try {

CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(psff);

CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(poligos);

CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(palign);

CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pchimera);

CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pclassify);

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

CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none",false,false); parameters.push_back(ppipeline);

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

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, "PipelineCommand", "setParameters");

exit(1);

}

try {

string helpString = "";

helpString += "The pipeline.pds command is designed to guide you through your analysis using mothur.\n";

helpString += "The pipeline.pds command parameters are pipeline, sff, oligos, align, chimera, classify, taxonomy and processors.\n";

helpString += "The sff parameter allows you to enter your sff file. It is required, if not using pipeline parameter.\n";

helpString += "The oligos parameter allows you to enter your oligos file. It is required, if not using pipeline parameter.\n";

helpString += "The align parameter allows you to enter a template to use with the aligner. It is required, if not using pipeline parameter.\n";

helpString += "The chimera parameter allows you to enter a template to use for chimera detection. It is required, if not using pipeline parameter.\n";

helpString += "The classify parameter allows you to enter a template to use for classification. It is required, if not using pipeline parameter.\n";

helpString += "The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required, if not using pipeline parameter.\n";

helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";

helpString += "The pipeline parameter allows you to enter your own pipeline file. This file should look like a mothur batchfile, but where you would be using a mothur generated file, you can use current instead.\n";

helpString += "Example: trim.seqs(processors=8, allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, fasta=may1.v13.fasta, oligos=may1.v13.oligos, qfile=may1.v13.qual)\n";

helpString += "then, you could enter unique.seqs(fasta=current), and mothur would use the .trim.fasta file from the trim.seqs command. \n";

helpString += "then you could enter align.seqs(candidate=current, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n";

helpString += "If no pipeline file is given then mothur will use Pat's pipeline. \n";

helpString += "Here is a list of the commands used in Pat's pipeline.\n";

helpString += "All paralellized commands will use the processors you entered.\n";

helpString += "The sffinfo command takes your sff file and extracts the fasta and quality files.\n";

helpString += "The trim.seqs command uses your oligos file and the quality and fasta files generated by sffinfo.\n";

helpString += "The trim.seqs command sets the following parameters: allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50.\n";

helpString += "The unique.seqs command uses the trimmed fasta file and removes redundant sequences, don't worry the names file generated by unique.seqs will be used in the pipeline to make sure they are included.\n";

helpString += "The align.seqs command aligns the unique sequences using the aligners default options. \n";

helpString += "The screen.seqs command screens the sequences using optimize=end-minlength. \n";

helpString += "The pipeline uses chimera.slayer to detect chimeras using the default options. \n";

helpString += "The pipeline removes all sequences determined to be chimeric by chimera.slayer. \n";

helpString += "The filter.seqs command filters the sequences using vertical=T, trump=. \n";

helpString += "The unique.seqs command uses the filtered fasta file and name file to remove sequences that have become redundant after filtering.\n";

helpString += "The pre.cluster command clusters sequences that have no more than 2 differences.\n";

helpString += "The dist.seqs command is used to generate a column and phylip formatted distance matrix using cutoff=0.20 for column.\n";

helpString += "The pipeline uses cluster with method=average, hard=T. \n";

helpString += "The classify.seqs command is used to classify the sequences using the bayesian method with a cutoff of 80.\n";

helpString += "The phylotype command is used to cluster the sequences based on their classification.\n";

helpString += "The clearcut command is used to generate a tree using neighbor=T. \n";

helpString += "The summary.single and summary.shared commands are run on the otu files from cluster and phylotype commands. \n";

helpString += "The summary.shared command uses calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc. \n";

helpString += "The summary.single command uses calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson. \n";

helpString += "The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n";

helpString += "The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n";

helpString += "The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n";

helpString += "\n";

return helpString;

}

catch(exception& e) {

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

exit(1);

}

try {

cFactory = CommandFactory::getInstance();

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; }

}

//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("sff");

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

}

it = parameters.find("oligos");

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

}

it = parameters.find("align");

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

}

it = parameters.find("chimera");

