try {

CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);

CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);

CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);

CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);

CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);

CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);

CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);

CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);

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, "MetaStatsCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "This command is based on the Metastats program, White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009).\n";

helpString += "The metastats command outputs a .metastats file. \n";

helpString += "The metastats command parameters are shared, iters, threshold, groups, label, design, sets and processors. The shared and design parameters are required, unless you have valid current files.\n";

helpString += "The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n";

helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n";

helpString += "The sets parameter allows you to specify which of the sets in your designfile you would like to analyze. The set names are separated by dashes. THe default is all sets in the designfile.\n";

helpString += "The iters parameter allows you to set number of bootstrap permutations for estimating null distribution of t statistic. The default is 1000. \n";

helpString += "The threshold parameter allows you to set the significance level to reject null hypotheses (default 0.05).\n";

helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";

helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";

helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";

helpString += "The metastats command should be in the following format: metastats(design=yourDesignFile).\n";

helpString += "Example metastats(design=temp.design, groups=A-B-C).\n";

helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";

helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

string pattern = "";

if (type == "metastats") { pattern = "[filename],[distance],[group],metastats"; }

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

return pattern;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = true; calledHelp = true;

setParameters();

vector<string> tempOutNames;

outputTypes["metastats"] = tempOutNames;

}

catch(exception& e) {

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

exit(1);

}

try {

abort = false; calledHelp = false;

allLines = 1;

//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;

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

map<string,string>::iterator it;

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["metastats"] = 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("design");

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

}

it = parameters.find("shared");

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

}

}

//check for required parameters

sharedfile = validParameter.validFile(parameters, "shared", true);

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

else if (sharedfile == "not found") { //if there is a current shared file, use it

sharedfile = m->getSharedFile();

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

else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }

}else { m->setSharedFile(sharedfile); }

//check for required parameters

designfile = validParameter.validFile(parameters, "design", true);

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

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

//if there is a current design file, use it

designfile = m->getDesignFile();

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

else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }

}else { m->setDesignFile(designfile); }

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

}

//check for optional parameter and set defaults

// ...at some point should added some additional type checking...

label = validParameter.validFile(parameters, "label", false);

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

else {

if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }

else { allLines = 1; }

}

groups = validParameter.validFile(parameters, "groups", false);

if (groups == "not found") { groups = ""; pickedGroups = false; }

else {

pickedGroups = true;

m->splitAtDash(groups, Groups);

m->setGroups(Groups);

}

sets = validParameter.validFile(parameters, "sets", false);

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

else {

m->splitAtDash(sets, Sets);

}

string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }

m->mothurConvert(temp, iters);

temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "0.05"; }

m->mothurConvert(temp, threshold);

temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }

m->setProcessors(temp);

m->mothurConvert(temp, processors);

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

//just used to convert files to test metastats online

/****************************************************/

bool convertInputToShared = false;

convertSharedToInput = false;

if (convertInputToShared) { convertToShared(sharedfile); return 0; }

/****************************************************/

designMap = new GroupMap(designfile);

designMap->readDesignMap();

input = new InputData(sharedfile, "sharedfile");

lookup = input->getSharedRAbundVectors();

string lastLabel = lookup[0]->getLabel();

//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.

set<string> processedLabels;

set<string> userLabels = labels;

//setup the pairwise comparions of sets for metastats

//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;

//make sure sets are all in designMap

SharedUtil* util = new SharedUtil();

vector<string> dGroups = designMap->getNamesOfGroups();

util->setGroups(Sets, dGroups);

delete util;

int numGroups = Sets.size();

for (int a=0; a<numGroups; a++) {

for (int l = 0; l < a; l++) {

vector<string> groups; groups.push_back(Sets[a]); groups.push_back(Sets[l]);

namesOfGroupCombos.push_back(groups);

}

}

//only 1 combo

if (numGroups == 2) { processors = 1; }

else if (numGroups < 2) { m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }

if(processors != 1){

int remainingPairs = namesOfGroupCombos.size();

int startIndex = 0;

for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {

int numPairs = remainingPairs; //case for last processor

if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }

lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs

startIndex = startIndex + numPairs;

remainingPairs = remainingPairs - numPairs;

}

}

//as long as you are not at the end of the file or done wih the lines you want

while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {

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

if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

process(lookup);

processedLabels.insert(lookup[0]->getLabel());

userLabels.erase(lookup[0]->getLabel());

