#include "parsefastaqcommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::setParameters(){
+ try {
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
+ 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, "ParseFastaQCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParseFastaQCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
+ helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+ helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+ helpString += "Example fastq.info(fastaq=test.fastaq).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseFastaQCommand::ParseFastaQCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
- abort = false;
+ abort = false; calledHelp = false;
- if(option == "help") { help(); abort = true; }
+ 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[] = {"fastaq", "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 (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = 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("fastaq");
+ it = parameters.find("fastq");
//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["fastaq"] = inputDir + it->second; }
+ if (path == "") { parameters["fastq"] = inputDir + it->second; }
}
}
//check for required parameters
- fastaQFile = validParameter.validFile(parameters, "fastaq", true);
- if (fastaQFile == "not found") { m->mothurOut("fastaq is a required parameter for the parse.fastaq command."); m->mothurOutEndLine(); abort = true; }
+ fastaQFile = validParameter.validFile(parameters, "fastq", true);
+ if (fastaQFile == "not found") { m->mothurOut("fastq is a required parameter for the fastq.info command."); m->mothurOutEndLine(); abort = true; }
else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
}
//**********************************************************************************************************************
-void ParseFastaQCommand::help(){
- try {
- m->mothurOut("The parse.fastaq command reads a fastaQ file and creates a fasta and quality file.\n");
- m->mothurOut("The parse.fastaq command parameter is fastaq, and it is required.\n");
- m->mothurOut("The parse.fastaq command should be in the following format: parse.fastaq(fastaq=yourFastaQFile).\n");
- m->mothurOut("Example parse.fastaq(fastaq=test.fastaq).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fastaq), '=' and yourFastaQFile.\n");
- m->mothurOutEndLine();
- }
- catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-ParseFastaQCommand::~ParseFastaQCommand() { /* do nothing */ }
-
-//**********************************************************************************************************************
-
int ParseFastaQCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
ofstream outFasta, outQual;
- m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile);
- m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile);
+ m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
+ m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile);
ifstream in;
m->openInputFile(fastaQFile, in);
if (qual == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
//sanity check sequence length and number of quality scores match
- if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
//convert quality scores
outFasta.close();
outQual.close();
- if (m->control_pressed) { remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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