try {

CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);

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

CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);

CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);

CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);

CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);

CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);

CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);

CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);

CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);

CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);

CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);

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, "GetSeqsCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n";

helpString += "It outputs a file containing only the sequences in the .accnos file.\n";

helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";

helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";

helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";

helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\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, "GetSeqsCommand", "getHelpString");

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["fasta"] = tempOutNames;

outputTypes["taxonomy"] = tempOutNames;

outputTypes["name"] = tempOutNames;

outputTypes["group"] = tempOutNames;

outputTypes["alignreport"] = tempOutNames;

outputTypes["list"] = tempOutNames;

outputTypes["qfile"] = tempOutNames;

outputTypes["accnosreport"] = tempOutNames;

}

catch(exception& e) {

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

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["taxonomy"] = tempOutNames;

outputTypes["name"] = tempOutNames;

outputTypes["group"] = tempOutNames;

outputTypes["alignreport"] = tempOutNames;

outputTypes["list"] = tempOutNames;

outputTypes["qfile"] = tempOutNames;

outputTypes["accnosreport"] = tempOutNames;

//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 = ""; }

//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("alignreport");

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

}

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("accnos");

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

}

it = parameters.find("accnos2");

//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["accnos2"] = inputDir + it->second; }

}

it = parameters.find("list");

//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["list"] = 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("group");

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

}

it = parameters.find("taxonomy");

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

}

it = parameters.find("qfile");

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

}

}

//check for required parameters

accnosfile = validParameter.validFile(parameters, "accnos", true);

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

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

accnosfile = m->getAccnosFile();

if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }

else {

m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();

abort = true;

}

}else { m->setAccnosFile(accnosfile); }

if (accnosfile2 == "not found") { accnosfile2 = ""; }

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

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

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

else { m->setFastaFile(fastafile); }

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

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

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

else { m->setNameFile(namefile); }

groupfile = validParameter.validFile(parameters, "group", true);

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

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

else { m->setGroupFile(groupfile); }

alignfile = validParameter.validFile(parameters, "alignreport", true);

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

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

listfile = validParameter.validFile(parameters, "list", true);

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

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

else { m->setListFile(listfile); }

taxfile = validParameter.validFile(parameters, "taxonomy", true);

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

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

else { m->setTaxonomyFile(taxfile); }

qualfile = validParameter.validFile(parameters, "qfile", true);

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

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

else { m->setQualFile(qualfile); }

accnosfile2 = validParameter.validFile(parameters, "accnos2", true);

if (accnosfile2 == "not open") { abort = true; }

else if (accnosfile2 == "not found") { accnosfile2 = ""; }

string usedDups = "true";

string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "true"; usedDups = ""; }

dups = m->isTrue(temp);

if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }

if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){

vector<string> files; files.push_back(fastafile); files.push_back(taxfile);

parser.getNameFile(files);

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

//get names you want to keep

readAccnos();

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

//read through the correct file and output lines you want to keep

if (namefile != "") { readName(); }

if (fastafile != "") { readFasta(); }

if (groupfile != "") { readGroup(); }

if (alignfile != "") { readAlign(); }

if (listfile != "") { readList(); }

if (taxfile != "") { readTax(); }

if (qualfile != "") { readQual(); }

if (accnosfile2 != "") { compareAccnos(); }

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

if (outputNames.size() != 0) {

m->mothurOutEndLine();

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

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("group");

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

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

}

itTypes = outputTypes.find("list");

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

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

}

itTypes = outputTypes.find("taxonomy");

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

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

}

itTypes = outputTypes.find("qfile");

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

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

}

}

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(fastafile, in);

string name;

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

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

Sequence currSeq(in);

name = currSeq.getName();

if (name != "") {

//if this name is in the accnos file

if (names.count(name) != 0) {

wroteSomething = true;

currSeq.printSequence(out);

selectedCount++;

}

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

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

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readFasta");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(qualfile, in);

string name;

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

string saveName = "";

string name = "";

string scores = "";

in >> name;

if (name.length() != 0) {

saveName = name.substr(1);

while (!in.eof()) {

char c = in.get();

if (c == 10 || c == 13){ break; }

else { name += c; }

}

m->gobble(in);

}

while(in){

char letter= in.get();

if(letter == '>'){ in.putback(letter); break; }

else{ scores += letter; }

}

m->gobble(in);

if (names.count(saveName) != 0) {

wroteSomething = true;

out << name << endl << scores;

selectedCount++;

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readQual");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(listfile, in);

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

selectedCount = 0;

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

//read in list vector

ListVector list(in);

//make a new list vector

ListVector newList;

newList.setLabel(list.getLabel());

//for each bin

for (int i = 0; i < list.getNumBins(); i++) {

//parse out names that are in accnos file

string binnames = list.get(i);

string newNames = "";

while (binnames.find_first_of(',') != -1) {

string name = binnames.substr(0,binnames.find_first_of(','));

binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());

//if that name is in the .accnos file, add it

if (names.count(name) != 0) { newNames += name + ","; selectedCount++; }

}

//get last name

if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; }

//if there are names in this bin add to new list

if (newNames != "") {

newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma

newList.push_back(newNames);

