2 * pipelinepdscommand.cpp
5 * Created by westcott on 10/5/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "pipelinepdscommand.h"
11 #include "sffinfocommand.h"
12 #include "commandoptionparser.hpp"
14 //**********************************************************************************************************************
15 vector<string> PipelineCommand::getValidParameters(){
17 string Array[] = {"sff","oligos","align","chimera","classify","taxonomy","pipeline","processors","outputdir","inputdir"};
18 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
22 m->errorOut(e, "PipelineCommand", "getValidParameters");
26 //**********************************************************************************************************************
27 vector<string> PipelineCommand::getRequiredParameters(){
29 vector<string> myArray;
33 m->errorOut(e, "PipelineCommand", "getRequiredParameters");
37 //**********************************************************************************************************************
38 vector<string> PipelineCommand::getRequiredFiles(){
40 vector<string> myArray;
44 m->errorOut(e, "PipelineCommand", "getRequiredFiles");
48 //**********************************************************************************************************************
49 PipelineCommand::PipelineCommand(string option) {
51 cFactory = CommandFactory::getInstance();
54 //allow user to run help
55 if(option == "help") { help(); abort = true; }
59 //valid paramters for this command
60 string AlignArray[] = {"sff","oligos","align","chimera","classify","taxonomy","pipeline","processors","outputdir","inputdir"};
61 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
63 OptionParser parser(option);
64 map<string, string> parameters = parser.getParameters();
66 ValidParameters validParameter;
67 map<string, string>::iterator it;
69 //check to make sure all parameters are valid for command
70 for (it = parameters.begin(); it != parameters.end(); it++) {
71 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
74 //if the user changes the input directory command factory will send this info to us in the output parameter
75 string inputDir = validParameter.validFile(parameters, "inputdir", false);
76 if (inputDir == "not found"){ inputDir = ""; }
79 it = parameters.find("sff");
80 //user has given a template file
81 if(it != parameters.end()){
82 path = m->hasPath(it->second);
83 //if the user has not given a path then, add inputdir. else leave path alone.
84 if (path == "") { parameters["sff"] = inputDir + it->second; }
87 it = parameters.find("oligos");
88 //user has given a template file
89 if(it != parameters.end()){
90 path = m->hasPath(it->second);
91 //if the user has not given a path then, add inputdir. else leave path alone.
92 if (path == "") { parameters["oligos"] = inputDir + it->second; }
95 it = parameters.find("align");
96 //user has given a template file
97 if(it != parameters.end()){
98 path = m->hasPath(it->second);
99 //if the user has not given a path then, add inputdir. else leave path alone.
100 if (path == "") { parameters["align"] = inputDir + it->second; }
103 it = parameters.find("chimera");
104 //user has given a template file
105 if(it != parameters.end()){
106 path = m->hasPath(it->second);
107 //if the user has not given a path then, add inputdir. else leave path alone.
108 if (path == "") { parameters["chimera"] = inputDir + it->second; }
111 it = parameters.find("classify");
112 //user has given a template file
113 if(it != parameters.end()){
114 path = m->hasPath(it->second);
115 //if the user has not given a path then, add inputdir. else leave path alone.
116 if (path == "") { parameters["classify"] = inputDir + it->second; }
119 it = parameters.find("taxonomy");
120 //user has given a template file
121 if(it != parameters.end()){
122 path = m->hasPath(it->second);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
127 it = parameters.find("pipeline");
128 //user has given a template file
129 if(it != parameters.end()){
130 path = m->hasPath(it->second);
131 //if the user has not given a path then, add inputdir. else leave path alone.
