//**********************************************************************************************************************
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::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ 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(){
try {
abort = true; calledHelp = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastafile); }
qualfile = validParameter.validFile(parameters, "qfile", true);
if (qualfile == "not open") { abort = true; qualfile = ""; }
qualfile = m->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setQualFile(qualfile); }
//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)) + "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; }
qFile.close();
out.close();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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;