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/*
* aligncommand.cpp
* Mothur
*
* Created by Sarah Westcott on 5/15/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
* This version of nast does everything I think that the greengenes nast server does and then some. I have added the
* feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
* method. This latter feature is perhaps most significant. nastPlus enables a user to use either a Needleman-Wunsch
* (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm. This is significant because it
* allows for a global alignment and not the local alignment provided by bLAst. Furthermore, it has the potential to
* provide a better alignment because of the banding method employed by blast (I'm not sure about this).
*
*/
#include "aligncommand.h"
//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
try {
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate);
CommandParameter psearch("search", "Multiple", "kmer-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch);
CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
CommandParameter palign("align", "Multiple", "needleman-gotoh-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pflip("flip", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pflip);
CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
abort = false; calledHelp = false;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string AlignCommand::getHelpString(){
try {
string helpString = "\n";
helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n";
helpString += "The align.seqs command parameters are " + getCommandParameters() + ".\n";
helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file.\n";
helpString += "The search parameter allows you to specify the method to find most similar reference sequence. Your options are: suffix or kmer. The default is kmer.\n";
helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman and noalign. The default is needleman.\n";
helpString += "The ksize parameter allows you to specify the kmer size for finding most similar reference to a given sequence. The default is 8.\n";
helpString += "The match parameter allows you to specify the bonus for having the same base. Default=1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. Default=-1.0.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. Default=-5.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. Default=-2.0.\n";
helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
helpString += " By default, mothur will align the reverse compliment of your sequences when the alignment process removes more than 50% of the bases indicating the read may be flipped. This process assembles the best possible alignment, and downstream analysis will remove any poor quality reads remaining.\n";
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.\n";
helpString += "The align.seqs command should be in the following format: ";
helpString += "align.seqs(reference=yourTemplateFile, fasta=yourUnalignedFastaFile)\n";
helpString += "Example: align.seqs(fasta=water.fasta, template=silva.v4.fasta)\n\n";
getCommonQuestions();
return helpString;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string AlignCommand::getCommonQuestions(){
try {
vector<string> questions, issues, qanswers, ianswers, howtos, hanswers;
string issue = "...template is not aligned, aborting. What do I do?"; issues.push_back(issue);
string ianswer = "\tMothur requires the reference file to be aligned to generate aligned sequences. You can download mothur's aligned silva references here, https://mothur.org/wiki/Silva_reference_files. For ITS sequences, see 'how to' below.\n"; ianswers.push_back(ianswer);
issue = "...xxx of your sequences generated alignments that eliminated too many bases... What does this mean?"; issues.push_back(issue);
ianswer = "\tBy default, mothur will align the reverse compliment of your sequences when the alignment process removes more than 50% of the bases indicating the read may be flipped. This process assembles the best possible alignment, and downstream analysis will remove any poor quality reads remaining.\n"; ianswers.push_back(ianswer);
string howto = "How do I 'align' ITS sequences?"; howtos.push_back(howto);
string hanswer = "\tYou really can't do an alignment because there isn't positional homology. You can use the pre.cluster and pairwise.seqs commands to generate a distance matrix from unaligned sequences.\n"; hanswers.push_back(hanswer);
howto = "How do I create a custom reference for the region I am studying?"; howtos.push_back(howto);
hanswer = "\tYou can tailor your reference using this method: http://blog.mothur.org/2016/07/07/Customization-for-your-region/.\n"; hanswers.push_back(hanswer);
string commonQuestions = util.getFormattedHelp(questions, qanswers, issues, ianswers, howtos, hanswers);
return commonQuestions;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "getCommonQuestions");
exit(1);
}
}
//**********************************************************************************************************************
string AlignCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],align"; } //makes file like: amazon.align
else if (type == "alignreport") { pattern = "[filename],align_report"; }
else if (type == "accnos") { pattern = "[filename],flip.accnos"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(string option) : Command() {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true;}
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
templateFileName = validParameter.validFile(parameters, "reference");
if (templateFileName == "not found") { m->mothurOut("[ERROR]: The reference parameter is a required for the align.seqs command, aborting.\n"); abort = true;
}else if (templateFileName == "not open") { abort = true; }