132 if (path == "") { parameters["pipeline"] = inputDir + it->second; }
136 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
138 pipeFilename = validParameter.validFile(parameters, "pipeline", true);
139 if (pipeFilename == "not found") { pipeFilename = ""; }
140 else if (pipeFilename == "not open") { pipeFilename = ""; abort = true; }
142 string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
143 convert(temp, processors);
145 if (pipeFilename != "") {
146 abort = readUsersPipeline();
148 sffFile = validParameter.validFile(parameters, "sff", true);
149 if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
150 else if (sffFile == "not open") { sffFile = ""; abort = true; }
152 oligosFile = validParameter.validFile(parameters, "oligos", true);
153 if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
154 else if (oligosFile == "not open") { oligosFile = ""; abort = true; }
156 alignFile = validParameter.validFile(parameters, "align", true);
157 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; }
158 else if (alignFile == "not open") { alignFile = ""; abort = true; }
160 chimeraFile = validParameter.validFile(parameters, "chimera", true);
161 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; }
162 else if (chimeraFile == "not open") { chimeraFile = ""; abort = true; }
164 classifyFile = validParameter.validFile(parameters, "classify", true);
165 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; }
166 else if (classifyFile == "not open") { classifyFile = ""; abort = true; }
168 taxonomyFile = validParameter.validFile(parameters, "taxonomy", true);
169 if (taxonomyFile == "not found") { m->mothurOut("taxonomy is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
170 else if (taxonomyFile == "not open") { taxonomyFile = ""; abort = true; }
175 catch(exception& e) {
176 m->errorOut(e, "PipelineCommand", "PipelineCommand");
180 //**********************************************************************************************************************
182 void PipelineCommand::help(){
184 m->mothurOut("The pipeline command is designed to guide you through your analysis using mothur.\n");
185 m->mothurOut("The pipeline command parameters are pipeline, sff, oligos, align, chimera, classify, taxonomy and processors.\n");
186 m->mothurOut("The sff parameter allows you to enter your sff file. It is required, if not using pipeline parameter.\n");
187 m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required, if not using pipeline parameter.\n");
188 m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required, if not using pipeline parameter.\n");
189 m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required, if not using pipeline parameter.\n");
190 m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required, if not using pipeline parameter.\n");
191 m->mothurOut("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");
192 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
193 m->mothurOut("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 mothurmade instead.\n");
194 m->mothurOut("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");
195 m->mothurOut("then, you could enter unique.seqs(fasta=mothurmade), and mothur would use the .trim.fasta file from the trim.seqs command. \n");
196 m->mothurOut("then you could enter align.seqs(candidate=mothurmade, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n");
197 m->mothurOut("If no pipeline file is given then mothur will use Pat's pipeline. \n\n");
198 m->mothurOut("Here is a list of the commands used in Pat's pipeline.\n");
199 m->mothurOut("All paralellized commands will use the processors you entered.\n");
200 m->mothurOut("The sffinfo command takes your sff file and extracts the fasta and quality files.\n");
201 m->mothurOut("The trim.seqs command uses your oligos file and the quality and fasta files generated by sffinfo.\n");
202 m->mothurOut("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");
203 m->mothurOut("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");
204 m->mothurOut("The align.seqs command aligns the unique sequences using the aligners default options. \n");
205 m->mothurOut("The screen.seqs command screens the sequences using optimize=end-minlength. \n");
206 m->mothurOut("The pipeline uses chimera.slayer to detect chimeras using the default options. \n");
207 m->mothurOut("The pipeline removes all sequences determined to be chimeric by chimera.slayer. \n");
