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);
228 m->setFastaFile(candidateFileNames[i]);
233 //make sure there is at least one valid file left
234 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
237 //check for optional parameter and set defaults
238 // ...at some point should added some additional type checking...
240 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
241 convert(temp, kmerSize);
243 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
244 convert(temp, match);
246 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
247 convert(temp, misMatch);
249 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
250 convert(temp, gapOpen);
252 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
253 convert(temp, gapExtend);
255 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
256 m->setProcessors(temp);
257 convert(temp, processors);
259 temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
260 flip = m->isTrue(temp);
262 temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
263 convert(temp, threshold);
265 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
266 if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
268 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
269 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; }
274 catch(exception& e) {
275 m->errorOut(e, "AlignCommand", "AlignCommand");
279 //**********************************************************************************************************************
280 AlignCommand::~AlignCommand(){
282 if (abort == false) {
283 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
288 //**********************************************************************************************************************
290 int AlignCommand::execute(){
292 if (abort == true) { if (calledHelp) { return 0; } return 2; }
294 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
295 int longestBase = templateDB->getLongestBase();
297 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
298 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
299 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
300 else if(align == "noalign") { alignment = new NoAlign(); }
302 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
303 m->mothurOutEndLine();
304 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
307 for (int s = 0; s < candidateFileNames.size(); s++) {
308 if (m->control_pressed) { outputTypes.clear(); return 0; }
310 m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
312 if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
313 string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
314 string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
315 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
316 bool hasAccnos = true;
318 int numFastaSeqs = 0;
319 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
320 int start = time(NULL);
323 int pid, numSeqsPerProcessor;
325 vector<unsigned long int> MPIPos;
326 MPIWroteAccnos = false;
329 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
330 MPI_Comm_size(MPI_COMM_WORLD, &processors);
333 MPI_File outMPIAlign;
334 MPI_File outMPIReport;
335 MPI_File outMPIAccnos;
337 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
338 int inMode=MPI_MODE_RDONLY;
340 char outAlignFilename[1024];
341 strcpy(outAlignFilename, alignFileName.c_str());
343 char outReportFilename[1024];
344 strcpy(outReportFilename, reportFileName.c_str());
346 char outAccnosFilename[1024];
347 strcpy(outAccnosFilename, accnosFileName.c_str());
349 char inFileName[1024];
350 strcpy(inFileName, candidateFileNames[s].c_str());
352 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
353 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
354 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
355 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
357 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
359 if (pid == 0) { //you are the root process
361 MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
363 //send file positions to all processes
364 for(int i = 1; i < processors; i++) {
365 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
366 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
369 //figure out how many sequences you have to align
370 numSeqsPerProcessor = numFastaSeqs / processors;
371 int startIndex = pid * numSeqsPerProcessor;
372 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
375 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
377 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
379 for (int i = 1; i < processors; i++) {
381 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
382 if (tempResult != 0) { MPIWroteAccnos = true; }
384 }else{ //you are a child process
385 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
386 MPIPos.resize(numFastaSeqs+1);
387 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
390 //figure out how many sequences you have to align
391 numSeqsPerProcessor = numFastaSeqs / processors;
392 int startIndex = pid * numSeqsPerProcessor;
393 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
397 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
399 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
401 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
405 MPI_File_close(&inMPI);
406 MPI_File_close(&outMPIAlign);
407 MPI_File_close(&outMPIReport);
408 MPI_File_close(&outMPIAccnos);
410 //delete accnos file if blank
412 //delete accnos file if its blank else report to user
413 if (MPIWroteAccnos) {
414 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
416 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
417 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
418 m->mothurOutEndLine();
421 //MPI_File_delete(outAccnosFilename, info);
423 remove(accnosFileName.c_str());
429 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
430 for (int i = 0; i < (positions.size()-1); i++) {