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

}

it = parameters.find("classify");

//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["classify"] = 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("pipeline");

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

}

}

outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }

pipeFilename = validParameter.validFile(parameters, "pipeline", true);

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

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

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

m->setProcessors(temp);

m->mothurConvert(temp, processors);

if (pipeFilename != "") {

abort = readUsersPipeline();

}else{

sffFile = validParameter.validFile(parameters, "sff", true);

if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }

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

else { m->setSFFFile(sffFile); }

oligosFile = validParameter.validFile(parameters, "oligos", true);

if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }

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

alignFile = validParameter.validFile(parameters, "align", true);

if (alignFile == "not found") { m->mothurOut("align is a required parameter for the pipeline command. Please provide the template to align with."); m->mothurOutEndLine(); abort = true; }

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

chimeraFile = validParameter.validFile(parameters, "chimera", true);

if (chimeraFile == "not found") { m->mothurOut("chimera is a required parameter for the pipeline command. Please provide the template to check for chimeras with."); m->mothurOutEndLine(); abort = true; }

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

classifyFile = validParameter.validFile(parameters, "classify", true);

if (classifyFile == "not found") { m->mothurOut("classify is a required parameter for the pipeline command. Please provide the template to use with the classifier."); m->mothurOutEndLine(); abort = true; }

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

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

if (taxonomyFile == "not found") { m->mothurOut("taxonomy is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }

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

}

}

}

catch(exception& e) {

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

exit(1);

}

try {

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

int start = time(NULL);

if (pipeFilename == "") {

createPatsPipeline();

//run Pats pipeline

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

m->mothurOutEndLine(); m->mothurOut("mothur > " + commands[i]); m->mothurOutEndLine();

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

CommandOptionParser parser(commands[i]);

string commandName = parser.getCommandString();

string options = parser.getOptionString();

#ifdef USE_MPI

int pid;

MPI_Comm_rank(MPI_COMM_WORLD, &pid);

if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {

#endif

//executes valid command

Command* command = cFactory->getCommand(commandName, options, "pipe");

command->execute();

//add output files to list

map<string, vector<string> > thisCommandsFile = command->getOutputFiles();

map<string, vector<string> >::iterator itMade;

for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {

vector<string> temp = itMade->second;

for (int j = 0; j < temp.size(); j++) { outputNames.push_back(temp[j]); }

}

#ifdef USE_MPI

}

#endif

}

}else { runUsersPipeline(); }

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

m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run the pipeline analysis."); m->mothurOutEndLine(); m->mothurOutEndLine();

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, "PipelineCommand", "execute");

exit(1);

}

try {

ifstream in;

m->openInputFile(pipeFilename, in);

string nextCommand = "";

map<string, vector<string> > mothurMadeFiles;

while(!in.eof()) {

nextCommand = m->getline(in); m->gobble(in);

if (nextCommand[0] != '#') {

bool error = false;

string commandName, options;

error = parseCommand(nextCommand, commandName, options);

if (error) { in.close(); return error; }

if (commandName == "pipeline.pds") { m->mothurOut("Cannot run the pipeline.pds command from inside the pipeline.pds command."); m->mothurOutEndLine(); in.close(); return true; }

error = checkForValidAndRequiredParameters(commandName, options, mothurMadeFiles);

if (error) { in.close(); return error; }

}

}

in.close();

return false;

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "readUsersPipeline");

exit(1);

}

try {

CommandOptionParser parser(nextCommand);

name = parser.getCommandString();

options = parser.getOptionString();

if (name == "") { return true; } //name == "" if () are not right

return false;

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "parseCommand");

exit(1);

}

try {

if (name == "system") { return false; }

//get shell of the command so we can check to make sure its valid without running it

Command* command = cFactory->getCommand(name);

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

vector<string> validParameters = command->setParameters();

OptionParser parser(options);

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

ValidParameters validParameter;

map<string, string>::iterator it;

map<string, vector<string> >::iterator itMade;

