//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- 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", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ 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); }
helpString += "The deunique.seqs command should be in the following format: \n";
helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n";
helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
+string DeUniqueSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
try {
abort = true; calledHelp = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
fastaFile = m->getFastaFile();
if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastaFile); }
//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"){
nameFile = m->getNameFile();
if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setNameFile(nameFile); }
}
}
ofstream out;
string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
int pos = outFastaFile.find("unique");
- if (pos != string::npos) {
- outFastaFile = outputDir + outFastaFile.substr(0, pos) + "redundant" + m->getExtension(fastaFile);
- }else{
- outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "redundant" + m->getExtension(fastaFile);
- }
+ if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
+ else { outFastaFile = outputDir + outFastaFile; }
+ map<string, string> variables;
+ variables["[filename]"] = outFastaFile;
+ outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);
readNamesFile();
- if (m->control_pressed) { out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+ if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
ifstream in;
m->openInputFile(fastaFile, in);
while (!in.eof()) {
- if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
Sequence seq(in); m->gobble(in);
}
}
- if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();