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.valid(parameters, "ksize"); if (temp == "not found"){ temp = "8"; }
util.mothurConvert(temp, kmerSize);
temp = validParameter.valid(parameters, "match"); if (temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, match);
temp = validParameter.valid(parameters, "mismatch"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, misMatch);
temp = validParameter.valid(parameters, "gapopen"); if (temp == "not found"){ temp = "-5.0"; }
util.mothurConvert(temp, gapOpen);
temp = validParameter.valid(parameters, "gapextend"); if (temp == "not found"){ temp = "-2.0"; }
util.mothurConvert(temp, gapExtend);
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "flip"); if (temp == "not found"){ temp = "t"; }
flip = util.isTrue(temp);
temp = validParameter.valid(parameters, "threshold"); if (temp == "not found"){ temp = "0.50"; }
util.mothurConvert(temp, threshold);
search = validParameter.valid(parameters, "search"); if (search == "not found"){ search = "kmer"; }
if ((search != "suffix") && (search != "kmer")) { m->mothurOut("invalid search option: choices are kmer or suffix.\n"); abort=true; }
align = validParameter.valid(parameters, "align"); if (align == "not found"){ align = "needleman"; }
if ((align != "needleman") && (align != "gotoh") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh or noalign.\n"); abort=true; }
}
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "AlignCommand");
exit(1);
}
}
//**********************************************************************************************************************
AlignCommand::~AlignCommand(){}
//**********************************************************************************************************************
int AlignCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
long long before = util.getRAMUsed(); long long total = util.getTotalRAM();
if (m->getDebug()) { m->mothurOut("[DEBUG]: RAM used before reading template " + toString(before) + " of total RAM available " + toString(total) + "\n"); }
templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, util.getRandomNumber(), true);
if (m->getControl_pressed()) { outputTypes.clear(); return 0; }
time_t start = time(nullptr);
m->mothurOut("\nAligning sequences from " + fastafile + " ...\n" );
if (outputdir == "") { outputdir += util.hasPath(fastafile); }
map<string, string> variables; variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string alignFileName = getOutputFileName("fasta", variables);
string reportFileName = getOutputFileName("alignreport", variables);
string accnosFileName = getOutputFileName("accnos", variables);
bool hasAccnos = true;
vector<long long> numFlipped;
numFlipped.push_back(0); //numflipped because reverse was better
numFlipped.push_back(0); //total number of sequences with over 50% of bases removed
long long numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, fastafile, numFlipped);
delete templateDB;
if (m->getControl_pressed()) { util.mothurRemove(accnosFileName); util.mothurRemove(alignFileName); util.mothurRemove(reportFileName); outputTypes.clear(); return 0; }
//delete accnos file if its blank else report to user
if (util.isBlank(accnosFileName)) { util.mothurRemove(accnosFileName); hasAccnos = false; }
else {
m->mothurOut("[WARNING]: " + toString(numFlipped[1]) + " of your sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well. flip=t");
}else{ m->mothurOut("\n[NOTE]: " + toString(numFlipped[0]) + " of your sequences were reversed to produce a better alignment."); }
m->mothurOutEndLine();
}
outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); }
m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " seconds to align " + toString(numFastaSeqs) + " sequences.\n");
//set align file as new current fastafile
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; current->setFastaFile(currentFasta); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
struct alignStruct {
OutputWriter* alignWriter;
OutputWriter* reportWriter;
OutputWriter* accnosWriter;
string inputFilename;
string alignMethod, search, templateFileName;
float match, misMatch, gapOpen, gapExtend, threshold;
bool flip;
long long numSeqs;
int kmerSize;
vector<long long> flippedResults;
linePair filePos;
MothurOut* m;
Utils util;
AlignmentDB* templateDB;
Alignment* alignment;
alignStruct (linePair fP, OutputWriter* aFName, OutputWriter* reFName, OutputWriter* ac, string fname, AlignmentDB* tfn, string al, float ma, float misMa, float gOpen, float gExtend, float thr, bool fl, int ks, string se) {
filePos.start = fP.start;
filePos.end = fP.end;
alignWriter = aFName;
reportWriter = reFName;
accnosWriter = ac;
inputFilename = fname;
numSeqs = 0;
m = MothurOut::getInstance();
match = ma;
misMatch = misMa;
gapOpen = gOpen;
gapExtend = gExtend;
threshold = thr;
flip = fl;
search = se;
kmerSize = ks;
flippedResults.resize(2, 0);
alignMethod = al;
templateDB = tfn;
int longestBase = templateDB->getLongestBase();
if (m->getDebug()) { m->mothurOut("[DEBUG]: template longest base = " + toString(longestBase) + " \n"); }
if(al == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(al == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(al == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(al + " is not a valid alignment option. I will run the command using needleman.\n");
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
}
~alignStruct() { delete alignment; }
};
//**********************************************************************************************************************
void alignDriver(alignStruct* params) {
try {
AlignReport report;
ifstream inFASTA; params->util.openInputFile(params->inputFilename, inFASTA);
inFASTA.seekg(params->filePos.start);
bool done = false;
long long count = 0;
long long numFlipped_0 = 0;
