a fastq file.\n";
+ helpString += "The make.fastq command parameters are fasta, qfile and format. fasta and qfile are required.\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger, illumina1.8+ or illumina, default=sanger.\n";
helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
}
}
//**********************************************************************************************************************
-string MakeFastQCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeFastQCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fastq") { outputFileName = "fastq"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fastq") { pattern = "[filename],fastq"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MakeFastQCommand::MakeFastQCommand(){
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
+
+ format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
+
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
+ abort=true;
+ }
+
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFile = getOutputFileName("fastq",variables);
outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
ofstream out;
ifstream fFile;
m->openInputFile(fastafile, fFile);
-
+
while (!fFile.eof() && !qFile.eof()) {
if (m->control_pressed) { break; }
try {
string qualScores;
- int controlChar = int('@');
-
- for (int i = 0; i < qual.size(); i++) {
+ for (int i = 0; i < qual.size(); i++) {
+ int controlChar = int('!');
+ if (format == "illumina") { controlChar = int('@'); }
+
int temp = qual[i] + controlChar;
char qualChar = (char) temp;