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

if (validParameter.isValidParameter(it->first, validParameters, it->second) != true) { return true; } // not valid

if (it->second == "current") {

itMade = mothurMadeFiles.find(it->first);

if (itMade == mothurMadeFiles.end()) {

m->mothurOut("You have the " + it->first + " listed as a current file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine();

return true;

}

}

}

//is the command missing any required

vector<CommandParameter> commandParameters = command->getParameters();

vector<string> requiredParameters;

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

if (commandParameters[i].required) {

requiredParameters.push_back(commandParameters[i].name);

}

}

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

it = parameters.find(requiredParameters[i]);

if (it == parameters.end()) {

string paraToLookFor = requiredParameters[i];

//does mothur have a current file for this?

itMade = mothurMadeFiles.find(requiredParameters[i]);

if (itMade == mothurMadeFiles.end()) {

m->mothurOut(name + " requires the " + requiredParameters[i] + " parameter, please correct."); m->mothurOutEndLine();

}

}

}

//update MothurMade

map<string, vector<string> > thisCommandsFile = command->getOutputFiles();

for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {

mothurMadeFiles[itMade->first] = itMade->second; //adds any new types

}

return false;

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "checkForValidAndRequiredParameters");

exit(1);

}

try {

ifstream in;

m->openInputFile(pipeFilename, in);

string nextCommand = "";

map<string, vector<string> > mothurMadeFiles;

while(!in.eof()) {

nextCommand = m->getline(in); m->gobble(in);

if (nextCommand[0] != '#') {

CommandOptionParser parser(nextCommand);

string commandName = parser.getCommandString();

string options = parser.getOptionString();

if ((options != "") && (commandName != "system")) {

bool error = fillInMothurMade(options, mothurMadeFiles);

if (error) { in.close(); return 0; }

}

m->mothurOutEndLine(); m->mothurOut("mothur > " + commandName + "(" + options + ")"); m->mothurOutEndLine();

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

#ifdef USE_MPI

int pid;

MPI_Comm_rank(MPI_COMM_WORLD, &pid);

if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {

#endif

//executes valid command

Command* command = cFactory->getCommand(commandName, options, "pipe");

command->execute();

//add output files to list

map<string, vector<string> > thisCommandsFile = command->getOutputFiles();

map<string, vector<string> >::iterator itMade;

map<string, vector<string> >::iterator it;

for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {

vector<string> temp = itMade->second;

for (int k = 0; k < temp.size(); k++) { outputNames.push_back(temp[k]); } //

//update Mothur Made for each file

it = mothurMadeFiles.find(itMade->first);

if (it == mothurMadeFiles.end()) { //new type

mothurMadeFiles[itMade->first] = temp;

}else{ //update existing type

vector<string> oldFileNames = it->second;

//look at new files, see if an old version of the file exists, if so update, else just add.

//for example you may have abrecovery.fasta and amazon.fasta as old files and you created a new amazon.trim.fasta.

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

//get base name

string root = m->getSimpleName(temp[k]);

string individual = "";

for(int i=0;i<root.length();i++){

if(root[i] == '.'){

root = individual;

break;

}else{

individual += root[i];

}

}

//look for that base name in oldfiles

int spot = -1;

for (int l = 0; l < oldFileNames.size(); l++) {

int pos = oldFileNames[l].find(root);

if (pos != string::npos) {

spot = l;

break;

}

}

//if you found it update it, else add it

if (spot != -1) {

mothurMadeFiles[it->first][spot] = temp[k];

}else{

mothurMadeFiles[it->first].push_back(temp[k]);

}

}

}

}

#ifdef USE_MPI

}

#endif

}

}

in.close();

return 0;

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "runUsersPipeline");

exit(1);

}

try {

OptionParser parser(options);

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

map<string, string>::iterator it;

map<string, vector<string> >::iterator itMade;

options = "";

//fill in mothurmade filenames

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

string paraType = it->first;

string tempOption = it->second;

if (tempOption == "current") {

itMade = mothurMadeFiles.find(paraType);

if (itMade == mothurMadeFiles.end()) {

m->mothurOut("Looking for a current " + paraType + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine();

return true;

