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"};
43 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
45 OptionParser parser(option);
46 map<string, string> parameters = parser.getParameters();
48 ValidParameters validParameter;
50 //check to make sure all parameters are valid for command
51 for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
52 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
55 //check for required parameters
56 templateFileName = validParameter.validFile(parameters, "template", true);
57 if (templateFileName == "not found") {
58 mothurOut("template is a required parameter for the align.seqs command.");
62 else if (templateFileName == "not open") { abort = true; }
64 candidateFileName = validParameter.validFile(parameters, "candidate", true);
65 if (candidateFileName == "not found") {
66 mothurOut("candidate is a required parameter for the align.seqs command.");
70 else if (candidateFileName == "not open") { abort = true; }
72 //check for optional parameter and set defaults
73 // ...at some point should added some additional type checking...
75 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
76 convert(temp, kmerSize);
78 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
81 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
82 convert(temp, misMatch);
84 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
85 convert(temp, gapOpen);
87 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
88 convert(temp, gapExtend);
90 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
91 convert(temp, processors);
93 search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
95 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
100 errorOut(e, "AlignCommand", "AlignCommand");
105 //**********************************************************************************************************************
107 AlignCommand::~AlignCommand(){
109 if (abort == false) {
110 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
116 //**********************************************************************************************************************
118 void AlignCommand::help(){
120 mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
121 mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
122 mothurOut("The template and candidate parameters are required.\n");
123 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");
124 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");
125 mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
126 mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
127 mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
128 mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n");
129 mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0.\n");
130 mothurOut("The align.seqs command should be in the following format: \n");
131 mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
132 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");
133 mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
135 catch(exception& e) {
136 errorOut(e, "AlignCommand", "help");
142 //**********************************************************************************************************************
144 int AlignCommand::execute(){
146 if (abort == true) { return 0; }
148 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
149 int longestBase = templateDB->getLongestBase();
151 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
152 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
153 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
154 else if(align == "noalign") { alignment = new NoAlign(); }
156 mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
158 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
160 mothurOut("Aligning sequences...");
163 string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
164 string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
166 int numFastaSeqs = 0;
167 int start = time(NULL);
169 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
172 openInputFile(candidateFileName, inFASTA);
173 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
176 lines.push_back(new linePair(0, numFastaSeqs));
178 driver(lines[0], alignFileName, reportFileName);
182 vector<int> positions;
183 processIDS.resize(0);
186 openInputFile(candidateFileName, inFASTA);
189 while(!inFASTA.eof()){
190 input = getline(inFASTA);
191 if (input.length() != 0) {
192 if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
197 numFastaSeqs = positions.size();
199 int numSeqsPerProcessor = numFastaSeqs / processors;
201 for (int i = 0; i < processors; i++) {
202 int startPos = positions[ i * numSeqsPerProcessor ];
203 if(i == processors - 1){
204 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
206 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
208 createProcesses(alignFileName, reportFileName);
210 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
211 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
213 for(int i=1;i<processors;i++){
214 appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
215 remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
217 appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
218 remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
224 openInputFile(candidateFileName, inFASTA);
225 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
228 lines.push_back(new linePair(0, numFastaSeqs));
230 driver(lines[0], alignFileName, reportFileName);
233 mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
239 catch(exception& e) {
240 errorOut(e, "AlignCommand", "execute");
245 //**********************************************************************************************************************
247 int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
249 ofstream alignmentFile;
250 openOutputFile(alignFName, alignmentFile);
251 NastReport report(reportFName);
254 openInputFile(candidateFileName, inFASTA);
256 inFASTA.seekg(line->start);
258 for(int i=0;i<line->numSeqs;i++){
260 Sequence* candidateSeq = new Sequence(inFASTA);
262 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
263 alignment->resize(candidateSeq->getUnaligned().length()+1);
266 report.setCandidate(candidateSeq);
268 Sequence temp = templateDB->findClosestSequence(candidateSeq);
269 Sequence* templateSeq = &temp;
271 report.setTemplate(templateSeq);
272 report.setSearchParameters(search, templateDB->getSearchScore());
274 Nast nast(alignment, candidateSeq, templateSeq);
276 report.setAlignmentParameters(align, alignment);
278 report.setNastParameters(nast);
280 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
288 alignmentFile.close();
293 catch(exception& e) {
294 errorOut(e, "AlignCommand", "driver");
299 /**************************************************************************************************/
301 void AlignCommand::createProcesses(string alignFileName, string reportFileName) {
303 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
305 // processIDS.resize(0);
307 //loop through and create all the processes you want
308 while (process != processors) {
312 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
315 driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp");
317 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
320 //force parent to wait until all the processes are done
321 for (int i=0;i<processors;i++) {
322 int temp = processIDS[i];
327 catch(exception& e) {
328 errorOut(e, "AlignCommand", "createProcesses");
333 /**************************************************************************************************/
335 void AlignCommand::appendAlignFiles(string temp, string filename) {
340 openOutputFileAppend(filename, output);
341 openInputFile(temp, input);
343 while(char c = input.get()){
344 if(input.eof()) { break; }
345 else { output << c; }
351 catch(exception& e) {
352 errorOut(e, "AlignCommand", "appendAlignFiles");
357 /**************************************************************************************************/
359 void AlignCommand::appendReportFiles(string temp, string filename) {
364 openOutputFileAppend(filename, output);
365 openInputFile(temp, input);
367 while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
369 while(char c = input.get()){
370 if(input.eof()) { break; }
371 else { output << c; }
377 catch(exception& e) {
378 errorOut(e, "AlignCommand", "appendReportFiles");
383 //**********************************************************************************************************************