5 * Created by westcott on 2/14/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "makefastqcommand.h"
11 #include "sequence.hpp"
12 #include "qualityscores.h"
14 //**********************************************************************************************************************
15 vector<string> MakeFastQCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
18 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqfile);
19 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
20 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
22 vector<string> myArray;
23 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
27 m->errorOut(e, "MakeFastQCommand", "setParameters");
31 //**********************************************************************************************************************
32 string MakeFastQCommand::getHelpString(){
34 string helpString = "";
35 helpString += "The make.fastq command read a fasta and quality file and creates a fastq file.\n";
36 helpString += "The make.fastq command parameters are fasta and qfile, both are required.\n";
37 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";
38 helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
39 helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
40 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
44 m->errorOut(e, "MakeFastQCommand", "getHelpString");
48 //**********************************************************************************************************************
49 string MakeFastQCommand::getOutputFileNameTag(string type, string inputName=""){
51 string outputFileName = "";
52 map<string, vector<string> >::iterator it;
54 //is this a type this command creates
55 it = outputTypes.find(type);
56 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
58 if (type == "fastq") { outputFileName = "fastq"; }
59 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
61 return outputFileName;
64 m->errorOut(e, "MakeFastQCommand", "getOutputFileNameTag");
68 //**********************************************************************************************************************
69 MakeFastQCommand::MakeFastQCommand(){
71 abort = true; calledHelp = true;
73 vector<string> tempOutNames;
74 outputTypes["fastq"] = tempOutNames;
77 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
81 //**********************************************************************************************************************
82 MakeFastQCommand::MakeFastQCommand(string option) {
84 abort = false; calledHelp = false;
86 //allow user to run help
87 if(option == "help") { help(); abort = true; calledHelp = true; }
88 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
91 vector<string> myArray = setParameters();
93 OptionParser parser(option);
94 map<string,string> parameters = parser.getParameters();
96 ValidParameters validParameter;
97 map<string,string>::iterator it;
99 //check to make sure all parameters are valid for command
100 for (it = parameters.begin(); it != parameters.end(); it++) {
101 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
104 //initialize outputTypes
105 vector<string> tempOutNames;
106 outputTypes["fastq"] = tempOutNames;
109 //if the user changes the input directory command factory will send this info to us in the output parameter
110 string inputDir = validParameter.validFile(parameters, "inputdir", false);
111 if (inputDir == "not found"){ inputDir = ""; }
114 it = parameters.find("fasta");
115 //user has given a template file
116 if(it != parameters.end()){
117 path = m->hasPath(it->second);
118 //if the user has not given a path then, add inputdir. else leave path alone.
119 if (path == "") { parameters["fasta"] = inputDir + it->second; }
122 it = parameters.find("qfile");
123 //user has given a template file
124 if(it != parameters.end()){
125 path = m->hasPath(it->second);
126 //if the user has not given a path then, add inputdir. else leave path alone.
127 if (path == "") { parameters["qfile"] = inputDir + it->second; }
132 //check for required parameters
133 fastafile = validParameter.validFile(parameters, "fasta", true);
134 if (fastafile == "not open") { abort = true; fastafile = ""; }
135 else if (fastafile == "not found") {
136 fastafile = m->getFastaFile();
137 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
138 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
139 }else { m->setFastaFile(fastafile); }
141 qualfile = validParameter.validFile(parameters, "qfile", true);
142 if (qualfile == "not open") { abort = true; qualfile = ""; }
143 else if (qualfile == "not found") {
144 qualfile = m->getQualFile();
145 if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
146 else { m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
147 }else { m->setQualFile(qualfile); }
149 //if the user changes the output directory command factory will send this info to us in the output parameter
150 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
155 catch(exception& e) {
156 m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand");
160 //**********************************************************************************************************************
162 int MakeFastQCommand::execute(){
165 if (abort == true) { if (calledHelp) { return 0; } return 2; }
168 string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
169 outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
172 m->openOutputFile(outputFile, out);
175 m->openInputFile(qualfile, qFile);
178 m->openInputFile(fastafile, fFile);
180 while (!fFile.eof() && !qFile.eof()) {
182 if (m->control_pressed) { break; }
184 Sequence currSeq(fFile); m->gobble(fFile);
185 QualityScores currQual(qFile); m->gobble(qFile);
187 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; }
190 out << '@' << currSeq.getName() << endl << currSeq.getAligned() << endl;
192 string qualityString = convertQual(currQual.getQualityScores());
195 out << '+' << currQual.getName() << endl << qualityString << endl;
204 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
206 m->mothurOutEndLine();
207 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
208 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
209 m->mothurOutEndLine();
214 catch(exception& e) {
215 m->errorOut(e, "MakeFastQCommand", "execute");
219 //**********************************************************************************************************************
220 string MakeFastQCommand::convertQual(vector<int> qual) {
224 int controlChar = int('@');
226 for (int i = 0; i < qual.size(); i++) {
227 int temp = qual[i] + controlChar;
228 char qualChar = (char) temp;
230 qualScores += qualChar;
235 catch(exception& e) {
236 m->errorOut(e, "MakeFastQCommand", "convertQual");
240 //**********************************************************************************************************************