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"
29 //**********************************************************************************************************************
31 AlignCommand::AlignCommand(string option){
33 // globaldata = GlobalData::getInstance();
36 //allow user to run help
37 if(option == "help") { help(); abort = true; }
41 //valid paramters for this command
42 string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
43 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
45 OptionParser parser(option);
46 map<string, string> parameters = parser.getParameters();
48 ValidParameters validParameter;
49 map<string, string>::iterator it;
51 //check to make sure all parameters are valid for command
52 for (it = parameters.begin(); it != parameters.end(); it++) {
53 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
56 //if the user changes the output directory command factory will send this info to us in the output parameter
57 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
60 //if the user changes the input directory command factory will send this info to us in the output parameter
61 string inputDir = validParameter.validFile(parameters, "inputdir", false);
63 if (inputDir == "not found"){ inputDir = ""; }
67 it = parameters.find("template");
69 //user has given a template file
70 if(it != parameters.end()){
71 path = hasPath(it->second);
72 //if the user has not given a path then, add inputdir. else leave path alone.
73 if (path == "") { parameters["template"] = inputDir + it->second; }
77 //check for required parameters
78 templateFileName = validParameter.validFile(parameters, "template", true);
80 if (templateFileName == "not found") {
81 mothurOut("template is a required parameter for the align.seqs command.");
84 }else if (templateFileName == "not open") { abort = true; }
86 candidateFileName = validParameter.validFile(parameters, "candidate", false);
87 if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true; }
89 splitAtDash(candidateFileName, candidateFileNames);
91 //go through files and make sure they are good, if not, then disregard them
92 for (int i = 0; i < candidateFileNames.size(); i++) {
94 string path = hasPath(candidateFileNames[i]);
95 //if the user has not given a path then, add inputdir. else leave path alone.
96 if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
101 ableToOpen = openInputFile(candidateFileNames[i], in);
102 if (ableToOpen == 1) {
103 mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
104 //erase from file list
105 candidateFileNames.erase(candidateFileNames.begin()+i);
111 //make sure there is at least one valid file left
112 if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
115 //check for optional parameter and set defaults
116 // ...at some point should added some additional type checking...
118 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
119 convert(temp, kmerSize);
121 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
122 convert(temp, match);
124 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
125 convert(temp, misMatch);
127 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
128 convert(temp, gapOpen);
130 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
131 convert(temp, gapExtend);
133 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
134 convert(temp, processors);
136 temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
139 temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
140 convert(temp, threshold);
142 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
144 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
148 catch(exception& e) {
149 errorOut(e, "AlignCommand", "AlignCommand");
154 //**********************************************************************************************************************
156 AlignCommand::~AlignCommand(){
158 if (abort == false) {
159 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
165 //**********************************************************************************************************************
167 void AlignCommand::help(){
169 mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
170 mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
171 mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
172 mothurOut("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.\n");
173 mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
174 mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
175 mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
176 mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
177 mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
178 mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
179 mothurOut("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.\n");
180 mothurOut("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.\n");
181 mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
182 mothurOut("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.\n");
183 mothurOut("The align.seqs command should be in the following format: \n");
184 mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
185 mothurOut("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)\n");
186 mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
188 catch(exception& e) {
189 errorOut(e, "AlignCommand", "help");
195 //**********************************************************************************************************************
197 int AlignCommand::execute(){
199 if (abort == true) { return 0; }
201 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
202 int longestBase = templateDB->getLongestBase();
204 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
205 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
206 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
207 else if(align == "noalign") { alignment = new NoAlign(); }
209 mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
211 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
214 for (int s = 0; s < candidateFileNames.size(); s++) {
215 mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
217 if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
218 string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
219 string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
220 string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
221 bool hasAccnos = true;
223 int numFastaSeqs = 0;
224 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
225 int start = time(NULL);
227 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
230 openInputFile(candidateFileNames[s], inFASTA);
231 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
234 lines.push_back(new linePair(0, numFastaSeqs));
236 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
238 //delete accnos file if its blank else report to user
239 if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
241 mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
243 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
244 }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
249 vector<int> positions;
250 processIDS.resize(0);
253 openInputFile(candidateFileNames[s], inFASTA);
