+++ /dev/null
-/*
- * 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"
-
-//**********************************************************************************************************************
-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);
-
- 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 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 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", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-MakeFastQCommand::MakeFastQCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fastq"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-MakeFastQCommand::MakeFastQCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //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();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fastq"] = tempOutNames;
-
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("fasta");
- //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["fasta"] = inputDir + it->second; }
- }
-
- it = parameters.find("qfile");
- //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["qfile"] = 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->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->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); }
-
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int MakeFastQCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
-
- string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
- outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
-
- ofstream out;
- m->openOutputFile(outputFile, out);
-
- ifstream qFile;
- m->openInputFile(qualfile, qFile);
-
- ifstream fFile;
- m->openInputFile(fastafile, fFile);
-
- while (!fFile.eof() && !qFile.eof()) {
-
- if (m->control_pressed) { break; }
-
- Sequence currSeq(fFile); m->gobble(fFile);
- QualityScores currQual(qFile); m->gobble(qFile);
-
- if (currSeq.getName() != currQual.getName()) { m->mothurOut("[ERROR]: mismatch between fasta and quality files. Found " + currSeq.getName() + " in fasta file and " + currQual.getName() + " in quality file."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- //print sequence
- out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
-
- string qualityString = convertQual(currQual.getQualityScores());
-
- //print quality info
- out << '+' << currQual.getName() << endl << qualityString << endl;
- }
-
- }
-
- fFile.close();
- qFile.close();
- out.close();
-
- 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();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string MakeFastQCommand::convertQual(vector<int> qual) {
- try {
- string qualScores;
-
- int controlChar = int('!');
-
- for (int i = 0; i < qual.size(); i++) {
- 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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