--- /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::getValidParameters(){
+ try {
+ string Array[] = {"fasta","qfile","outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MakeFastQCommand::MakeFastQCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["fastq"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
+ 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);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MakeFastQCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "getRequiredFiles");
+ 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 {
+ //valid paramters for this command
+ string Array[] = {"fasta","qfile", "outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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; }
+ }
+
+ 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; }
+
+ 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; }
+
+ //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);
+ }
+}
+//**********************************************************************************************************************
+
+void MakeFastQCommand::help(){
+ try {
+ /*m->mothurOut("The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
+ m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
+ m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is 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 groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n");
+ m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
+ m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+ m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\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";
+ 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++) { remove(outputNames[i].c_str()); } 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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