431 lines.push_back(new linePair(positions[i], positions[(i+1)]));
433 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
435 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
437 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
440 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
443 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
445 //delete accnos file if its blank else report to user
446 if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
448 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
450 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
451 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
452 m->mothurOutEndLine();
459 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
461 if (pid == 0) { //only one process should output to screen
464 outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
465 outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
466 if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); }
472 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
473 m->mothurOutEndLine();
474 m->mothurOutEndLine();
477 //set align file as new current fastafile
478 string currentFasta = "";
479 itTypes = outputTypes.find("fasta");
480 if (itTypes != outputTypes.end()) {
481 if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
484 m->mothurOutEndLine();
485 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
486 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
487 m->mothurOutEndLine();
491 catch(exception& e) {
492 m->errorOut(e, "AlignCommand", "execute");
497 //**********************************************************************************************************************
499 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
501 ofstream alignmentFile;
502 m->openOutputFile(alignFName, alignmentFile);
505 m->openOutputFile(accnosFName, accnosFile);
507 NastReport report(reportFName);
510 m->openInputFile(filename, inFASTA);
512 inFASTA.seekg(filePos->start);
519 if (m->control_pressed) { return 0; }
521 Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
522 report.setCandidate(candidateSeq);
524 int origNumBases = candidateSeq->getNumBases();
525 string originalUnaligned = candidateSeq->getUnaligned();
526 int numBasesNeeded = origNumBases * threshold;
528 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
529 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
530 alignment->resize(candidateSeq->getUnaligned().length()+1);
533 Sequence temp = templateDB->findClosestSequence(candidateSeq);
534 Sequence* templateSeq = &temp;
536 float searchScore = templateDB->getSearchScore();
538 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
543 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
544 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
545 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
546 //so this bool tells you if you need to delete it
548 //if there is a possibility that this sequence should be reversed
549 if (candidateSeq->getNumBases() < numBasesNeeded) {
551 string wasBetter = "";
552 //if the user wants you to try the reverse
555 //get reverse compliment
556 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
557 copy->reverseComplement();
560 Sequence temp2 = templateDB->findClosestSequence(copy);
561 Sequence* templateSeq2 = &temp2;
563 searchScore = templateDB->getSearchScore();
565 nast2 = new Nast(alignment, copy, templateSeq2);
567 //check if any better
568 if (copy->getNumBases() > candidateSeq->getNumBases()) {
569 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
570 templateSeq = templateSeq2;
573 needToDeleteCopy = true;
574 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
576 wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
582 //create accnos file with names
583 accnosFile << candidateSeq->getName() << wasBetter << endl;
586 report.setTemplate(templateSeq);
587 report.setSearchParameters(search, searchScore);
588 report.setAlignmentParameters(align, alignment);
589 report.setNastParameters(*nast);
591 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
595 if (needToDeleteCopy) { delete copy; }
601 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
602 unsigned long int pos = inFASTA.tellg();
603 if ((pos == -1) || (pos >= filePos->end)) { break; }
605 if (inFASTA.eof()) { break; }
609 if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
613 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
615 alignmentFile.close();
621 catch(exception& e) {
622 m->errorOut(e, "AlignCommand", "driver");
626 //**********************************************************************************************************************
628 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
630 string outputString = "";
631 MPI_Status statusReport;
632 MPI_Status statusAlign;
633 MPI_Status statusAccnos;
636 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
641 outputString = report.getHeaders();
642 int length = outputString.length();
644 char* buf = new char[length];
645 memcpy(buf, outputString.c_str(), length);
647 MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
652 for(int i=0;i<num;i++){
654 if (m->control_pressed) { return 0; }
657 int length = MPIPos[start+i+1] - MPIPos[start+i];
659 char* buf4 = new char[length];
660 //memcpy(buf4, outputString.c_str(), length);
662 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
664 string tempBuf = buf4;
668 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
670 istringstream iss (tempBuf,istringstream::in);
672 Sequence* candidateSeq = new Sequence(iss);
673 report.setCandidate(candidateSeq);
675 int origNumBases = candidateSeq->getNumBases();
676 string originalUnaligned = candidateSeq->getUnaligned();
677 int numBasesNeeded = origNumBases * threshold;
679 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
680 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