208 m->mothurOut("The filter.seqs command filters the sequences using vertical=T, trump=. \n");
209 m->mothurOut("The unique.seqs command uses the filtered fasta file and name file to remove sequences that have become redundant after filtering.\n");
210 m->mothurOut("The pre.cluster command clusters sequences that have no more than 2 differences.\n");
211 m->mothurOut("The dist.seqs command is used to generate a column and phylip formatted distance matrix using cutoff=0.20 for column.\n");
212 m->mothurOut("The pipeline uses cluster with method=average, hard=T. \n");
213 m->mothurOut("The classify.seqs command is used to classify the sequences using the bayesian method with a cutoff of 80.\n");
214 m->mothurOut("The phylotype command is used to cluster the sequences based on their classification.\n");
215 m->mothurOut("The clearcut command is used to generate a tree using neighbor=T. \n");
216 m->mothurOut("The summary.single and summary.shared commands are run on the otu files from cluster and phylotype commands. \n");
217 m->mothurOut("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");
218 m->mothurOut("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");
219 m->mothurOut("The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n");
220 m->mothurOut("The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n");
221 m->mothurOut("The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n");
222 m->mothurOut("\n\n");
224 catch(exception& e) {
225 m->errorOut(e, "PipelineCommand", "help");
230 //**********************************************************************************************************************
232 PipelineCommand::~PipelineCommand(){}
234 //**********************************************************************************************************************
236 int PipelineCommand::execute(){
238 if (abort == true) { return 0; }
240 int start = time(NULL);
242 if (pipeFilename == "") {
243 createPatsPipeline();
246 for (int i = 0; i < commands.size(); i++) {
247 m->mothurOutEndLine(); m->mothurOut("mothur > " + commands[i]); m->mothurOutEndLine();
249 if (m->control_pressed) { return 0; }
251 CommandOptionParser parser(commands[i]);
252 string commandName = parser.getCommandString();
253 string options = parser.getOptionString();
257 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
259 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
262 //executes valid command
263 Command* command = cFactory->getCommand(commandName, options, "pipe");
266 //add output files to list
267 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
268 map<string, vector<string> >::iterator itMade;
269 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
270 vector<string> temp = itMade->second;
271 for (int j = 0; j < temp.size(); j++) { outputNames.push_back(temp[j]); }
279 }else { runUsersPipeline(); }
281 if (m->control_pressed) { return 0; }
283 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run the pipeline analysis."); m->mothurOutEndLine(); m->mothurOutEndLine();
285 m->mothurOutEndLine();
286 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
287 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
288 m->mothurOutEndLine();
292 catch(exception& e) {
293 m->errorOut(e, "PipelineCommand", "execute");
297 //**********************************************************************************************************************
299 bool PipelineCommand::readUsersPipeline(){
303 m->openInputFile(pipeFilename, in);
305 string nextCommand = "";
307 map<string, vector<string> > mothurMadeFiles;
310 nextCommand = m->getline(in); m->gobble(in);
312 if (nextCommand[0] != '#') {
315 string commandName, options;
316 error = parseCommand(nextCommand, commandName, options);
318 if (error) { in.close(); return error; }
319 if (commandName == "pipeline.pds") { m->mothurOut("Cannot run the pipeline.pds command from inside the pipeline.pds command."); m->mothurOutEndLine(); in.close(); return true; }
321 error = checkForValidAndRequiredParameters(commandName, options, mothurMadeFiles);
323 if (error) { in.close(); return error; }
331 catch(exception& e) {
332 m->errorOut(e, "PipelineCommand", "readUsersPipeline");
336 //**********************************************************************************************************************
338 bool PipelineCommand::parseCommand(string nextCommand, string& name, string& options){
340 CommandOptionParser parser(nextCommand);
341 name = parser.getCommandString();
342 options = parser.getOptionString();
