5 * Created by Sarah Westcott on 5/15/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
8 * This version of nast does everything I think that the greengenes nast server does and then some. I have added the
9 * feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
10 * method. This latter feature is perhaps most significant. nastPlus enables a user to use either a Needleman-Wunsch
11 * (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm. This is significant because it
12 * allows for a global alignment and not the local alignment provided by bLAst. Furthermore, it has the potential to
13 * provide a better alignment because of the banding method employed by blast (I'm not sure about this).
17 #include "aligncommand.h"
18 #include "sequence.hpp"
20 #include "gotohoverlap.hpp"
21 #include "needlemanoverlap.hpp"
22 #include "blastalign.hpp"
23 #include "noalign.hpp"
26 #include "nastreport.hpp"
28 //**********************************************************************************************************************
29 vector<string> AlignCommand::setParameters(){
31 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
32 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
33 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
34 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
35 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
36 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
37 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
38 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
39 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
40 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
41 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
42 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
43 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
44 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
46 vector<string> myArray;
47 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
51 m->errorOut(e, "AlignCommand", "setParameters");
55 //**********************************************************************************************************************
56 string AlignCommand::getHelpString(){
58 string helpString = "";
59 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
60 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
61 helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
62 helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.";
63 helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
64 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.";
65 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
66 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.";
67 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
68 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.";
69 helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.";
70 helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
71 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
72 helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.";
73 helpString += "The align.seqs command should be in the following format:";
74 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
75 helpString += "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)";
76 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
80 m->errorOut(e, "AlignCommand", "getHelpString");
84 //**********************************************************************************************************************
85 AlignCommand::AlignCommand(){
87 abort = true; calledHelp = true;
89 vector<string> tempOutNames;
90 outputTypes["fasta"] = tempOutNames;
91 outputTypes["alignreport"] = tempOutNames;
92 outputTypes["accnos"] = tempOutNames;
95 m->errorOut(e, "AlignCommand", "AlignCommand");
99 //**********************************************************************************************************************
100 AlignCommand::AlignCommand(string option) {
102 abort = false; calledHelp = false;
104 //allow user to run help
105 if(option == "help") { help(); abort = true; calledHelp = true;}
106 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
109 vector<string> myArray = setParameters();
111 OptionParser parser(option);
112 map<string, string> parameters = parser.getParameters();
114 ValidParameters validParameter("align.seqs");
115 map<string, string>::iterator it;
117 //check to make sure all parameters are valid for command
118 for (it = parameters.begin(); it != parameters.end(); it++) {
119 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
122 //initialize outputTypes
123 vector<string> tempOutNames;
124 outputTypes["fasta"] = tempOutNames;
125 outputTypes["alignreport"] = tempOutNames;
126 outputTypes["accnos"] = tempOutNames;
128 //if the user changes the output directory command factory will send this info to us in the output parameter
129 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
132 //if the user changes the input directory command factory will send this info to us in the output parameter
133 string inputDir = validParameter.validFile(parameters, "inputdir", false);
135 if (inputDir == "not found"){ inputDir = ""; }
139 it = parameters.find("reference");
141 //user has given a template file
142 if(it != parameters.end()){
143 path = m->hasPath(it->second);
144 //if the user has not given a path then, add inputdir. else leave path alone.
145 if (path == "") { parameters["reference"] = inputDir + it->second; }
149 //check for required parameters
150 templateFileName = validParameter.validFile(parameters, "reference", true);
152 if (templateFileName == "not found") {
153 m->mothurOut("reference is a required parameter for the align.seqs command.");
154 m->mothurOutEndLine();
156 }else if (templateFileName == "not open") { abort = true; }
158 candidateFileName = validParameter.validFile(parameters, "fasta", false);
159 if (candidateFileName == "not found") {
160 //if there is a current fasta file, use it
161 string filename = m->getFastaFile();
162 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
163 else { m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
165 m->splitAtDash(candidateFileName, candidateFileNames);
167 //go through files and make sure they are good, if not, then disregard them
168 for (int i = 0; i < candidateFileNames.size(); i++) {
169 //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
172 if (candidateFileNames[i] == "current") {
173 candidateFileNames[i] = m->getFastaFile();
174 if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
176 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
177 //erase from file list
178 candidateFileNames.erase(candidateFileNames.begin()+i);
185 if (inputDir != "") {
186 string path = m->hasPath(candidateFileNames[i]);
187 //if the user has not given a path then, add inputdir. else leave path alone.
