try {

CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);

CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);

CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);

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, "DeconvoluteCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The unique.seqs command reads a fastafile and creates a name or count file.\n";

helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";

helpString += "If the sequence is unique the second column will just contain its name. \n";

helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\n";

helpString += "The unique.seqs command should be in the following format: \n";

helpString += "unique.seqs(fasta=yourFastaFile) \n";

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

string pattern = "";

if (type == "fasta") { pattern = "[filename],unique,[extension]"; }

else if (type == "name") { pattern = "[filename],names-[filename],[tag],names"; }

else if (type == "count") { pattern = "[filename],count_table-[filename],[tag],count_table"; }

else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }

return pattern;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["fasta"] = tempOutNames;

outputTypes["name"] = tempOutNames;

outputTypes["count"] = tempOutNames;

}

catch(exception& e) {

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

outputTypes["name"] = tempOutNames;

outputTypes["count"] = 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; }

}

it = parameters.find("count");

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

}

}

//check for required parameters

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

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

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

inFastaName = m->getFastaFile();

if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " 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(inFastaName); }

//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(inFastaName); //if user entered a file with a path then preserve it

}

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

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

else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }

else { m->setNameFile(oldNameMapFName); }

countfile = validParameter.validFile(parameters, "count", true);

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

else if (countfile == "not found") { countfile = ""; }

else { m->setCountTableFile(countfile); }

if ((countfile != "") && (oldNameMapFName != "")) { m->mothurOut("When executing a unique.seqs command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }

if (countfile == "") {

if (oldNameMapFName == "") {

vector<string> files; files.push_back(inFastaName);

parser.getNameFile(files);

}

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

//prepare filenames and open files

map<string, string> variables;

variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));

string outNameFile = getOutputFileName("name", variables);

string outCountFile = getOutputFileName("count", variables);

variables["[extension]"] = m->getExtension(inFastaName);

string outFastaFile = getOutputFileName("fasta", variables);

map<string, string> nameMap;

map<string, string>::iterator itNames;

if (oldNameMapFName != "") {

m->readNames(oldNameMapFName, nameMap);

if (oldNameMapFName == outNameFile){

//prepare filenames and open files

map<string, string> mvariables;

mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));

mvariables["[tag]"] = "unique";

outNameFile = getOutputFileName("name", mvariables);

}

}

CountTable ct;

if (countfile != "") {

ct.readTable(countfile, true, false);

if (countfile == outCountFile){

//prepare filenames and open files

map<string, string> mvariables;

mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));

mvariables["[tag]"] = "unique";

outCountFile = getOutputFileName("count", mvariables); }

}

if (m->control_pressed) { return 0; }

ifstream in;

m->openInputFile(inFastaName, in);

ofstream outFasta;

m->openOutputFile(outFastaFile, outFasta);

map<string, string> sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3.

map<string, string>::iterator itStrings;

set<string> nameInFastaFile; //for sanity checking

set<string>::iterator itname;

vector<string> nameFileOrder;

int count = 0;

while (!in.eof()) {

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

Sequence seq(in);

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

//sanity checks

itname = nameInFastaFile.find(seq.getName());

if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); }

else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct."); m->mothurOutEndLine(); }

itStrings = sequenceStrings.find(seq.getAligned());

if (itStrings == sequenceStrings.end()) { //this is a new unique sequence

//output to unique fasta file

seq.printSequence(outFasta);

if (oldNameMapFName != "") {

itNames = nameMap.find(seq.getName());

if (itNames == nameMap.end()) { //namefile and fastafile do not match

m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();

}else {

sequenceStrings[seq.getAligned()] = itNames->second;

nameFileOrder.push_back(seq.getAligned());

}

}else if (countfile != "") {

ct.getNumSeqs(seq.getName()); //checks to make sure seq is in table

sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned());

}else { sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned()); }

}else { //this is a dup

if (oldNameMapFName != "") {

itNames = nameMap.find(seq.getName());

if (itNames == nameMap.end()) { //namefile and fastafile do not match

m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();

}else {

sequenceStrings[seq.getAligned()] += "," + itNames->second;

}

}else if (countfile != "") {

int num = ct.getNumSeqs(seq.getName()); //checks to make sure seq is in table

if (num != 0) { //its in the table

ct.mergeCounts(itStrings->second, seq.getName()); //merges counts and saves in uniques name

}

}else { sequenceStrings[seq.getAligned()] += "," + seq.getName(); }

}

count++;

}

m->gobble(in);

if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }

}

if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }

in.close();

outFasta.close();

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

//print new names file

ofstream outNames;

if (countfile == "") { m->openOutputFile(outNameFile, outNames); outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile); }

else { m->openOutputFile(outCountFile, outNames); ct.printHeaders(outNames); outputTypes["count"].push_back(outCountFile); outputNames.push_back(outCountFile); }

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

if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }

itStrings = sequenceStrings.find(nameFileOrder[i]);

if (itStrings != sequenceStrings.end()) {

if (countfile == "") {

//get rep name

int pos = (itStrings->second).find_first_of(',');

if (pos == string::npos) { // only reps itself

outNames << itStrings->second << '\t' << itStrings->second << endl;

}else {

outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;

}

}else { ct.printSeq(outNames, itStrings->second); }

}else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; }

}

outNames.close();

if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }

m->mothurOutEndLine();

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

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

for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }

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); }

}

itTypes = outputTypes.find("name");

if (itTypes != outputTypes.end()) {

if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }

}

itTypes = outputTypes.find("count");

if (itTypes != outputTypes.end()) {

if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }

}

return 0;

}

catch(exception& e) {

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

exit(1);

}