}else{

vector<string> temp = itMade->second;

if (temp.size() > 1) {

//ask user which file to use

m->mothurOut("More than one file has been created for the " + paraType + " parameter. "); m->mothurOutEndLine();

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

m->mothurOut(toString(i) + " - " + temp[i]); m->mothurOutEndLine();

}

m->mothurOut("Please select the number of the file you would like to use: ");

int num = 0;

cin >> num;

m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();

if ((num < 0) || (num > (temp.size()-1))) { m->mothurOut("Not a valid response, quitting."); m->mothurOutEndLine(); return true; }

else {

tempOption = temp[num];

}

//clears buffer so next command doesn't have error

string s;

getline(cin, s);

vector<string> newTemp;

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

if (i == num) { newTemp.push_back(temp[i]); }

else {

m->mothurOut("Would you like to remove " + temp[i] + " as an option for " + paraType + ", (y/n): "); m->mothurOutEndLine();

string response;

cin >> response;

m->mothurOutJustToLog(response); m->mothurOutEndLine();

if (response == "n") { newTemp.push_back(temp[i]); }

//clears buffer so next command doesn't have error

string s;

getline(cin, s);

}

}

mothurMadeFiles[paraType] = newTemp;

}else if (temp.size() == 0){

m->mothurOut("Sorry, we seem to think you created a " + paraType + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine();

return true;

}else{

tempOption = temp[0];

}

}

}

options += it->first + "=" + tempOption + ", ";

}

//rip off extra comma

options = options.substr(0, (options.length()-2));

return false;

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "fillInMothurMade");

exit(1);

}

try {

//sff.info command

string thisCommand = "sffinfo(sff=" + sffFile + ")";

commands.push_back(thisCommand);

//trim.seqs command

string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";

string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";

thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=current, allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=current)";

commands.push_back(thisCommand);

//unique.seqs

string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";

qualFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";

thisCommand = "unique.seqs(fasta=current)";

commands.push_back(thisCommand);

//align.seqs

string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);

thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=current, template=" + alignFile + ")";

commands.push_back(thisCommand);

//screen.seqs

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";

thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=current, name=current, group=current, optimize=end-minlength)";

commands.push_back(thisCommand);

//chimera.slayer

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);

nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);

groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);

thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=current, template=" + chimeraFile + ")";

commands.push_back(thisCommand);

//remove.seqs

string accnosFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.accnos";

thisCommand = "remove.seqs(fasta=current, name=current, group=current, accnos=current, dups=T)";

commands.push_back(thisCommand);

//filter.seqs

nameFile = m->getRootName(m->getSimpleName(nameFile)) + "pick" + m->getExtension(nameFile);

groupFile = m->getRootName(m->getSimpleName(groupFile)) + "pick" + m->getExtension(groupFile);

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "pick" + m->getExtension(fastaFile);

thisCommand = "filter.seqs(processors=" + toString(processors) + ", fasta=current, vertical=T, trump=.)";

commands.push_back(thisCommand);

//unique.seqs

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "filter.fasta";

thisCommand = "unique.seqs(fasta=current, name=current)";

commands.push_back(thisCommand);

//pre.cluster

nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);

thisCommand = "pre.cluster(fasta=current, name=current, diffs=2)";

commands.push_back(thisCommand);

//dist.seqs

nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster.names";

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster" + m->getExtension(fastaFile);

thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=current, cutoff=0.20)";

commands.push_back(thisCommand);

//dist.seqs

string columnFile = m->getRootName(m->getSimpleName(fastaFile)) + "dist";

thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=current, output=lt)";

commands.push_back(thisCommand);

//read.dist

string phylipFile = m->getRootName(m->getSimpleName(fastaFile)) + "phylip.dist";

thisCommand = "read.dist(column=current, name=current)";

commands.push_back(thisCommand);

