//**********************************************************************************************************************
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 pformat("format", "Multiple", "sanger-illumina-solexa", "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);
+ 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 ppacbio("pacbio", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppacbio);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "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); }
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, 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 format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ 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 += "The pacbio parameter allows you to indicate .... When set to true, quality scores of 0 will results in a corresponding base of N. Default=F.\n";
helpString += "Example fastq.info(fastaq=test.fastaq).\n";
helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
return helpString;
}
}
//**********************************************************************************************************************
-string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ParseFastaQCommand::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 == "fasta") { outputFileName = "fasta"; }
- else if (type == "qfile") { outputFileName = "qual"; }
- 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, "ParseFastaQCommand", "getOutputFileNameTag");
- exit(1);
- }
+ 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 {
fasta = m->isTrue(temp);
temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; }
- qual = m->isTrue(temp);
+ qual = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "pacbio", false); if(temp == "not found"){ temp = "F"; }
+ pacbio = 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();
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, 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)) + getOutputFileNameTag("fasta");
- string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
+ 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); }
string name = m->getline(in); m->gobble(in);
if (name == "") { m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else { name = name.substr(1); }
+ else {
+ name = name.substr(1);
+ m->checkName(name);
+ }
//read sequence
string sequence = m->getline(in); m->gobble(in);
string name2 = m->getline(in); m->gobble(in);
if (name2 == "") { m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else { name2 = name2.substr(1); }
+ else {
+ name2 = name2.substr(1);
+ m->checkName(name2);
+ }
//read quality scores
string quality = m->getline(in); m->gobble(in);
if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- //print sequence info to files
- if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
-
- if (qual) {
- vector<int> qualScores = convertQual(quality);
+ vector<int> qualScores;
+ if (qual) {
+ qualScores = convertQual(quality);
outQual << ">" << name << endl;
for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
outQual << endl;
}
+
+ if (m->control_pressed) { break; }
+
+ if (pacbio) {
+ if (!qual) { qualScores = convertQual(quality); } //get scores if we didn't already
+ for (int i = 0; i < qualScores.size(); i++) {
+ if (qualScores[i] == 0){ sequence[i] = 'N'; }
+ }
+ }
+
+ //print sequence info to files
+ if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
+
}
in.close();
if (fasta) { outFasta.close(); }
if (qual) { outQual.close(); }
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); outputNames.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
//set fasta file as new current fastafile
string current = "";
try {
vector<int> qualScores;
+ bool negativeScores = false;
+
for (int i = 0; i < qual.length(); i++) {
int temp = 0;
temp = int(qual[i]);
if (format == "illumina") {
temp -= 64; //char '@'
+ }else if (format == "illumina1.8+") {
+ temp -= int('!'); //char '!'
}else if (format == "solexa") {
temp = int(convertTable[temp]); //convert to sanger
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}else {
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}
+ if (temp < -5) { negativeScores = true; }
qualScores.push_back(temp);
}
+ if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n"); m->control_pressed = true; }
+
return qualScores;
}
catch(exception& e) {
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