}

}

//print new listvector

if (newList.getNumBins() != 0) {

wroteSomething = true;

newList.print(out);

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readList");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(namefile, in);

string name, firstCol, secondCol;

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

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

in >> firstCol;

in >> secondCol;

string hold = "";

if (dups) { hold = secondCol; }

vector<string> parsedNames;

m->splitAtComma(secondCol, parsedNames);

vector<string> validSecond;

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

if (names.count(parsedNames[i]) != 0) {

validSecond.push_back(parsedNames[i]);

}

}

if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone

for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }

out << firstCol << '\t' << hold << endl;

wroteSomething = true;

selectedCount += parsedNames.size();

}else {

selectedCount += validSecond.size();

//if the name in the first column is in the set then print it and any other names in second column also in set

if (names.count(firstCol) != 0) {

wroteSomething = true;

out << firstCol << '\t';

//you know you have at least one valid second since first column is valid

for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }

out << validSecond[validSecond.size()-1] << endl;

//make first name in set you come to first column and then add the remaining names to second column

}else {

//you want part of this row

if (validSecond.size() != 0) {

wroteSomething = true;

out << validSecond[0] << '\t';

//you know you have at least one valid second since first column is valid

for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }

out << validSecond[validSecond.size()-1] << endl;

}

}

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readName");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(groupfile, in);

string name, group;

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

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

in >> name; //read from first column

in >> group; //read from second column

//if this name is in the accnos file

if (names.count(name) != 0) {

wroteSomething = true;

out << name << '\t' << group << endl;

selectedCount++;

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readGroup");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(taxfile, in);

string name, tax;

bool wroteSomething = false;

int selectedCount = 0;

while(!in.eof()){

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

in >> name; //read from first column

in >> tax; //read from second column

//if this name is in the accnos file

if (names.count(name) != 0) {

wroteSomething = true;

out << name << '\t' << tax << endl;

selectedCount++;

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readTax");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(alignfile, in);

string name, junk;

bool wroteSomething = false;

int selectedCount = 0;

//read column headers

for (int i = 0; i < 16; i++) {

if (!in.eof()) { in >> junk; out << junk << '\t'; }

else { break; }

}

out << endl;

while(!in.eof()){

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

in >> name; //read from first column

//if this name is in the accnos file

if (names.count(name) != 0) {

wroteSomething = true;

selectedCount++;

out << name << '\t';

//read rest

for (int i = 0; i < 15; i++) {

if (!in.eof()) { in >> junk; out << junk << '\t'; }

else { break; }

}

out << endl;

}else {//still read just don't do anything with it

//read rest

for (int i = 0; i < 15; i++) {

if (!in.eof()) { in >> junk; }

else { break; }

}

}

m->gobble(in);

}

in.close();

out.close();

if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }

outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);

m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readAlign");

exit(1);

}

try {

ifstream in;

m->openInputFile(accnosfile, in);

string name;

while(!in.eof()){

in >> name;

names.insert(name);

m->gobble(in);

}

in.close();

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readAccnos");

exit(1);

}

try {

string thisOutputDir = outputDir;

if (outputDir == "") { thisOutputDir += m->hasPath(accnosfile); }

string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";

ofstream out;

m->openOutputFile(outputFileName, out);

ifstream in;

m->openInputFile(accnosfile2, in);

string name;

set<string> namesAccnos2;

set<string> namesDups;

set<string> namesAccnos = names;

map<string, int> nameCount;

if (namefile != "") {

ifstream inName;

m->openInputFile(namefile, inName);

while(!inName.eof()){

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

string thisname, repnames;

inName >> thisname; m->gobble(inName); //read from first column

inName >> repnames; //read from second column

int num = m->getNumNames(repnames);

nameCount[thisname] = num;

m->gobble(inName);

}

inName.close();

}

while(!in.eof()){

in >> name;

if (namesAccnos.count(name) == 0){ //name unique to accnos2

int pos = name.find_last_of('_');

string tempName = name;

if (pos != string::npos) { tempName = tempName.substr(pos+1); cout << tempName << endl; }

if (namesAccnos.count(tempName) == 0){

namesAccnos2.insert(name);

}else { //you are in both so erase

namesAccnos.erase(name);

namesDups.insert(name);

}

}else { //you are in both so erase

namesAccnos.erase(name);

namesDups.insert(name);

}

m->gobble(in);

}

in.close();

out << "Names in both files : " + toString(namesDups.size()) << endl;

m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();

for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {

out << (*it);

if (namefile != "") { out << '\t' << nameCount[(*it)]; }

out << endl;

}

out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;

m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();

for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {

out << (*it);

if (namefile != "") { out << '\t' << nameCount[(*it)]; }

out << endl;

}

out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;

m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();

for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {

out << (*it);

if (namefile != "") { out << '\t' << nameCount[(*it)]; }

out << endl;

}

out.close();

outputNames.push_back(outputFileName); outputTypes["accnosreport"].push_back(outputFileName);

return 0;

}

catch(exception& e) {

m->errorOut(e, "GetSeqsCommand", "readAccnos");

exit(1);

}