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 "referencedb.h"
20 //**********************************************************************************************************************
21 vector<string> AlignCommand::setParameters(){
23 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
24 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
25 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
26 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
27 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
28 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
29 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
30 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
31 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
32 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
33 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
34 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
35 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
36 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
37 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
39 vector<string> myArray;
40 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
44 m->errorOut(e, "AlignCommand", "setParameters");
48 //**********************************************************************************************************************
49 string AlignCommand::getHelpString(){
51 string helpString = "";
52 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
53 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
54 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.";
55 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.";
56 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.";
57 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.";
58 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
59 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.";
60 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
61 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.";
62 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.";
63 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.";
64 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
65 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
66 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.";
67 helpString += "The align.seqs command should be in the following format:";
68 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
69 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)";
70 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
74 m->errorOut(e, "AlignCommand", "getHelpString");
78 //**********************************************************************************************************************
79 AlignCommand::AlignCommand(){
81 abort = true; calledHelp = true;
83 vector<string> tempOutNames;
84 outputTypes["fasta"] = tempOutNames;
85 outputTypes["alignreport"] = tempOutNames;
86 outputTypes["accnos"] = tempOutNames;
89 m->errorOut(e, "AlignCommand", "AlignCommand");
93 //**********************************************************************************************************************
94 AlignCommand::AlignCommand(string option) {
96 abort = false; calledHelp = false;
97 ReferenceDB* rdb = ReferenceDB::getInstance();
99 //allow user to run help
100 if(option == "help") { help(); abort = true; calledHelp = true;}
101 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
104 vector<string> myArray = setParameters();
106 OptionParser parser(option);
107 map<string, string> parameters = parser.getParameters();
109 ValidParameters validParameter("align.seqs");
110 map<string, string>::iterator it;
112 //check to make sure all parameters are valid for command
113 for (it = parameters.begin(); it != parameters.end(); it++) {
114 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
117 //initialize outputTypes
118 vector<string> tempOutNames;
119 outputTypes["fasta"] = tempOutNames;
120 outputTypes["alignreport"] = tempOutNames;
121 outputTypes["accnos"] = tempOutNames;
123 //if the user changes the output directory command factory will send this info to us in the output parameter
124 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
127 //if the user changes the input directory command factory will send this info to us in the output parameter
128 string inputDir = validParameter.validFile(parameters, "inputdir", false);
130 if (inputDir == "not found"){ inputDir = ""; }
134 it = parameters.find("reference");
136 //user has given a template file
137 if(it != parameters.end()){
138 path = m->hasPath(it->second);
139 //if the user has not given a path then, add inputdir. else leave path alone.
140 if (path == "") { parameters["reference"] = inputDir + it->second; }
144 candidateFileName = validParameter.validFile(parameters, "fasta", false);
145 if (candidateFileName == "not found") {
146 //if there is a current fasta file, use it
147 string filename = m->getFastaFile();
148 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
149 else { m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
151 m->splitAtDash(candidateFileName, candidateFileNames);
153 //go through files and make sure they are good, if not, then disregard them
154 for (int i = 0; i < candidateFileNames.size(); i++) {
155 //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
158 if (candidateFileNames[i] == "current") {
159 candidateFileNames[i] = m->getFastaFile();
160 if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
162 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
163 //erase from file list
164 candidateFileNames.erase(candidateFileNames.begin()+i);
171 if (inputDir != "") {
172 string path = m->hasPath(candidateFileNames[i]);
173 //if the user has not given a path then, add inputdir. else leave path alone.
174 if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
179 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
182 //if you can't open it, try default location
183 if (ableToOpen == 1) {
184 if (m->getDefaultPath() != "") { //default path is set
185 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
186 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
188 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
190 candidateFileNames[i] = tryPath;
194 //if you can't open it, try output location
195 if (ableToOpen == 1) {
196 if (m->getOutputDir() != "") { //default path is set
197 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
198 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
200 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
202 candidateFileNames[i] = tryPath;
208 if (ableToOpen == 1) {
209 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
210 //erase from file list
211 candidateFileNames.erase(candidateFileNames.begin()+i);
214 m->setFastaFile(candidateFileNames[i]);
219 //make sure there is at least one valid file left
220 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
223 //check for optional parameter and set defaults
224 // ...at some point should added some additional type checking...
