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.\n");
187 m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required.\n");
188 m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required.\n");
189 m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required.\n");
190 m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required.\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.\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("First column contains the command name, and the second column contains the parameter options or 'defaults', meaning use defaults. You may leave out file options.\n");
195 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");
196 m->mothurOut("then, you could enter unique.seqs(fasta=mothurmade), and mothur would use the .trim.fasta file from the trim.seqs command. \n");
197 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");
198 m->mothurOut("If no pipeline file is given then mothur will use Pat's pipeline. \n\n");
199 m->mothurOut("Here is a list of the commands used in Pat's pipeline.\n");
200 m->mothurOut("All paralellized commands will use the processors you entered.\n");
201 m->mothurOut("The sffinfo command takes your sff file and extracts the fasta and quality files.\n");
202 m->mothurOut("The trim.seqs command uses your oligos file and the quality and fasta files generated by sffinfo.\n");
203 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");
204 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");
205 m->mothurOut("The align.seqs command aligns the unique sequences using the aligners default options. \n");
206 m->mothurOut("The screen.seqs command screens the sequences using optimize=end-minlength. \n");
207 m->mothurOut("The pipeline uses chimera.slayer to detect chimeras using the default options. \n");
208 m->mothurOut("The pipeline removes all sequences determined to be chimeric by chimera.slayer. \n");
209 m->mothurOut("The filter.seqs command filters the sequences using vertical=T, trump=. \n");
210 m->mothurOut("The unique.seqs command uses the filtered fasta file and name file to remove sequences that have become redundant after filtering.\n");
211 m->mothurOut("The pre.cluster command clusters sequences that have no more than 2 differences.\n");
212 m->mothurOut("The dist.seqs command is used to generate a column and phylip formatted distance matrix using cutoff=0.20 for column.\n");
213 m->mothurOut("The pipeline uses cluster with method=average, hard=T. \n");
214 m->mothurOut("The classify.seqs command is used to classify the sequences using the bayesian method with a cutoff of 80.\n");
215 m->mothurOut("The phylotype command is used to cluster the sequences based on their classification.\n");
216 m->mothurOut("The clearcut command is used to generate a tree using neighbor=T. \n");
217 m->mothurOut("The summary.single and summary.shared commands are run on the otu files from cluster and phylotype commands. \n");
218 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");
219 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");
220 m->mothurOut("The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n");
221 m->mothurOut("The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n");
222 m->mothurOut("The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n");
223 m->mothurOut("\n\n");
225 catch(exception& e) {
226 m->errorOut(e, "PipelineCommand", "help");
231 //**********************************************************************************************************************
233 PipelineCommand::~PipelineCommand(){}
235 //**********************************************************************************************************************
237 int PipelineCommand::execute(){
239 if (abort == true) { return 0; }
241 int start = time(NULL);
243 if (pipeFilename == "") {
244 createPatsPipeline();
247 for (int i = 0; i < commands.size(); i++) {
248 m->mothurOutEndLine(); m->mothurOut("mothur > " + commands[i]); m->mothurOutEndLine();
250 if (m->control_pressed) { return 0; }
252 CommandOptionParser parser(commands[i]);
253 string commandName = parser.getCommandString();
254 string options = parser.getOptionString();
258 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
260 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
263 //executes valid command
264 Command* command = cFactory->getCommand(commandName, options, "pipe");
267 //add output files to list
268 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
269 map<string, vector<string> >::iterator itMade;
270 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
271 vector<string> temp = itMade->second;
272 for (int j = 0; j < temp.size(); j++) { outputNames.push_back(temp[j]); }
280 }else { runUsersPipeline(); }
282 if (m->control_pressed) { return 0; }
284 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run the pipeline analysis."); m->mothurOutEndLine(); m->mothurOutEndLine();
286 m->mothurOutEndLine();
287 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
288 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
289 m->mothurOutEndLine();
293 catch(exception& e) {
294 m->errorOut(e, "PipelineCommand", "execute");
298 //**********************************************************************************************************************
300 bool PipelineCommand::readUsersPipeline(){
304 m->openInputFile(pipeFilename, in);