344 if (name == "") { return true; } //name == "" if () are not right
348 catch(exception& e) {
349 m->errorOut(e, "PipelineCommand", "parseCommand");
353 //**********************************************************************************************************************
355 bool PipelineCommand::checkForValidAndRequiredParameters(string name, string options, map<string, vector<string> >& mothurMadeFiles){
358 if (name == "system") { return false; }
360 if (name == "system") { return false; }
362 //get shell of the command so we can check to make sure its valid without running it
363 Command* command = cFactory->getCommand(name);
365 //check to make sure all parameters are valid for command
366 vector<string> validParameters = command->getValidParameters();
368 OptionParser parser(options);
369 map<string, string> parameters = parser.getParameters();
371 ValidParameters validParameter;
372 map<string, string>::iterator it;
373 map<string, vector<string> >::iterator itMade;
375 for (it = parameters.begin(); it != parameters.end(); it++) {
377 if (validParameter.isValidParameter(it->first, validParameters, it->second) != true) { return true; } // not valid
378 if (it->second == "mothurmade") {
379 itMade = mothurMadeFiles.find(it->first);
381 if (itMade == mothurMadeFiles.end()) {
382 if ((name == "align.seqs") && (it->first == "candidate")) {} //do nothing about candidate
384 m->mothurOut("You have the " + it->first + " listed as a mothurmade file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine();
391 //is the command missing any required
392 vector<string> requiredParameters = command->getRequiredParameters();
397 if (requiredParameters.size() > 2) {
398 if (requiredParameters[(requiredParameters.size()-1)] == "or") { hasOr = true; }
401 for (int i = 0; i < requiredParameters.size(); i++) {
402 it = parameters.find(requiredParameters[i]);
404 if (it != parameters.end()) { numFound++; }
406 if (!hasOr) { m->mothurOut(name + " requires the " + requiredParameters[i] + " parameter, please correct."); m->mothurOutEndLine(); }
410 // if all are needed and not all are found
411 if ((!hasOr) && (numFound != requiredParameters.size())) { return true; }
412 //if one is needed and none are found
413 else if ((hasOr) && (numFound == 0)) { return true; }
416 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
417 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
418 mothurMadeFiles[itMade->first] = itMade->second; //adds any new types
423 catch(exception& e) {
424 m->errorOut(e, "PipelineCommand", "checkForValidAndRequiredParameters");
428 //**********************************************************************************************************************
429 int PipelineCommand::runUsersPipeline(){
432 m->openInputFile(pipeFilename, in);
434 string nextCommand = "";
436 map<string, vector<string> > mothurMadeFiles;
439 nextCommand = m->getline(in); m->gobble(in);
441 if (nextCommand[0] != '#') {
442 CommandOptionParser parser(nextCommand);
443 string commandName = parser.getCommandString();
444 string options = parser.getOptionString();
446 if ((options != "") && (commandName != "system")) {
447 bool error = fillInMothurMade(options, mothurMadeFiles);
448 if (error) { in.close(); return 0; }
451 m->mothurOutEndLine(); m->mothurOut("mothur > " + commandName + "(" + options + ")"); m->mothurOutEndLine();
453 if (m->control_pressed) { return 0; }
457 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
459 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
462 //executes valid command
463 Command* command = cFactory->getCommand(commandName, options, "pipe");
466 //add output files to list
467 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
468 map<string, vector<string> >::iterator itMade;
469 map<string, vector<string> >::iterator it;
470 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
472 vector<string> temp = itMade->second;
473 for (int k = 0; k < temp.size(); k++) { outputNames.push_back(temp[k]); } //
475 //update Mothur Made for each file
476 it = mothurMadeFiles.find(itMade->first);
478 if (it == mothurMadeFiles.end()) { //new type
480 mothurMadeFiles[itMade->first] = temp;
482 }else{ //update existing type
483 vector<string> oldFileNames = it->second;
484 //look at new files, see if an old version of the file exists, if so update, else just add.
485 //for example you may have abrecovery.fasta and amazon.fasta as old files and you created a new amazon.trim.fasta.