}

if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {

string saveLabel = lookup[0]->getLabel();

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }

lookup = input->getSharedRAbundVectors(lastLabel);

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

process(lookup);

processedLabels.insert(lookup[0]->getLabel());

userLabels.erase(lookup[0]->getLabel());

//restore real lastlabel to save below

lookup[0]->setLabel(saveLabel);

}

lastLabel = lookup[0]->getLabel();

//prevent memory leak

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }

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

//get next line to process

lookup = input->getSharedRAbundVectors();

}

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

//output error messages about any remaining user labels

set<string>::iterator it;

bool needToRun = false;

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

m->mothurOut("Your file does not include the label " + *it);

if (processedLabels.count(lastLabel) != 1) {

m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();

needToRun = true;

}else {

m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();

}

}

//run last label if you need to

if (needToRun == true) {

for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }

lookup = input->getSharedRAbundVectors(lastLabel);

m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();

process(lookup);

for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }

}

//reset groups parameter

m->clearGroups();

delete input;

delete designMap;

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

return 0;

}

catch(exception& e) {

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

exit(1);

}

try {

if(processors == 1){

driver(0, namesOfGroupCombos.size(), thisLookUp);

}else{

int process = 1;

vector<int> processIDS;

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)

//loop through and create all the processes you want

while (process != processors) {

int pid = fork();

if (pid > 0) {

processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later

process++;

}else if (pid == 0){

driver(lines[process].start, lines[process].num, thisLookUp);

exit(0);

}else {

m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();

for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }

exit(0);

}

}

//do my part

driver(lines[0].start, lines[0].num, thisLookUp);

//force parent to wait until all the processes are done

for (int i=0;i<(processors-1);i++) {

int temp = processIDS[i];

wait(&temp);

}

#else

//////////////////////////////////////////////////////////////////////////////////////////////////////

//Windows version shared memory, so be careful when passing variables through the summarySharedData struct.

//Above fork() will clone, so memory is separate, but that's not the case with windows,

//Taking advantage of shared memory to pass results vectors.

//////////////////////////////////////////////////////////////////////////////////////////////////////

vector<metastatsData*> pDataArray;

DWORD dwThreadIdArray[processors-1];

HANDLE hThreadArray[processors-1];

//Create processor worker threads.

for( int i=1; i<processors; i++ ){

//make copy of lookup so we don't get access violations

vector<SharedRAbundVector*> newLookup;

vector<string> designMapGroups;

for (int k = 0; k < thisLookUp.size(); k++) {

SharedRAbundVector* temp = new SharedRAbundVector();

temp->setLabel(thisLookUp[k]->getLabel());

temp->setGroup(thisLookUp[k]->getGroup());

newLookup.push_back(temp);

designMapGroups.push_back(designMap->getGroup(thisLookUp[k]->getGroup()));

}

//for each bin

for (int k = 0; k < thisLookUp[0]->getNumBins(); k++) {

if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }

for (int j = 0; j < thisLookUp.size(); j++) { newLookup[j]->push_back(thisLookUp[j]->getAbundance(k), thisLookUp[j]->getGroup()); }

}

// Allocate memory for thread data.

metastatsData* tempSum = new metastatsData(sharedfile, outputDir, m, lines[i].start, lines[i].num, namesOfGroupCombos, newLookup, designMapGroups, iters, threshold);

pDataArray.push_back(tempSum);

processIDS.push_back(i);

hThreadArray[i-1] = CreateThread(NULL, 0, MyMetastatsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);

}

//do my part

driver(lines[0].start, lines[0].num, thisLookUp);

//Wait until all threads have terminated.

WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);

//Close all thread handles and free memory allocations.

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

if (pDataArray[i]->count != (pDataArray[i]->num)) {

m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->num) + " groups assigned to it, quitting. \n"); m->control_pressed = true;

}

for (int j = 0; j < pDataArray[i]->thisLookUp.size(); j++) { delete pDataArray[i]->thisLookUp[j]; }

for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {

outputNames.push_back(pDataArray[i]->outputNames[j]);

outputTypes["metastats"].push_back(pDataArray[i]->outputNames[j]);

}

CloseHandle(hThreadArray[i]);

delete pDataArray[i];

}

#endif

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "MetaStatsCommand", "process");

exit(1);

}

try {

//for each combo

for (int c = start; c < (start+num); c++) {

//get set names

string setA = namesOfGroupCombos[c][0];

string setB = namesOfGroupCombos[c][1];