306 string nextCommand = "";
308 map<string, vector<string> > mothurMadeFiles;
311 nextCommand = m->getline(in); m->gobble(in);
313 if (nextCommand[0] != '#') {
316 string commandName, options;
317 error = parseCommand(nextCommand, commandName, options);
319 if (error) { in.close(); return error; }
320 if (commandName == "pipeline.pds") { m->mothurOut("Cannot run the pipeline.pds command from inside the pipeline.pds command."); m->mothurOutEndLine(); in.close(); return true; }
322 error = checkForValidAndRequiredParameters(commandName, options, mothurMadeFiles);
324 if (error) { in.close(); return error; }
332 catch(exception& e) {
333 m->errorOut(e, "PipelineCommand", "readUsersPipeline");
337 //**********************************************************************************************************************
339 bool PipelineCommand::parseCommand(string nextCommand, string& name, string& options){
341 CommandOptionParser parser(nextCommand);
342 name = parser.getCommandString();
343 options = parser.getOptionString();
345 if (name == "") { return true; } //name == "" if () are not right
349 catch(exception& e) {
350 m->errorOut(e, "PipelineCommand", "parseCommand");
354 //**********************************************************************************************************************
356 bool PipelineCommand::checkForValidAndRequiredParameters(string name, string options, map<string, vector<string> >& mothurMadeFiles){
359 if (name == "system") { return false; }
361 //get shell of the command so we can check to make sure its valid without running it
362 Command* command = cFactory->getCommand(name);
364 //check to make sure all parameters are valid for command
365 vector<string> validParameters = command->getValidParameters();
367 OptionParser parser(options);
368 map<string, string> parameters = parser.getParameters();
370 ValidParameters validParameter;
371 map<string, string>::iterator it;
372 map<string, vector<string> >::iterator itMade;
374 for (it = parameters.begin(); it != parameters.end(); it++) {
375 if (validParameter.isValidParameter(it->first, validParameters, it->second) != true) { return true; } // not valid
376 if (it->second == "mothurmade") {
377 itMade = mothurMadeFiles.find(it->first);
379 if (itMade == mothurMadeFiles.end()) {
380 if ((name == "align.seqs") && (it->first == "candidate")) {} //do nothing about candidate
382 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();
389 //is the command missing any required
390 vector<string> requiredParameters = command->getRequiredParameters();
395 if (requiredParameters.size() > 2) {
396 if (requiredParameters[(requiredParameters.size()-1)] == "or") { hasOr = true; }
399 for (int i = 0; i < requiredParameters.size(); i++) {
400 it = parameters.find(requiredParameters[i]);
402 if (it != parameters.end()) { numFound++; }
404 if (!hasOr) { m->mothurOut(name + " requires the " + requiredParameters[i] + " parameter, please correct."); m->mothurOutEndLine(); }
408 // if all are needed and not all are found
409 if ((!hasOr) && (numFound != requiredParameters.size())) { return true; }
410 //if one is needed and none are found
411 else if ((hasOr) && (numFound == 0)) { return true; }
414 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
415 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
416 mothurMadeFiles[itMade->first] = itMade->second; //adds any new types
421 catch(exception& e) {
422 m->errorOut(e, "PipelineCommand", "checkForValidAndRequiredParameters");
426 //**********************************************************************************************************************
427 int PipelineCommand::runUsersPipeline(){
430 m->openInputFile(pipeFilename, in);
432 string nextCommand = "";
434 map<string, vector<string> > mothurMadeFiles;
437 nextCommand = m->getline(in); m->gobble(in);
439 if (nextCommand[0] != '#') {
440 CommandOptionParser parser(nextCommand);
441 string commandName = parser.getCommandString();
442 string options = parser.getOptionString();
445 bool error = fillInMothurMade(options, mothurMadeFiles);
446 if (error) { in.close(); return 0; }
449 m->mothurOutEndLine(); m->mothurOut("mothur > " + commandName + "(" + options + ")"); m->mothurOutEndLine();
451 if (m->control_pressed) { return 0; }
455 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
457 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
460 //executes valid command
461 Command* command = cFactory->getCommand(commandName, options, "pipe");
464 //add output files to list
465 map<string, vector<string> > thisCommandsFile = command->getOutputFiles();
466 map<string, vector<string> >::iterator itMade;
467 map<string, vector<string> >::iterator it;
468 for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) {
470 vector<string> temp = itMade->second;
471 for (int k = 0; k < temp.size(); k++) { outputNames.push_back(temp[k]); } //
473 //update Mothur Made for each file
474 it = mothurMadeFiles.find(itMade->first);
476 if (it == mothurMadeFiles.end()) { //new type
478 mothurMadeFiles[itMade->first] = temp;
480 }else{ //update existing type
481 vector<string> oldFileNames = it->second;
482 //look at new files, see if an old version of the file exists, if so update, else just add.
483 //for example you may have abrecovery.fasta and amazon.fasta as old files and you created a new amazon.trim.fasta.