226 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
227 m->mothurConvert(temp, kmerSize);
229 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
230 m->mothurConvert(temp, match);
232 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
233 m->mothurConvert(temp, misMatch);
235 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
236 m->mothurConvert(temp, gapOpen);
238 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
239 m->mothurConvert(temp, gapExtend);
241 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
242 m->setProcessors(temp);
243 m->mothurConvert(temp, processors);
245 temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
246 flip = m->isTrue(temp);
248 temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
249 save = m->isTrue(temp);
251 if (save) { //clear out old references
255 //this has to go after save so that if the user sets save=t and provides no reference we abort
256 templateFileName = validParameter.validFile(parameters, "reference", true);
257 if (templateFileName == "not found") {
258 //check for saved reference sequences
259 if (rdb->referenceSeqs.size() != 0) {
260 templateFileName = "saved";
262 m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
263 m->mothurOutEndLine();
266 }else if (templateFileName == "not open") { abort = true; }
267 else { if (save) { rdb->setSavedReference(templateFileName); } }
269 temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
270 m->mothurConvert(temp, threshold);
272 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
273 if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
275 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
276 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; }
281 catch(exception& e) {
282 m->errorOut(e, "AlignCommand", "AlignCommand");
286 //**********************************************************************************************************************
287 AlignCommand::~AlignCommand(){
289 if (abort == false) {
290 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
294 //**********************************************************************************************************************
296 int AlignCommand::execute(){
298 if (abort == true) { if (calledHelp) { return 0; } return 2; }
300 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
302 for (int s = 0; s < candidateFileNames.size(); s++) {
303 if (m->control_pressed) { outputTypes.clear(); return 0; }
305 m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
307 if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
308 string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
309 string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
310 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
311 bool hasAccnos = true;
313 int numFastaSeqs = 0;
314 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
315 int start = time(NULL);
318 int pid, numSeqsPerProcessor;
320 vector<unsigned long long> MPIPos;
321 MPIWroteAccnos = false;
324 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
325 MPI_Comm_size(MPI_COMM_WORLD, &processors);
328 MPI_File outMPIAlign;
329 MPI_File outMPIReport;
330 MPI_File outMPIAccnos;
332 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
333 int inMode=MPI_MODE_RDONLY;
335 char outAlignFilename[1024];
336 strcpy(outAlignFilename, alignFileName.c_str());
338 char outReportFilename[1024];
339 strcpy(outReportFilename, reportFileName.c_str());
341 char outAccnosFilename[1024];
342 strcpy(outAccnosFilename, accnosFileName.c_str());
344 char inFileName[1024];
345 strcpy(inFileName, candidateFileNames[s].c_str());
347 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
348 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
349 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
350 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
352 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
354 if (pid == 0) { //you are the root process
356 MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
358 //send file positions to all processes
359 for(int i = 1; i < processors; i++) {
360 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
361 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
364 //figure out how many sequences you have to align
365 numSeqsPerProcessor = numFastaSeqs / processors;
366 int startIndex = pid * numSeqsPerProcessor;
367 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
370 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
372 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
374 for (int i = 1; i < processors; i++) {
376 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
377 if (tempResult != 0) { MPIWroteAccnos = true; }
379 }else{ //you are a child process
380 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
381 MPIPos.resize(numFastaSeqs+1);
382 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
385 //figure out how many sequences you have to align
386 numSeqsPerProcessor = numFastaSeqs / processors;
387 int startIndex = pid * numSeqsPerProcessor;
388 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
392 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
394 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
396 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
400 MPI_File_close(&inMPI);
401 MPI_File_close(&outMPIAlign);
402 MPI_File_close(&outMPIReport);
403 MPI_File_close(&outMPIAccnos);
405 //delete accnos file if blank
407 //delete accnos file if its blank else report to user
408 if (MPIWroteAccnos) {
409 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
411 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
412 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
413 m->mothurOutEndLine();
416 //MPI_File_delete(outAccnosFilename, info);
418 m->mothurRemove(accnosFileName);
424 vector<unsigned long long> positions;
425 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
426 positions = m->divideFile(candidateFileNames[s], processors);
427 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
429 if (processors == 1) {
