#include "sequence.hpp"
//**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getValidParameters(){
+vector<string> ParseFastaQCommand::setParameters(){
try {
- string Array[] = {"fastq", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ParseFastaQCommand::ParseFastaQCommand(){
- try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+ m->errorOut(e, "ParseFastaQCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredParameters(){
+string ParseFastaQCommand::getHelpString(){
try {
- string Array[] = {"fastq"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ 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", "getRequiredParameters");
+ m->errorOut(e, "ParseFastaQCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredFiles(){
+ParseFastaQCommand::ParseFastaQCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "getRequiredFiles");
+ 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[] = {"fastq", "outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = 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);
}
//**********************************************************************************************************************
-void ParseFastaQCommand::help(){
- try {
- m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
- m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
- m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
- m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\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); outputTypes["fasta"].push_back(fastaFile);
- m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qual"].push_back(qualFile);
+ 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
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();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }