//**********************************************************************************************************************
vector<string> ReverseSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,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); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string ReverseSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],rc,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],rc,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ReverseSeqsCommand::ReverseSeqsCommand(){
try {
ofstream outFASTA;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
- fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
+ variables["[extension]"] = m->getExtension(fastaFileName);
+ fastaReverseFileName = getOutputFileName("fasta", variables);
m->openOutputFile(fastaReverseFileName, outFASTA);
while(!inFASTA.eof()){
ofstream outQual;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
- string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
- m->openOutputFile(qualReverseFileName, outQual);
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
+ variables["[extension]"] = m->getExtension(qualFileName);
+ string qualReverseFileName = getOutputFileName("qfile", variables);
+ m->openOutputFile(qualReverseFileName, outQual);
while(!inQual.eof()){
if (m->control_pressed) { inQual.close(); outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for(int i=0;i<outputNames.size();i++){
m->mothurOut(outputNames[i]);
m->mothurOutEndLine();