430 lines.push_back(new linePair(0, 1000));
432 positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs);
434 //figure out how many sequences you have to process
435 int numSeqsPerProcessor = numFastaSeqs / processors;
436 for (int i = 0; i < processors; i++) {
437 int startIndex = i * numSeqsPerProcessor;
438 if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
439 lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
445 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
447 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
450 if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear(); return 0; }
452 //delete accnos file if its blank else report to user
453 if (m->isBlank(accnosFileName)) { m->mothurRemove(accnosFileName); hasAccnos = false; }
455 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
457 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
458 }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
459 m->mothurOutEndLine();
466 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
468 if (pid == 0) { //only one process should output to screen
471 outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
472 outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
473 if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); }
479 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
480 m->mothurOutEndLine();
481 m->mothurOutEndLine();
484 //set align file as new current fastafile
485 string currentFasta = "";
486 itTypes = outputTypes.find("fasta");
487 if (itTypes != outputTypes.end()) {
488 if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
491 m->mothurOutEndLine();
492 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
493 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
494 m->mothurOutEndLine();
498 catch(exception& e) {
499 m->errorOut(e, "AlignCommand", "execute");
504 //**********************************************************************************************************************
505 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
507 ofstream alignmentFile;
508 m->openOutputFile(alignFName, alignmentFile);
511 m->openOutputFile(accnosFName, accnosFile);
513 NastReport report(reportFName);
516 m->openInputFile(filename, inFASTA);
518 inFASTA.seekg(filePos->start);
523 //moved this into driver to avoid deep copies in windows paralellized version
524 Alignment* alignment;
525 int longestBase = templateDB->getLongestBase();
526 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
527 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
528 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
529 else if(align == "noalign") { alignment = new NoAlign(); }
531 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
532 m->mothurOutEndLine();
533 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
538 if (m->control_pressed) { break; }
540 Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
541 report.setCandidate(candidateSeq);
543 int origNumBases = candidateSeq->getNumBases();
544 string originalUnaligned = candidateSeq->getUnaligned();
545 int numBasesNeeded = origNumBases * threshold;
547 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
548 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
549 alignment->resize(candidateSeq->getUnaligned().length()+1);
552 Sequence temp = templateDB->findClosestSequence(candidateSeq);
553 Sequence* templateSeq = &temp;
555 float searchScore = templateDB->getSearchScore();
557 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
562 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
563 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
564 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
565 //so this bool tells you if you need to delete it
567 //if there is a possibility that this sequence should be reversed
568 if (candidateSeq->getNumBases() < numBasesNeeded) {
570 string wasBetter = "";
571 //if the user wants you to try the reverse
574 //get reverse compliment
575 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
576 copy->reverseComplement();
579 Sequence temp2 = templateDB->findClosestSequence(copy);
580 Sequence* templateSeq2 = &temp2;
582 searchScore = templateDB->getSearchScore();
584 nast2 = new Nast(alignment, copy, templateSeq2);
586 //check if any better
587 if (copy->getNumBases() > candidateSeq->getNumBases()) {
588 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
589 templateSeq = templateSeq2;
592 needToDeleteCopy = true;
593 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
595 wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
601 //create accnos file with names
602 accnosFile << candidateSeq->getName() << wasBetter << endl;
605 report.setTemplate(templateSeq);
606 report.setSearchParameters(search, searchScore);
607 report.setAlignmentParameters(align, alignment);
608 report.setNastParameters(*nast);
610 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
614 if (needToDeleteCopy) { delete copy; }
620 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
621 unsigned long long pos = inFASTA.tellg();
622 if ((pos == -1) || (pos >= filePos->end)) { break; }
624 if (inFASTA.eof()) { break; }
628 if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
632 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
635 alignmentFile.close();
641 catch(exception& e) {
642 m->errorOut(e, "AlignCommand", "driver");
646 //**********************************************************************************************************************
648 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
650 string outputString = "";
651 MPI_Status statusReport;
652 MPI_Status statusAlign;
653 MPI_Status statusAccnos;
656 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
661 outputString = report.getHeaders();
662 int length = outputString.length();
664 char* buf = new char[length];
665 memcpy(buf, outputString.c_str(), length);
667 MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
672 Alignment* alignment;
673 int longestBase = templateDB->getLongestBase();
674 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