485 for (int k = 0; k < temp.size(); k++) {
488 string root = m->getSimpleName(temp[k]);
489 string individual = "";
490 for(int i=0;i<root.length();i++){
495 individual += root[i];
499 //look for that base name in oldfiles
501 for (int l = 0; l < oldFileNames.size(); l++) {
502 int pos = oldFileNames[l].find(root);
503 if (pos != string::npos) {
509 //if you found it update it, else add it
511 mothurMadeFiles[it->first][spot] = temp[k];
513 mothurMadeFiles[it->first].push_back(temp[k]);
527 catch(exception& e) {
528 m->errorOut(e, "PipelineCommand", "runUsersPipeline");
532 //**********************************************************************************************************************
533 bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<string> >& mothurMadeFiles){
535 OptionParser parser(options);
536 map<string, string> parameters = parser.getParameters();
537 map<string, string>::iterator it;
538 map<string, vector<string> >::iterator itMade;
542 //fill in mothurmade filenames
543 for (it = parameters.begin(); it != parameters.end(); it++) {
544 string paraType = it->first;
545 string tempOption = it->second;
547 if (tempOption == "mothurmade") {
549 if (it->first == "candidate") { paraType = "fasta"; }
551 itMade = mothurMadeFiles.find(paraType);
553 if (itMade == mothurMadeFiles.end()) {
554 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();
557 vector<string> temp = itMade->second;
559 if (temp.size() > 1) {
560 //ask user which file to use
561 m->mothurOut("More than one file has been created for the " + paraType + " parameter. "); m->mothurOutEndLine();
562 for (int i = 0; i < temp.size(); i++) {
563 m->mothurOut(toString(i) + " - " + temp[i]); m->mothurOutEndLine();
566 m->mothurOut("Please select the number of the file you would like to use: ");
569 m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
571 if ((num < 0) || (num > (temp.size()-1))) { m->mothurOut("Not a valid response, quitting."); m->mothurOutEndLine(); return true; }
573 tempOption = temp[num];
576 //clears buffer so next command doesn't have error
580 vector<string> newTemp;
581 for (int i = 0; i < temp.size(); i++) {
582 if (i == num) { newTemp.push_back(temp[i]); }
584 m->mothurOut("Would you like to remove " + temp[i] + " as an option for " + paraType + ", (y/n): "); m->mothurOutEndLine();
587 m->mothurOutJustToLog(response); m->mothurOutEndLine();
589 if (response == "n") { newTemp.push_back(temp[i]); }
591 //clears buffer so next command doesn't have error
597 mothurMadeFiles[paraType] = newTemp;
600 }else if (temp.size() == 0){
601 m->mothurOut("Sorry, we seem to think you created a " + paraType + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine();
604 tempOption = temp[0];
609 options += it->first + "=" + tempOption + ", ";
612 //rip off extra comma
613 options = options.substr(0, (options.length()-2));
617 catch(exception& e) {
618 m->errorOut(e, "PipelineCommand", "fillInMothurMade");
623 //**********************************************************************************************************************
624 void PipelineCommand::createPatsPipeline(){
628 string thisCommand = "sffinfo(sff=" + sffFile + ")";
629 commands.push_back(thisCommand);
632 string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
633 string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
634 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 + ")";
635 commands.push_back(thisCommand);
638 string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";
639 qualFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
640 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
641 thisCommand = "unique.seqs(fasta=" + fastaFile + ")";
642 commands.push_back(thisCommand);
645 string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
646 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
647 thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
648 commands.push_back(thisCommand);
651 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
652 thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
653 commands.push_back(thisCommand);
656 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
657 nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
658 groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
659 thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
660 commands.push_back(thisCommand);
663 string accnosFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.accnos";
664 thisCommand = "remove.seqs(fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", accnos=" + accnosFile + ", dups=T)";
665 commands.push_back(thisCommand);
668 nameFile = m->getRootName(m->getSimpleName(nameFile)) + "pick" + m->getExtension(nameFile);
669 groupFile = m->getRootName(m->getSimpleName(groupFile)) + "pick" + m->getExtension(groupFile);
670 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "pick" + m->getExtension(fastaFile);
671 thisCommand = "filter.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", vertical=T, trump=.)";
672 commands.push_back(thisCommand);
675 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "filter.fasta";
