#include "qualityscores.h"
//**********************************************************************************************************************
-vector<string> MakeFastQCommand::getValidParameters(){
+vector<string> MakeFastQCommand::setParameters(){
try {
- string Array[] = {"fasta","qfile","outputdir","inputdir" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "getValidParameters");
+ m->errorOut(e, "MakeFastQCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-MakeFastQCommand::MakeFastQCommand(){
+string MakeFastQCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fastq"] = tempOutNames;
+ string helpString = "";
+ 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";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
+ m->errorOut(e, "MakeFastQCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MakeFastQCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","qfile"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "getRequiredParameters");
- exit(1);
- }
+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);
+ }
}
//**********************************************************************************************************************
-vector<string> MakeFastQCommand::getRequiredFiles(){
+MakeFastQCommand::MakeFastQCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fastq"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "getRequiredFiles");
+ m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","qfile", "outputdir","inputdir" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["qfile"] = inputDir + it->second; }
}
-
- it = parameters.find("list");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["list"] = inputDir + it->second; }
- }
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; fastafile = ""; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") {
+ 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 = ""; }
- else if (qualfile == "not found") { qualfile = ""; m->mothurOut("You must provide a quality file."); m->mothurOutEndLine(); abort = true; }
+ else if (qualfile == "not found") {
+ 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;
+ }
+
}
}
//**********************************************************************************************************************
-void MakeFastQCommand::help(){
- try {
- m->mothurOut("The make.fastq command read a fasta and quality file and creates a fastq file.\n");
- m->mothurOut("The make.fastq command parameters are fasta and qfile, both are required.\n");
- m->mothurOut("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");
- m->mothurOut("The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n");
- m->mothurOut("Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int MakeFastQCommand::execute(){
try {
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;
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