675 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
676 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
677 else if(align == "noalign") { alignment = new NoAlign(); }
679 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
680 m->mothurOutEndLine();
681 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
685 for(int i=0;i<num;i++){
687 if (m->control_pressed) { delete alignment; return 0; }
690 int length = MPIPos[start+i+1] - MPIPos[start+i];
692 char* buf4 = new char[length];
693 //memcpy(buf4, outputString.c_str(), length);
695 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
697 string tempBuf = buf4;
701 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
703 istringstream iss (tempBuf,istringstream::in);
705 Sequence* candidateSeq = new Sequence(iss);
706 report.setCandidate(candidateSeq);
708 int origNumBases = candidateSeq->getNumBases();
709 string originalUnaligned = candidateSeq->getUnaligned();
710 int numBasesNeeded = origNumBases * threshold;
712 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
713 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
714 alignment->resize(candidateSeq->getUnaligned().length()+1);
717 Sequence temp = templateDB->findClosestSequence(candidateSeq);
718 Sequence* templateSeq = &temp;
720 float searchScore = templateDB->getSearchScore();
722 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
726 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
727 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
728 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
729 //so this bool tells you if you need to delete it
731 //if there is a possibility that this sequence should be reversed
732 if (candidateSeq->getNumBases() < numBasesNeeded) {
734 string wasBetter = "";
735 //if the user wants you to try the reverse
737 //get reverse compliment
738 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
739 copy->reverseComplement();
742 Sequence temp2 = templateDB->findClosestSequence(copy);
743 Sequence* templateSeq2 = &temp2;
745 searchScore = templateDB->getSearchScore();
747 nast2 = new Nast(alignment, copy, templateSeq2);
749 //check if any better
750 if (copy->getNumBases() > candidateSeq->getNumBases()) {
751 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
752 templateSeq = templateSeq2;
755 needToDeleteCopy = true;
756 wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
758 wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
764 //create accnos file with names
765 outputString = candidateSeq->getName() + wasBetter + "\n";
767 //send results to parent
768 int length = outputString.length();
770 char* buf = new char[length];
771 memcpy(buf, outputString.c_str(), length);
773 MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
775 MPIWroteAccnos = true;
778 report.setTemplate(templateSeq);
779 report.setSearchParameters(search, searchScore);
780 report.setAlignmentParameters(align, alignment);
781 report.setNastParameters(*nast);
783 outputString = ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
785 //send results to parent
786 int length = outputString.length();
787 char* buf2 = new char[length];
788 memcpy(buf2, outputString.c_str(), length);
790 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
794 outputString = report.getReport();
796 //send results to parent
797 length = outputString.length();
798 char* buf3 = new char[length];
799 memcpy(buf3, outputString.c_str(), length);
801 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
805 if (needToDeleteCopy) { delete copy; }
810 if((i+1) % 100 == 0){ cout << (toString(i+1)) << endl; }
813 if((num) % 100 != 0){ cout << (toString(num)) << endl; }
817 catch(exception& e) {
818 m->errorOut(e, "AlignCommand", "driverMPI");
823 /**************************************************************************************************/
825 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
828 processIDS.resize(0);
829 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
832 //loop through and create all the processes you want
833 while (process != processors) {
837 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
840 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
842 //pass numSeqs to parent
844 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
845 m->openOutputFile(tempFile, out);
851 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
852 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
858 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
860 //force parent to wait until all the processes are done
861 for (int i=0;i<processIDS.size();i++) {
862 int temp = processIDS[i];
866 vector<string> nonBlankAccnosFiles;
867 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
868 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
870 for (int i = 0; i < processIDS.size(); i++) {
872 string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp";
873 m->openInputFile(tempFile, in);
874 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
875 in.close(); m->mothurRemove(tempFile);
877 appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
878 m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
880 appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
881 m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
883 if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
884 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
885 }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp")); }
889 //append accnos files
890 if (nonBlankAccnosFiles.size() != 0) {
891 rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
893 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
894 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
895 m->mothurRemove(nonBlankAccnosFiles[h]);
897 }else { //recreate the accnosfile if needed
899 m->openOutputFile(accnosFName, out);
903 //////////////////////////////////////////////////////////////////////////////////////////////////////
904 //Windows version shared memory, so be careful when passing variables through the alignData struct.