487 for (int k = 0; k < temp.size(); k++) {
490 string root = m->getSimpleName(temp[k]);
491 string individual = "";
492 for(int i=0;i<root.length();i++){
497 individual += root[i];
501 //look for that base name in oldfiles
503 for (int l = 0; l < oldFileNames.size(); l++) {
504 int pos = oldFileNames[l].find(root);
505 if (pos != string::npos) {
511 //if you found it update it, else add it
513 mothurMadeFiles[it->first][spot] = temp[k];
515 mothurMadeFiles[it->first].push_back(temp[k]);
529 catch(exception& e) {
530 m->errorOut(e, "PipelineCommand", "runUsersPipeline");
534 //**********************************************************************************************************************
535 bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<string> >& mothurMadeFiles){
538 OptionParser parser(options);
539 map<string, string> parameters = parser.getParameters();
540 map<string, string>::iterator it;
541 map<string, vector<string> >::iterator itMade;
545 //fill in mothurmade filenames
546 for (it = parameters.begin(); it != parameters.end(); it++) {
547 string paraType = it->first;
548 string tempOption = it->second;
550 if (tempOption == "mothurmade") {
552 if (it->first == "candidate") { paraType = "fasta"; }
554 itMade = mothurMadeFiles.find(paraType);
556 if (itMade == mothurMadeFiles.end()) {
557 m->mothurOut("Looking for a mothurmade " + paraType + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine();
560 vector<string> temp = itMade->second;
562 if (temp.size() > 1) {
563 //ask user which file to use
564 m->mothurOut("More than one file has been created for the " + paraType + " parameter. "); m->mothurOutEndLine();
565 for (int i = 0; i < temp.size(); i++) {
566 m->mothurOut(toString(i) + " - " + temp[i]); m->mothurOutEndLine();
569 m->mothurOut("Please select the number of the file you would like to use: ");
572 m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
574 if ((num < 0) || (num > (temp.size()-1))) { m->mothurOut("Not a valid response, quitting."); m->mothurOutEndLine(); return true; }
576 tempOption = temp[num];
579 //clears buffer so next command doesn't have error
583 vector<string> newTemp;
584 for (int i = 0; i < temp.size(); i++) {
585 if (i == num) { newTemp.push_back(temp[i]); }
587 m->mothurOut("Would you like to remove " + temp[i] + " as an option for " + paraType + ", (y/n): "); m->mothurOutEndLine();
590 m->mothurOutJustToLog(response); m->mothurOutEndLine();
592 if (response == "n") { newTemp.push_back(temp[i]); }
594 //clears buffer so next command doesn't have error
600 mothurMadeFiles[paraType] = newTemp;
603 }else if (temp.size() == 0){
604 m->mothurOut("Sorry, we seem to think you created a " + paraType + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine();
607 tempOption = temp[0];
612 options += it->first + "=" + tempOption + ", ";
615 //rip off extra comma
616 options = options.substr(0, (options.length()-2));
620 catch(exception& e) {
621 m->errorOut(e, "PipelineCommand", "fillInMothurMade");
626 //**********************************************************************************************************************
627 void PipelineCommand::createPatsPipeline(){
631 string thisCommand = "sffinfo(sff=" + sffFile + ")";
632 commands.push_back(thisCommand);
635 string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
636 string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
637 thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
638 commands.push_back(thisCommand);
641 string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";
642 qualFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
643 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
644 thisCommand = "unique.seqs(fasta=" + fastaFile + ")";
645 commands.push_back(thisCommand);
648 string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
649 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
650 thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
651 commands.push_back(thisCommand);
654 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
655 thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
656 commands.push_back(thisCommand);
659 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
660 nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
661 groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
662 thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
663 commands.push_back(thisCommand);
666 string accnosFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.accnos";
667 thisCommand = "remove.seqs(fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", accnos=" + accnosFile + ", dups=T)";
668 commands.push_back(thisCommand);
671 nameFile = m->getRootName(m->getSimpleName(nameFile)) + "pick" + m->getExtension(nameFile);
672 groupFile = m->getRootName(m->getSimpleName(groupFile)) + "pick" + m->getExtension(groupFile);
673 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "pick" + m->getExtension(fastaFile);
674 thisCommand = "filter.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", vertical=T, trump=.)";
675 commands.push_back(thisCommand);
678 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "filter.fasta";