//get filename

map<string, string> variables;

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

variables["[distance]"] = thisLookUp[0]->getLabel();

variables["[group]"] = setA + "-" + setB;

string outputFileName = getOutputFileName("metastats",variables);

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

//int nameLength = outputFileName.length();

//char * output = new char[nameLength];

//strcpy(output, outputFileName.c_str());

//build matrix from shared rabunds

//double** data;

//data = new double*[thisLookUp[0]->getNumBins()];

vector< vector<double> > data2; data2.resize(thisLookUp[0]->getNumBins());

vector<SharedRAbundVector*> subset;

int setACount = 0;

int setBCount = 0;

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

string thisGroup = thisLookUp[i]->getGroup();

//is this group for a set we want to compare??

//sorting the sets by putting setB at the back and setA in the front

if ((designMap->getGroup(thisGroup) == setB)) {

subset.push_back(thisLookUp[i]);

setBCount++;

}else if ((designMap->getGroup(thisGroup) == setA)) {

subset.insert(subset.begin()+setACount, thisLookUp[i]);

setACount++;

}

}

if ((setACount == 0) || (setBCount == 0)) {

m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();

outputNames.pop_back();

}else {

//fill data

for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {

//data[j] = new double[subset.size()];

data2[j].resize(subset.size(), 0.0);

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

data2[j][i] = (subset[i]->getAbundance(j));

}

}

m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();

//metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);

if (convertSharedToInput) { convertToInput(subset, outputFileName); }

m->mothurOutEndLine();

MothurMetastats mothurMeta(threshold, iters);

mothurMeta.runMetastats(outputFileName , data2, setACount);

m->mothurOutEndLine();

m->mothurOutEndLine();

}

//free memory

//delete output;

//for(int i = 0; i < thisLookUp[0]->getNumBins(); i++) { delete[] data[i]; }

//delete[] data;

}

return 0;

}

catch(exception& e) {

m->errorOut(e, "MetaStatsCommand", "driver");

exit(1);

}

try {

ifstream in;

m->openInputFile(filename, in);

string header = m->getline(in); m->gobble(in);

vector<string> groups = m->splitWhiteSpace(header);

vector<SharedRAbundFloatVector*> newLookup;

cout << groups.size() << endl;

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

cout << "creating group " << groups[i] << endl;

SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();

temp->setLabel("0.03");

temp->setGroup(groups[i]);

newLookup.push_back(temp);

}

int otuCount = 0;

while (!in.eof()) {

if (m->control_pressed) { break; }

string otuname;

in >> otuname; m->gobble(in);

otuCount++;

cout << otuname << endl;

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

double temp;

in >> temp; m->gobble(in);

newLookup[i]->push_back(temp, groups[i]);

}

m->gobble(in);

}

in.close();

ofstream out;

m->openOutputFile(filename+".shared", out);

out << "label\tgroup\tnumOTUs\t";

string snumBins = toString(otuCount);

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

string binLabel = "Otu";

string sbinNumber = toString(i+1);

if (sbinNumber.length() < snumBins.length()) {

int diff = snumBins.length() - sbinNumber.length();

for (int h = 0; h < diff; h++) { binLabel += "0"; }

}

binLabel += sbinNumber;

out << binLabel << '\t';

}

out << endl;

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

out << "0.03" << '\t' << groups[i] << '\t';

newLookup[i]->print(out);

}

out.close();

cout << filename+".shared" << endl;

return 0;

}

catch(exception& e) {

m->errorOut(e, "MetaStatsCommand", "convertToShared");

exit(1);

}

try {

ofstream out;

m->openOutputFile(thisfilename+".matrix", out);

out << "\t";

for (int i = 0; i < subset.size()-1; i++) {

out << subset[i]->getGroup() << '\t';

}

out << subset[subset.size()-1]->getGroup() << endl;

for (int i = 0; i < subset[0]->getNumBins(); i++) {

out << m->currentSharedBinLabels[i] << '\t';

for (int j = 0; j < subset.size()-1; j++) {

out << subset[j]->getAbundance(i) << '\t';

}

out << subset[subset.size()-1]->getAbundance(i) << endl;

}

out.close();

cout << thisfilename+".matrix" << endl;

return 0;

}

catch(exception& e) {

m->errorOut(e, "MetaStatsCommand", "convertToInput");

exit(1);

}