256 while(!inFASTA.eof()){
257 input = getline(inFASTA);
258 if (input.length() != 0) {
259 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
264 numFastaSeqs = positions.size();
266 int numSeqsPerProcessor = numFastaSeqs / processors;
268 for (int i = 0; i < processors; i++) {
269 long int startPos = positions[ i * numSeqsPerProcessor ];
270 if(i == processors - 1){
271 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
273 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
276 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
278 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
279 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
281 //append alignment and report files
282 for(int i=1;i<processors;i++){
283 appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
284 remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
286 appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
287 remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
290 vector<string> nonBlankAccnosFiles;
291 //delete blank accnos files generated with multiple processes
292 for(int i=0;i<processors;i++){
293 if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
294 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
295 }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
298 //append accnos files
299 if (nonBlankAccnosFiles.size() != 0) {
300 rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
302 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
303 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
304 remove(nonBlankAccnosFiles[h].c_str());
306 mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
308 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
309 }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
311 }else{ hasAccnos = false; }
315 openInputFile(candidateFileNames[s], inFASTA);
316 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
319 lines.push_back(new linePair(0, numFastaSeqs));
321 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
323 //delete accnos file if its blank else report to user
324 if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
326 mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
328 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
329 }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
335 mothurOut("Output File Names: " + alignFileName + ", " + reportFileName);
336 if (hasAccnos) { mothurOut(", " + accnosFileName + "."); }
337 else { mothurOut("."); }
340 mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
347 catch(exception& e) {
348 errorOut(e, "AlignCommand", "execute");
353 //**********************************************************************************************************************
355 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
357 ofstream alignmentFile;
358 openOutputFile(alignFName, alignmentFile);
361 openOutputFile(accnosFName, accnosFile);
363 NastReport report(reportFName);
366 openInputFile(filename, inFASTA);
368 inFASTA.seekg(line->start);
370 for(int i=0;i<line->numSeqs;i++){
372 Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
373 int origNumBases = candidateSeq->getNumBases();
374 string originalUnaligned = candidateSeq->getUnaligned();
375 int numBasesNeeded = origNumBases * threshold;
377 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
378 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
379 alignment->resize(candidateSeq->getUnaligned().length()+1);
382 Sequence temp = templateDB->findClosestSequence(candidateSeq);
383 Sequence* templateSeq = &temp;
385 float searchScore = templateDB->getSearchScore();
387 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
391 bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
392 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
393 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
394 //so this bool tells you if you need to delete it
396 //if there is a possibility that this sequence should be reversed
397 if (candidateSeq->getNumBases() < numBasesNeeded) {
399 string wasBetter = "";
400 //if the user wants you to try the reverse
402 //get reverse compliment
403 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
404 copy->reverseComplement();
407 Sequence temp2 = templateDB->findClosestSequence(copy);
408 Sequence* templateSeq2 = &temp2;
410 searchScore = templateDB->getSearchScore();
412 nast2 = new Nast(alignment, copy, templateSeq2);
414 //check if any better
415 if (copy->getNumBases() > candidateSeq->getNumBases()) {
416 candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
417 templateSeq = templateSeq2;
420 needToDeleteCopy = true;
422 wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
428 //create accnos file with names
429 accnosFile << candidateSeq->getName() << wasBetter << endl;
432 report.setCandidate(candidateSeq);
433 report.setTemplate(templateSeq);
434 report.setSearchParameters(search, searchScore);
435 report.setAlignmentParameters(align, alignment);
436 report.setNastParameters(*nast);
438 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
442 if (needToDeleteCopy) { delete copy; }
447 if((i+1) % 100 == 0){ mothurOut(toString(i+1)); mothurOutEndLine(); }
450 if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine(); }
452 alignmentFile.close();
458 catch(exception& e) {
459 errorOut(e, "AlignCommand", "driver");
464 /**************************************************************************************************/
466 void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
468 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
470 // processIDS.resize(0);
472 //loop through and create all the processes you want
473 while (process != processors) {
477 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
480 driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
482 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
485 //force parent to wait until all the processes are done
486 for (int i=0;i<processors;i++) {
487 int temp = processIDS[i];
492 catch(exception& e) {
493 errorOut(e, "AlignCommand", "createProcesses");
498 /**************************************************************************************************/
500 void AlignCommand::appendAlignFiles(string temp, string filename) {
505 openOutputFileAppend(filename, output);
506 openInputFile(temp, input);
508 while(char c = input.get()){
509 if(input.eof()) { break; }
510 else { output << c; }
516 catch(exception& e) {
517 errorOut(e, "AlignCommand", "appendAlignFiles");
521 //**********************************************************************************************************************
523 void AlignCommand::appendReportFiles(string temp, string filename) {
528 openOutputFileAppend(filename, output);
529 openInputFile(temp, input);
531 while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
533 while(char c = input.get()){
534 if(input.eof()) { break; }
535 else { output << c; }
541 catch(exception& e) {
542 errorOut(e, "AlignCommand", "appendReportFiles");
547 //**********************************************************************************************************************