188 if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
193 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
196 //if you can't open it, try default location
197 if (ableToOpen == 1) {
198 if (m->getDefaultPath() != "") { //default path is set
199 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
200 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
202 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
204 candidateFileNames[i] = tryPath;
208 //if you can't open it, try output location
209 if (ableToOpen == 1) {
210 if (m->getOutputDir() != "") { //default path is set
211 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
212 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
214 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
216 candidateFileNames[i] = tryPath;
222 if (ableToOpen == 1) {
223 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
224 //erase from file list
225 candidateFileNames.erase(candidateFileNames.begin()+i);
231 //make sure there is at least one valid file left
232 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
235 //check for optional parameter and set defaults
236 // ...at some point should added some additional type checking...
238 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
239 convert(temp, kmerSize);
241 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
242 convert(temp, match);
244 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
245 convert(temp, misMatch);
247 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
248 convert(temp, gapOpen);
250 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
251 convert(temp, gapExtend);
253 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
254 m->setProcessors(temp);
255 convert(temp, processors);
257 temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
258 flip = m->isTrue(temp);
260 temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
261 convert(temp, threshold);
263 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
264 if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
266 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
267 if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
272 catch(exception& e) {
273 m->errorOut(e, "AlignCommand", "AlignCommand");
277 //**********************************************************************************************************************
278 AlignCommand::~AlignCommand(){
280 if (abort == false) {
281 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
286 //**********************************************************************************************************************
288 int AlignCommand::execute(){
290 if (abort == true) { if (calledHelp) { return 0; } return 2; }
292 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
293 int longestBase = templateDB->getLongestBase();
295 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
296 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
297 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
298 else if(align == "noalign") { alignment = new NoAlign(); }
300 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
301 m->mothurOutEndLine();
302 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
305 for (int s = 0; s < candidateFileNames.size(); s++) {
306 if (m->control_pressed) { outputTypes.clear(); return 0; }
308 m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
310 if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
311 string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
312 string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
313 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
314 bool hasAccnos = true;
316 int numFastaSeqs = 0;
317 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
318 int start = time(NULL);
321 int pid, numSeqsPerProcessor;
323 vector<unsigned long int> MPIPos;
324 MPIWroteAccnos = false;
327 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
328 MPI_Comm_size(MPI_COMM_WORLD, &processors);
331 MPI_File outMPIAlign;
332 MPI_File outMPIReport;
333 MPI_File outMPIAccnos;
335 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
336 int inMode=MPI_MODE_RDONLY;
338 char outAlignFilename[1024];
339 strcpy(outAlignFilename, alignFileName.c_str());
341 char outReportFilename[1024];
342 strcpy(outReportFilename, reportFileName.c_str());
344 char outAccnosFilename[1024];
345 strcpy(outAccnosFilename, accnosFileName.c_str());
347 char inFileName[1024];
348 strcpy(inFileName, candidateFileNames[s].c_str());
350 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
351 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
352 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
353 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
355 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
357 if (pid == 0) { //you are the root process
359 MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
361 //send file positions to all processes
362 for(int i = 1; i < processors; i++) {
363 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
364 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
367 //figure out how many sequences you have to align
368 numSeqsPerProcessor = numFastaSeqs / processors;
369 int startIndex = pid * numSeqsPerProcessor;
370 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
373 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
375 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
377 for (int i = 1; i < processors; i++) {
379 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
380 if (tempResult != 0) { MPIWroteAccnos = true; }
382 }else{ //you are a child process
383 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
384 MPIPos.resize(numFastaSeqs+1);
385 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
388 //figure out how many sequences you have to align
389 numSeqsPerProcessor = numFastaSeqs / processors;
390 int startIndex = pid * numSeqsPerProcessor;
391 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
395 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
397 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
399 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
403 MPI_File_close(&inMPI);