905 //Above fork() will clone, so memory is separate, but that's not the case with windows,
906 //////////////////////////////////////////////////////////////////////////////////////////////////////
908 vector<alignData*> pDataArray;
909 DWORD dwThreadIdArray[processors-1];
910 HANDLE hThreadArray[processors-1];
912 //Create processor worker threads.
913 for( int i=0; i<processors-1; i++ ){
915 //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
917 // Allocate memory for thread data.
918 string extension = "";
919 if (i != 0) { extension = toString(i) + ".temp"; }
921 alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
922 pDataArray.push_back(tempalign);
923 processIDS.push_back(i);
925 //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
926 //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
927 hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
930 //need to check for line ending error
932 m->openInputFile(filename, inFASTA);
933 inFASTA.seekg(lines[processors-1]->start-1);
934 char c = inFASTA.peek();
936 if (c != '>') { //we need to move back
937 lines[processors-1]->start--;
940 //using the main process as a worker saves time and memory
941 //do my part - do last piece because windows is looking for eof
942 num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
944 //Wait until all threads have terminated.
945 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
947 //Close all thread handles and free memory allocations.
948 for(int i=0; i < pDataArray.size(); i++){
949 num += pDataArray[i]->count;
950 CloseHandle(hThreadArray[i]);
951 delete pDataArray[i];
954 vector<string> nonBlankAccnosFiles;
955 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
956 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
958 for (int i = 1; i < processors; i++) {
959 appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
960 m->mothurRemove((alignFileName + toString(i) + ".temp"));
962 appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
963 m->mothurRemove((reportFileName + toString(i) + ".temp"));
965 if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
966 nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
967 }else { m->mothurRemove((accnosFName + toString(i) + ".temp")); }
970 //append accnos files
971 if (nonBlankAccnosFiles.size() != 0) {
972 rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
974 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
975 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
976 m->mothurRemove(nonBlankAccnosFiles[h]);
978 }else { //recreate the accnosfile if needed
980 m->openOutputFile(accnosFName, out);
987 catch(exception& e) {
988 m->errorOut(e, "AlignCommand", "createProcesses");
992 /**************************************************************************************************/
994 void AlignCommand::appendAlignFiles(string temp, string filename) {
999 m->openOutputFileAppend(filename, output);
1000 m->openInputFile(temp, input);
1002 while(char c = input.get()){
1003 if(input.eof()) { break; }
1004 else { output << c; }
1010 catch(exception& e) {
1011 m->errorOut(e, "AlignCommand", "appendAlignFiles");
1015 //**********************************************************************************************************************
1017 void AlignCommand::appendReportFiles(string temp, string filename) {
1022 m->openOutputFileAppend(filename, output);
1023 m->openInputFile(temp, input);
1025 while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
1027 while(char c = input.get()){
1028 if(input.eof()) { break; }
1029 else { output << c; }
1035 catch(exception& e) {
1036 m->errorOut(e, "AlignCommand", "appendReportFiles");
1040 //**********************************************************************************************************************