//**********************************************************************************************************************
vector<string> ParseFastaQCommand::setParameters(){
try {
- CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
- CommandParameter pfasta("fasta", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pqual("qfile", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pqual);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "","",false,false,true); 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); }
try {
string helpString = "";
helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
- helpString += "The fastq.info command parameters are fastq, fasta and qfile; fastq is required.\n";
- helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+ helpString += "The fastq.info command parameters are fastq, fasta, qfile and format; fastq is required.\n";
+ helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa or illumina, default=sanger.\n";
helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
helpString += "Example fastq.info(fastaq=test.fastaq).\n";
}
}
//**********************************************************************************************************************
+string ParseFastaQCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],fasta"; }
+ else if (type == "qfile") { pattern = "[filename],qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(){
try {
abort = true; calledHelp = true;
temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; }
qual = m->isTrue(temp);
+ format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
+
+ if ((format != "sanger") && (format != "illumina") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+ abort=true;
+ }
+
if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
- string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
- string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ string fastaFile = getOutputFileName("fasta",variables);
+ string qualFile = getOutputFileName("qfile",variables);
ofstream outFasta, outQual;
if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
ifstream in;
m->openInputFile(fastaQFile, in);
+
+ //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
+ for (int i = -64; i < 65; i++) {
+ char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
+ convertTable.push_back(temp);
+ }
while (!in.eof()) {
try {
vector<int> qualScores;
- int controlChar = int('!');
-
for (int i = 0; i < qual.length(); i++) {
- int temp = int(qual[i]);
- temp -= controlChar;
-
+
+ int temp = 0;
+ temp = int(qual[i]);
+ if (format == "illumina") {
+ temp -= 64; //char '@'
+ }else if (format == "solexa") {
+ temp = int(convertTable[temp]); //convert to sanger
+ temp -= int('!'); //char '!'
+ }else {
+ temp -= int('!'); //char '!'
+ }
qualScores.push_back(temp);
}