404 MPI_File_close(&outMPIAlign);
405 MPI_File_close(&outMPIReport);
406 MPI_File_close(&outMPIAccnos);
408 //delete accnos file if blank
410 //delete accnos file if its blank else report to user
411 if (MPIWroteAccnos) {
412 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
414 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
415 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
416 m->mothurOutEndLine();
419 //MPI_File_delete(outAccnosFilename, info);
421 remove(accnosFileName.c_str());
427 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
428 for (int i = 0; i < (positions.size()-1); i++) {
429 lines.push_back(new linePair(positions[i], positions[(i+1)]));
431 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
433 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
435 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
438 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
441 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
443 //delete accnos file if its blank else report to user
444 if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
446 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
448 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
449 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
450 m->mothurOutEndLine();
457 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
459 if (pid == 0) { //only one process should output to screen
462 outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
463 outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
464 if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); }
470 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
471 m->mothurOutEndLine();
472 m->mothurOutEndLine();
475 //set align file as new current fastafile
476 string currentFasta = "";
477 itTypes = outputTypes.find("fasta");
478 if (itTypes != outputTypes.end()) {
479 if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
482 m->mothurOutEndLine();
483 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
484 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
485 m->mothurOutEndLine();
489 catch(exception& e) {
490 m->errorOut(e, "AlignCommand", "execute");
495 //**********************************************************************************************************************
497 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
499 ofstream alignmentFile;
500 m->openOutputFile(alignFName, alignmentFile);
503 m->openOutputFile(accnosFName, accnosFile);
505 NastReport report(reportFName);
508 m->openInputFile(filename, inFASTA);
510 inFASTA.seekg(filePos->start);
517 if (m->control_pressed) { return 0; }
519 Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
520 report.setCandidate(candidateSeq);
522 int origNumBases = candidateSeq->getNumBases();
523 string originalUnaligned = candidateSeq->getUnaligned();
524 int numBasesNeeded = origNumBases * threshold;
526 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
527 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
528 alignment->resize(candidateSeq->getUnaligned().length()+1);
531 Sequence temp = templateDB->findClosestSequence(candidateSeq);
532 Sequence* templateSeq = &temp;
534 float searchScore = templateDB->getSearchScore();
536 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
541 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
542 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
543 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
544 //so this bool tells you if you need to delete it
546 //if there is a possibility that this sequence should be reversed
547 if (candidateSeq->getNumBases() < numBasesNeeded) {
549 string wasBetter = "";
550 //if the user wants you to try the reverse
553 //get reverse compliment
554 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
555 copy->reverseComplement();
558 Sequence temp2 = templateDB->findClosestSequence(copy);
559 Sequence* templateSeq2 = &temp2;
561 searchScore = templateDB->getSearchScore();
563 nast2 = new Nast(alignment, copy, templateSeq2);
565 //check if any better
566 if (copy->getNumBases() > candidateSeq->getNumBases()) {
567 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
568 templateSeq = templateSeq2;
571 needToDeleteCopy = true;
572 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
574 wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
580 //create accnos file with names
581 accnosFile << candidateSeq->getName() << wasBetter << endl;
584 report.setTemplate(templateSeq);
585 report.setSearchParameters(search, searchScore);
586 report.setAlignmentParameters(align, alignment);
587 report.setNastParameters(*nast);
589 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
593 if (needToDeleteCopy) { delete copy; }
599 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
600 unsigned long int pos = inFASTA.tellg();
601 if ((pos == -1) || (pos >= filePos->end)) { break; }
603 if (inFASTA.eof()) { break; }
607 if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
611 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
613 alignmentFile.close();
619 catch(exception& e) {
620 m->errorOut(e, "AlignCommand", "driver");
624 //**********************************************************************************************************************
626 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
628 string outputString = "";
629 MPI_Status statusReport;
630 MPI_Status statusAlign;
631 MPI_Status statusAccnos;
634 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
639 outputString = report.getHeaders();
640 int length = outputString.length();
642 char* buf = new char[length];
643 memcpy(buf, outputString.c_str(), length);
645 MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
650 for(int i=0;i<num;i++){
652 if (m->control_pressed) { return 0; }
655 int length = MPIPos[start+i+1] - MPIPos[start+i];
657 char* buf4 = new char[length];
658 //memcpy(buf4, outputString.c_str(), length);
660 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
662 string tempBuf = buf4;
666 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
668 istringstream iss (tempBuf,istringstream::in);
670 Sequence* candidateSeq = new Sequence(iss);
671 report.setCandidate(candidateSeq);
