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/*
* makefastqcommand.cpp
* mothur
*
* Created by westcott on 2/14/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "makefastqcommand.h"
#include "sequence.hpp"
#include "qualityscores.h"
#include "fastqread.h"
//**********************************************************************************************************************
vector<string> MakeFastQCommand::setParameters(){
try {
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-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fastq"] = tempOutNames;
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", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MakeFastQCommand::getHelpString(){
try {
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, solexa, illumina1.8+ or illumina, default=illumina1.8+.\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";
;
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MakeFastQCommand", "getHelpString");
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->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MakeFastQCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MakeFastQCommand::MakeFastQCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { abort = true; fastafile = ""; }
else if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}else { current->setFastaFile(fastafile); }
qualfile = validParameter.validFile(parameters, "qfile");
if (qualfile == "not open") { abort = true; qualfile = ""; }
else if (qualfile == "not found") {
qualfile = current->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter.\n"); }
else { m->mothurOut("You have no current qualfile and the qfile parameter is required.\n"); abort = true; }
}else { current->setQualFile(qualfile); }
if (outputdir == ""){ outputdir = util.hasPath(fastafile); }
format = validParameter.valid(parameters, "format"); if (format == "not found"){ format = "illumina1.8+"; }
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;
}
}
}
catch(exception& e) {
m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MakeFastQCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outputFile = getOutputFileName("fastq",variables);
outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
ofstream out;
util.openOutputFile(outputFile, out);
ifstream qFile;
util.openInputFile(qualfile, qFile);
ifstream fFile;
util.openInputFile(fastafile, fFile);
while (!fFile.eof() && !qFile.eof()) {
if (m->getControl_pressed()) { break; }
Sequence currSeq(fFile); gobble(fFile);
QualityScores currQual(qFile); gobble(qFile);
FastqRead fread(currSeq, currQual, format);
fread.printFastq(out);
}
fFile.close();
qFile.close();
out.close();
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MakeFastQCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
string MakeFastQCommand::convertQual(vector<int> qual) {
try {
string qualScores;
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;
qualScores += qualChar;
}
return qualScores;
}
catch(exception& e) {
m->errorOut(e, "MakeFastQCommand", "convertQual");
exit(1);
}
}
//**********************************************************************************************************************
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