//cluster

thisCommand = "cluster(method=average, hard=T)";

commands.push_back(thisCommand);

string listFile = m->getRootName(m->getSimpleName(columnFile)) + "an.list";

string rabundFile = m->getRootName(m->getSimpleName(columnFile)) + "an.rabund";

//degap.seqs

thisCommand = "degap.seqs(fasta=current)";

commands.push_back(thisCommand);

//classify.seqs

fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "ng.fasta";

thisCommand = "classify.seqs(processors=" + toString(processors) + ", fasta=current, name=current, template=" + classifyFile + ", taxonomy=" + taxonomyFile + ", cutoff=80)";

commands.push_back(thisCommand);

string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFile));

RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));

if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }

RippedTaxName += ".";

string fastaTaxFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "taxonomy";

string taxSummaryFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "tax.summary";

//phylotype

thisCommand = "phylotype(taxonomy=current, name=current)";

commands.push_back(thisCommand);

string phyloListFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.list";

string phyloRabundFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.rabund";

//clearcut

thisCommand = "clearcut(phylip=current, neighbor=T)";

commands.push_back(thisCommand);

string treeFile = m->getRootName(m->getSimpleName(phylipFile)) + "tre";

//read.otu

thisCommand = "make.shared(list=" + listFile + ", group=" + groupFile + ", label=0.03)";

commands.push_back(thisCommand);

string sharedFile = m->getRootName(m->getSimpleName(listFile)) + "shared";

//read.otu

thisCommand = "make.shared(list=" + phyloListFile + ", group=" + groupFile + ", label=1)";

commands.push_back(thisCommand);

string phyloSharedFile = m->getRootName(m->getSimpleName(phyloListFile)) + "shared";

//read.otu

thisCommand = "set.current(shared=" + sharedFile + ")";

commands.push_back(thisCommand);

//summary.single

thisCommand = "summary.single(shared=current, calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";

commands.push_back(thisCommand);

//summary.shared

thisCommand = "summary.shared(shared=current, calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";

commands.push_back(thisCommand);

//read.otu

//thisCommand = "read.otu(rabund=" + rabundFile + ", label=0.03)";

//commands.push_back(thisCommand);

//summary.single

thisCommand = "summary.single(rabund=" + rabundFile + ", label=0.03, calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";

commands.push_back(thisCommand);

//read.otu

thisCommand = "set.current(shared=" + phyloSharedFile + ")";

commands.push_back(thisCommand);

//summary.single

thisCommand = "summary.single(shared=current, calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";

commands.push_back(thisCommand);

//summary.shared

thisCommand = "summary.shared(shared=current, calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";

commands.push_back(thisCommand);

//read.otu

//thisCommand = "read.otu(rabund=" + phyloRabundFile + ", label=1)";

//commands.push_back(thisCommand);

//summary.single

thisCommand = "summary.single(rabund=" + phyloRabundFile + ", label=1, calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";

commands.push_back(thisCommand);

//classify.otu

thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + listFile + ", cutoff=51, label=0.03)";

commands.push_back(thisCommand);

//classify.otu

thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + phyloListFile + ", cutoff=51, label=1)";

commands.push_back(thisCommand);

//read.tree

thisCommand = "set.current(tree=" + treeFile + ", name=" + nameFile + ", group=" + groupFile + ")";

commands.push_back(thisCommand);

//phylo.diversity

thisCommand = "phylo.diversity(tree=current, group=current, name=current, iters=100,rarefy=T)";

commands.push_back(thisCommand);

//unifrac.weighted

thisCommand = "unifrac.weighted(tree=current, group=current, name=current, random=false, distance=true, groups=all, processors=" + toString(processors) + ")";

commands.push_back(thisCommand);

//unifrac.unweighted

thisCommand = "unifrac.unweighted(tree=current, group=current, name=current, random=false, distance=true, processors=" + toString(processors) + ")";

commands.push_back(thisCommand);

}

catch(exception& e) {

m->errorOut(e, "PipelineCommand", "createPatsPipeline");

exit(1);

}