679 thisCommand = "unique.seqs(fasta=" + fastaFile + ", name=" + nameFile + ")";
680 commands.push_back(thisCommand);
683 nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
684 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
685 thisCommand = "pre.cluster(fasta=" + fastaFile + ", name=" + nameFile + ", diffs=2)";
686 commands.push_back(thisCommand);
689 nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster.names";
690 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster" + m->getExtension(fastaFile);
691 thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", cutoff=0.20)";
692 commands.push_back(thisCommand);
695 string columnFile = m->getRootName(m->getSimpleName(fastaFile)) + "dist";
696 thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", output=lt)";
697 commands.push_back(thisCommand);
700 string phylipFile = m->getRootName(m->getSimpleName(fastaFile)) + "phylip.dist";
701 thisCommand = "read.dist(column=" + columnFile + ", name=" + nameFile + ")";
702 commands.push_back(thisCommand);
705 thisCommand = "cluster(method=average, hard=T)";
706 commands.push_back(thisCommand);
708 string listFile = m->getRootName(m->getSimpleName(columnFile)) + "an.list";
709 string rabundFile = m->getRootName(m->getSimpleName(columnFile)) + "an.rabund";
712 thisCommand = "degap.seqs(fasta=" + fastaFile + ")";
713 commands.push_back(thisCommand);
716 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "ng.fasta";
717 thisCommand = "classify.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", template=" + classifyFile + ", taxonomy=" + taxonomyFile + ", cutoff=80)";
718 commands.push_back(thisCommand);
720 string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFile));
721 RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
722 if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
723 RippedTaxName += ".";
725 string fastaTaxFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "taxonomy";
726 string taxSummaryFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "tax.summary";
729 thisCommand = "phylotype(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ")";
730 commands.push_back(thisCommand);
732 string phyloListFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.list";
733 string phyloRabundFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.rabund";
736 thisCommand = "clearcut(phylip=" + phylipFile + ", neighbor=T)";
737 commands.push_back(thisCommand);
739 string treeFile = m->getRootName(m->getSimpleName(phylipFile)) + "tre";
742 thisCommand = "read.otu(list=" + listFile + ", group=" + groupFile + ", label=0.03)";
743 commands.push_back(thisCommand);
745 string sharedFile = m->getRootName(m->getSimpleName(listFile)) + "shared";
748 thisCommand = "read.otu(list=" + phyloListFile + ", group=" + groupFile + ", label=1)";
749 commands.push_back(thisCommand);
751 string phyloSharedFile = m->getRootName(m->getSimpleName(phyloListFile)) + "shared";
754 thisCommand = "read.otu(shared=" + sharedFile + ")";
755 commands.push_back(thisCommand);
758 thisCommand = "summary.single(calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";
759 commands.push_back(thisCommand);
762 thisCommand = "summary.shared(calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";
763 commands.push_back(thisCommand);
766 thisCommand = "read.otu(rabund=" + rabundFile + ", label=0.03)";
767 commands.push_back(thisCommand);
770 thisCommand = "summary.single(calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";
771 commands.push_back(thisCommand);
774 thisCommand = "read.otu(shared=" + phyloSharedFile + ")";
775 commands.push_back(thisCommand);
778 thisCommand = "summary.single(calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";
779 commands.push_back(thisCommand);
782 thisCommand = "summary.shared(calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";
783 commands.push_back(thisCommand);
786 thisCommand = "read.otu(rabund=" + phyloRabundFile + ", label=1)";
787 commands.push_back(thisCommand);
790 thisCommand = "summary.single(calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson, size=5000)";
791 commands.push_back(thisCommand);
794 thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + listFile + ", cutoff=51, label=0.03)";
795 commands.push_back(thisCommand);
798 thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + phyloListFile + ", cutoff=51, label=1)";
799 commands.push_back(thisCommand);
802 thisCommand = "read.tree(tree=" + treeFile + ", name=" + nameFile + ", group=" + groupFile + ")";
803 commands.push_back(thisCommand);
806 thisCommand = "phylo.diversity(iters=100,rarefy=T)";
807 commands.push_back(thisCommand);
810 thisCommand = "unifrac.weighted(random=false, distance=true, groups=all, processors=" + toString(processors) + ")";
811 commands.push_back(thisCommand);
814 thisCommand = "unifrac.unweighted(random=false, distance=true, processors=" + toString(processors) + ")";
815 commands.push_back(thisCommand);
819 catch(exception& e) {
820 m->errorOut(e, "PipelineCommand", "createPatsPipeline");
825 //**********************************************************************************************************************