try {

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); }

return myArray;

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n";

helpString += "The deunique.seqs command parameters are fasta and name, both are required, unless you have valid current name and fasta files.\n";

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";

return helpString;

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString");

exit(1);

}

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);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["fasta"] = tempOutNames;

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand");

exit(1);

}

try {

abort = false; calledHelp = false;

//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();

OptionParser parser(option);

map<string,string> parameters = parser.getParameters();

ValidParameters validParameter;

map<string, string>::iterator it;

//check to make sure all parameters are valid for command

for (it = parameters.begin(); it != parameters.end(); it++) {

if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }

}

//initialize outputTypes

vector<string> tempOutNames;

outputTypes["fasta"] = 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("fasta");

//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["fasta"] = inputDir + it->second; }

}

it = parameters.find("name");

//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["name"] = inputDir + it->second; }

}

}

//check for required parameters

fastaFile = validParameter.validFile(parameters, "fasta", true);

if (fastaFile == "not open") { abort = true; }

else if (fastaFile == "not found") {

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"){

outputDir = "";

outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it

}

nameFile = validParameter.validFile(parameters, "name", true);

if (nameFile == "not open") { abort = true; }

else if (nameFile == "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); }

}

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "DeUniqueSeqsCommand");

exit(1);

}

try {

if (abort == true) { if (calledHelp) { return 0; } return 2; }

//prepare filenames and open files

ofstream out;

string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));

int pos = outFastaFile.find("unique");

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(); m->mothurRemove(outFastaFile); return 0; }

ifstream in;

m->openInputFile(fastaFile, in);

while (!in.eof()) {

if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }

Sequence seq(in); m->gobble(in);

if (seq.getName() != "") {

//look for sequence name in nameMap

map<string, string>::iterator it = nameMap.find(seq.getName());

if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }

else {

vector<string> names;

m->splitAtComma(it->second, names);

//output sequences

for (int i = 0; i < names.size(); i++) {

out << ">" << names[i] << endl;

out << seq.getAligned() << endl;

}

//remove seq from name map so we can check for seqs in namefile not in fastafile later

nameMap.erase(it);

}

}

}

in.close();

out.close();

if (nameMap.size() != 0) { //then there are names in the namefile not in the fastafile

for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {

m->mothurOut(it->first + " is not in your fasta file, but is in your name file. Please correct."); m->mothurOutEndLine();

}

}

if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }

m->mothurOutEndLine();

m->mothurOut("Output File Names: "); m->mothurOutEndLine();

m->mothurOut(outFastaFile); m->mothurOutEndLine();

outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);

m->mothurOutEndLine();

//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); }

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "execute");

exit(1);

}

try {

ifstream inNames;

m->openInputFile(nameFile, inNames);

string name, names;

map<string, string>::iterator it;

while(inNames){

if(m->control_pressed) { break; }

inNames >> name; m->gobble(inNames);

inNames >> names;

it = nameMap.find(name);

if (it == nameMap.end()) { nameMap[name] = names; }

else { m->mothurOut("[ERROR]: Your namefile already contains " + name + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }

m->gobble(inNames);

}

inNames.close();

return 0;

}

catch(exception& e) {

m->errorOut(e, "DeUniqueSeqsCommand", "readNamesFile");

exit(1);

}