676 thisCommand = "unique.seqs(fasta=" + fastaFile + ", name=" + nameFile + ")";
677 commands.push_back(thisCommand);
680 nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
681 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
682 thisCommand = "pre.cluster(fasta=" + fastaFile + ", name=" + nameFile + ", diffs=2)";
683 commands.push_back(thisCommand);
686 nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster.names";
687 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "precluster" + m->getExtension(fastaFile);
688 thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", cutoff=0.20)";
689 commands.push_back(thisCommand);
692 string columnFile = m->getRootName(m->getSimpleName(fastaFile)) + "dist";
693 thisCommand = "dist.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", output=lt)";
694 commands.push_back(thisCommand);
697 string phylipFile = m->getRootName(m->getSimpleName(fastaFile)) + "phylip.dist";
698 thisCommand = "read.dist(column=" + columnFile + ", name=" + nameFile + ")";
699 commands.push_back(thisCommand);
702 thisCommand = "cluster(method=average, hard=T)";
703 commands.push_back(thisCommand);
705 string listFile = m->getRootName(m->getSimpleName(columnFile)) + "an.list";
706 string rabundFile = m->getRootName(m->getSimpleName(columnFile)) + "an.rabund";
709 thisCommand = "degap.seqs(fasta=" + fastaFile + ")";
710 commands.push_back(thisCommand);
713 fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "ng.fasta";
714 thisCommand = "classify.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", template=" + classifyFile + ", taxonomy=" + taxonomyFile + ", cutoff=80)";
715 commands.push_back(thisCommand);
717 string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFile));
718 RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
719 if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
720 RippedTaxName += ".";
722 string fastaTaxFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "taxonomy";
723 string taxSummaryFile = m->getRootName(m->getSimpleName(fastaFile)) + RippedTaxName + "tax.summary";
726 thisCommand = "phylotype(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ")";
727 commands.push_back(thisCommand);
729 string phyloListFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.list";
730 string phyloRabundFile = m->getRootName(m->getSimpleName(fastaTaxFile)) + "tx.rabund";
733 thisCommand = "clearcut(phylip=" + phylipFile + ", neighbor=T)";
734 commands.push_back(thisCommand);
736 string treeFile = m->getRootName(m->getSimpleName(phylipFile)) + "tre";
739 thisCommand = "read.otu(list=" + listFile + ", group=" + groupFile + ", label=0.03)";
740 commands.push_back(thisCommand);
742 string sharedFile = m->getRootName(m->getSimpleName(listFile)) + "shared";
745 thisCommand = "read.otu(list=" + phyloListFile + ", group=" + groupFile + ", label=1)";
746 commands.push_back(thisCommand);
748 string phyloSharedFile = m->getRootName(m->getSimpleName(phyloListFile)) + "shared";
751 thisCommand = "read.otu(shared=" + sharedFile + ")";
752 commands.push_back(thisCommand);
755 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)";
756 commands.push_back(thisCommand);
759 thisCommand = "summary.shared(calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";
760 commands.push_back(thisCommand);
763 thisCommand = "read.otu(rabund=" + rabundFile + ", label=0.03)";
764 commands.push_back(thisCommand);
767 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)";
768 commands.push_back(thisCommand);
771 thisCommand = "read.otu(shared=" + phyloSharedFile + ")";
772 commands.push_back(thisCommand);
775 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)";
776 commands.push_back(thisCommand);
779 thisCommand = "summary.shared(calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc)";
780 commands.push_back(thisCommand);
783 thisCommand = "read.otu(rabund=" + phyloRabundFile + ", label=1)";
784 commands.push_back(thisCommand);
787 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)";
788 commands.push_back(thisCommand);
791 thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + listFile + ", cutoff=51, label=0.03)";
792 commands.push_back(thisCommand);
795 thisCommand = "classify.otu(taxonomy=" + fastaTaxFile + ", name=" + nameFile + ", list=" + phyloListFile + ", cutoff=51, label=1)";
796 commands.push_back(thisCommand);
799 thisCommand = "read.tree(tree=" + treeFile + ", name=" + nameFile + ", group=" + groupFile + ")";
800 commands.push_back(thisCommand);
803 thisCommand = "phylo.diversity(iters=100,rarefy=T)";
804 commands.push_back(thisCommand);
807 thisCommand = "unifrac.weighted(random=false, distance=true, groups=all, processors=" + toString(processors) + ")";
808 commands.push_back(thisCommand);
811 thisCommand = "unifrac.unweighted(random=false, distance=true, processors=" + toString(processors) + ")";
812 commands.push_back(thisCommand);
816 catch(exception& e) {
817 m->errorOut(e, "PipelineCommand", "createPatsPipeline");
822 //**********************************************************************************************************************