673 int origNumBases = candidateSeq->getNumBases();
674 string originalUnaligned = candidateSeq->getUnaligned();
675 int numBasesNeeded = origNumBases * threshold;
677 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
678 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
679 alignment->resize(candidateSeq->getUnaligned().length()+1);
682 Sequence temp = templateDB->findClosestSequence(candidateSeq);
683 Sequence* templateSeq = &temp;
685 float searchScore = templateDB->getSearchScore();
687 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
691 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
692 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
693 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
694 //so this bool tells you if you need to delete it
696 //if there is a possibility that this sequence should be reversed
697 if (candidateSeq->getNumBases() < numBasesNeeded) {
699 string wasBetter = "";
700 //if the user wants you to try the reverse
702 //get reverse compliment
703 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
704 copy->reverseComplement();
707 Sequence temp2 = templateDB->findClosestSequence(copy);
708 Sequence* templateSeq2 = &temp2;
710 searchScore = templateDB->getSearchScore();
712 nast2 = new Nast(alignment, copy, templateSeq2);
714 //check if any better
715 if (copy->getNumBases() > candidateSeq->getNumBases()) {
716 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
717 templateSeq = templateSeq2;
720 needToDeleteCopy = true;
721 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
723 wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
729 //create accnos file with names
730 outputString = candidateSeq->getName() + wasBetter + "\n";
732 //send results to parent
733 int length = outputString.length();
735 char* buf = new char[length];
736 memcpy(buf, outputString.c_str(), length);
738 MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
740 MPIWroteAccnos = true;
743 report.setTemplate(templateSeq);
744 report.setSearchParameters(search, searchScore);
745 report.setAlignmentParameters(align, alignment);
746 report.setNastParameters(*nast);
748 outputString = ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
750 //send results to parent
751 int length = outputString.length();
752 char* buf2 = new char[length];
753 memcpy(buf2, outputString.c_str(), length);
755 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
759 outputString = report.getReport();
761 //send results to parent
762 length = outputString.length();
763 char* buf3 = new char[length];
764 memcpy(buf3, outputString.c_str(), length);
766 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
770 if (needToDeleteCopy) { delete copy; }
775 if((i+1) % 100 == 0){ cout << (toString(i+1)) << endl; }
778 if((num) % 100 != 0){ cout << (toString(num)) << endl; }
782 catch(exception& e) {
783 m->errorOut(e, "AlignCommand", "driverMPI");
788 /**************************************************************************************************/
790 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
792 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
793 processIDS.resize(0);
796 // processIDS.resize(0);
798 //loop through and create all the processes you want
799 while (process != processors) {
803 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
806 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
808 //pass numSeqs to parent
810 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
811 m->openOutputFile(tempFile, out);
817 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
818 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
824 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
826 //force parent to wait until all the processes are done
827 for (int i=0;i<processIDS.size();i++) {
828 int temp = processIDS[i];
832 vector<string> nonBlankAccnosFiles;
833 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
834 else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
836 for (int i = 0; i < processIDS.size(); i++) {
838 string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp";
839 m->openInputFile(tempFile, in);
840 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
841 in.close(); remove(tempFile.c_str());
843 appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
844 remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
846 appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
847 remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
849 if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
850 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
851 }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str()); }
855 //append accnos files
856 if (nonBlankAccnosFiles.size() != 0) {
857 rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
859 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
860 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
861 remove(nonBlankAccnosFiles[h].c_str());
863 }else { //recreate the accnosfile if needed
865 m->openOutputFile(accnosFName, out);
872 catch(exception& e) {
873 m->errorOut(e, "AlignCommand", "createProcesses");
877 /**************************************************************************************************/
879 void AlignCommand::appendAlignFiles(string temp, string filename) {
884 m->openOutputFileAppend(filename, output);
885 m->openInputFile(temp, input);
887 while(char c = input.get()){
888 if(input.eof()) { break; }
889 else { output << c; }
895 catch(exception& e) {
896 m->errorOut(e, "AlignCommand", "appendAlignFiles");
900 //**********************************************************************************************************************
902 void AlignCommand::appendReportFiles(string temp, string filename) {
907 m->openOutputFileAppend(filename, output);
908 m->openInputFile(temp, input);
910 while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
912 while(char c = input.get()){
913 if(input.eof()) { break; }
914 else { output << c; }
920 catch(exception& e) {
921 m->errorOut(e, "AlignCommand", "appendReportFiles");
925 //**********************************************************************************************************************