681 alignment->resize(candidateSeq->getUnaligned().length()+1);
684 Sequence temp = templateDB->findClosestSequence(candidateSeq);
685 Sequence* templateSeq = &temp;
687 float searchScore = templateDB->getSearchScore();
689 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
693 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
694 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
695 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
696 //so this bool tells you if you need to delete it
698 //if there is a possibility that this sequence should be reversed
699 if (candidateSeq->getNumBases() < numBasesNeeded) {
701 string wasBetter = "";
702 //if the user wants you to try the reverse
704 //get reverse compliment
705 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
706 copy->reverseComplement();
709 Sequence temp2 = templateDB->findClosestSequence(copy);
710 Sequence* templateSeq2 = &temp2;
712 searchScore = templateDB->getSearchScore();
714 nast2 = new Nast(alignment, copy, templateSeq2);
716 //check if any better
717 if (copy->getNumBases() > candidateSeq->getNumBases()) {
718 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
719 templateSeq = templateSeq2;
722 needToDeleteCopy = true;
723 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
725 wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
731 //create accnos file with names
732 outputString = candidateSeq->getName() + wasBetter + "\n";
734 //send results to parent
735 int length = outputString.length();
737 char* buf = new char[length];
738 memcpy(buf, outputString.c_str(), length);
740 MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
742 MPIWroteAccnos = true;
745 report.setTemplate(templateSeq);
746 report.setSearchParameters(search, searchScore);
747 report.setAlignmentParameters(align, alignment);
748 report.setNastParameters(*nast);
750 outputString = ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
752 //send results to parent
753 int length = outputString.length();
754 char* buf2 = new char[length];
755 memcpy(buf2, outputString.c_str(), length);
757 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
761 outputString = report.getReport();
763 //send results to parent
764 length = outputString.length();
765 char* buf3 = new char[length];
766 memcpy(buf3, outputString.c_str(), length);
768 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
772 if (needToDeleteCopy) { delete copy; }
777 if((i+1) % 100 == 0){ cout << (toString(i+1)) << endl; }
780 if((num) % 100 != 0){ cout << (toString(num)) << endl; }
784 catch(exception& e) {
785 m->errorOut(e, "AlignCommand", "driverMPI");
790 /**************************************************************************************************/
792 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
794 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
795 processIDS.resize(0);
798 // processIDS.resize(0);
800 //loop through and create all the processes you want
801 while (process != processors) {
805 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
808 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
810 //pass numSeqs to parent
812 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
813 m->openOutputFile(tempFile, out);
819 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
820 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
826 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
828 //force parent to wait until all the processes are done
829 for (int i=0;i<processIDS.size();i++) {
830 int temp = processIDS[i];
834 vector<string> nonBlankAccnosFiles;
835 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
836 else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
838 for (int i = 0; i < processIDS.size(); i++) {
840 string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp";
841 m->openInputFile(tempFile, in);
842 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
843 in.close(); remove(tempFile.c_str());
845 appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
846 remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
848 appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
849 remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
851 if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
852 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
853 }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str()); }
857 //append accnos files
858 if (nonBlankAccnosFiles.size() != 0) {
859 rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
861 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
862 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
863 remove(nonBlankAccnosFiles[h].c_str());
865 }else { //recreate the accnosfile if needed
867 m->openOutputFile(accnosFName, out);
874 catch(exception& e) {
875 m->errorOut(e, "AlignCommand", "createProcesses");
879 /**************************************************************************************************/
881 void AlignCommand::appendAlignFiles(string temp, string filename) {
886 m->openOutputFileAppend(filename, output);
887 m->openInputFile(temp, input);
889 while(char c = input.get()){
890 if(input.eof()) { break; }
891 else { output << c; }
897 catch(exception& e) {
898 m->errorOut(e, "AlignCommand", "appendAlignFiles");
902 //**********************************************************************************************************************
904 void AlignCommand::appendReportFiles(string temp, string filename) {
909 m->openOutputFileAppend(filename, output);
910 m->openInputFile(temp, input);
912 while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
914 while(char c = input.get()){
915 if(input.eof()) { break; }
916 else { output << c; }
922 catch(exception& e) {
923 m->errorOut(e, "AlignCommand", "appendReportFiles");
927 //**********************************************************************************************************************