long long numFlipped_1 = 0;
while (!done) {
if (params->m->getControl_pressed()) { break; }
Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
report.setCandidate(candidateSeq);
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * params->threshold;
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
if (candidateSeq->getUnaligned().length()+1 > params->alignment->getnRows()) {
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + candidateSeq->getName() + " " + toString(candidateSeq->getUnaligned().length()) + " " + toString(params->alignment->getnRows()) + " \n"); }
params->alignment->resize(candidateSeq->getUnaligned().length()+2);
}
float searchScore;
Sequence temp = params->templateDB->findClosestSequence(candidateSeq, searchScore);
Sequence* templateSeq = new Sequence(temp.getName(), temp.getAligned());
Nast* nast = new Nast(params->alignment, candidateSeq, templateSeq);
Sequence* copy;
Nast* nast2;
bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
//since nast does not make a copy of hte sequence passed, and it is used by the reporter below
//you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
//so this bool tells you if you need to delete it
//if there is a possibility that this sequence should be reversed
if (candidateSeq->getNumBases() < numBasesNeeded) {
numFlipped_1++;
//if the user wants you to try the reverse
if (params->flip) {
//get reverse compliment
copy = new Sequence(candidateSeq->getName(), originalUnaligned);
copy->reverseComplement();
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: flipping " + candidateSeq->getName() + " \n"); }
//rerun alignment
Sequence temp2 = params->templateDB->findClosestSequence(copy, searchScore);
Sequence* templateSeq2 = new Sequence(temp2.getName(), temp2.getAligned());
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: closest template " + temp2.getName() + " \n"); }
nast2 = new Nast(params->alignment, copy, templateSeq2);
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: completed Nast2 " + candidateSeq->getName() + " flipped numBases = " + toString(copy->getNumBases()) + " old numbases = " + toString(candidateSeq->getNumBases()) +" \n"); }
//check if any better
if (copy->getNumBases() > candidateSeq->getNumBases()) {
candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
delete templateSeq;
templateSeq = templateSeq2;
delete nast;
nast = nast2;
needToDeleteCopy = true;
params->accnosWriter->write(candidateSeq->getName()+ '\n');
numFlipped_0++;
}else{
delete nast2;
delete templateSeq2;
delete copy;
}
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: done.\n"); }
}
}
report.setTemplate(templateSeq);
report.setSearchParameters(params->search, searchScore);
report.setAlignmentParameters(params->alignMethod, params->alignment);
report.setNastParameters(*nast);
params->alignWriter->write('>' + candidateSeq->getName() + '\n' + candidateSeq->getAligned() + '\n');
params->reportWriter->write(report.getSeqReport());
delete nast;
delete templateSeq;
if (needToDeleteCopy) { delete copy; }
count++;
}
delete candidateSeq;
#if defined NON_WINDOWS
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= params->filePos.end)) { break; }
#else
if (count == params->filePos.end) { break; }
#endif
//report progress
if((count) % 1000 == 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }
}
//report progress
if((count) % 1000 != 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }
params->numSeqs += count;
params->flippedResults[0] += numFlipped_0;
params->flippedResults[1] += numFlipped_1;
inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "AlignCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
//void alignDriver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename, vector<long long>& numFlipped,MothurOut* m, string align, float match, float misMatch, float gapOpen, float gapExtend, float threshold, bool flip, AlignmentDB* templateDB, string search, long long& count) {
long long AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename, vector<long long>& numFlipped) {
try {
vector<linePair> lines;
vector<double> positions;
#if defined NON_WINDOWS
positions = util.divideFile(filename, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
long long numFastaSeqs = 0;
positions = util.setFilePosFasta(filename, numFastaSeqs);
if (numFastaSeqs < processors) { processors = numFastaSeqs; m->mothurOut("Reducing processors to " + toString(numFastaSeqs) + ".\n"); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
#endif
//create array of worker threads
vector<std::thread*> workerThreads;
vector<alignStruct*> data;
long long num = 0;
for (int i = 0; i < numFlipped.size(); i++) { numFlipped[i] = 0; }
time_t start, end;
time(&start);
AlignReport nast; ofstream out; util.openOutputFile(reportFileName, out);
nast.printHeaders(out); out.close();
auto synchronizedOutputAlignFile = std::make_shared<SynchronizedOutputFile>(alignFileName);
auto synchronizedOutputReportFile = std::make_shared<SynchronizedOutputFile>(reportFileName, true);
auto synchronizedOutputAccnosFile = std::make_shared<SynchronizedOutputFile>(accnosFName);
for (int i = 0; i < processors-1; i++) {
OutputWriter* threadAlignWriter = new OutputWriter(synchronizedOutputAlignFile);
OutputWriter* threadReportWriter = new OutputWriter(synchronizedOutputReportFile);
OutputWriter* threadAccnosWriter = new OutputWriter(synchronizedOutputAccnosFile);
alignStruct* dataBundle = new alignStruct(lines[i+1], threadAlignWriter, threadReportWriter, threadAccnosWriter, filename, templateDB, align, match, misMatch, gapOpen, gapExtend, threshold, flip, kmerSize, search);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(alignDriver, dataBundle));
}
OutputWriter* threadAlignWriter = new OutputWriter(synchronizedOutputAlignFile);
OutputWriter* threadReportWriter = new OutputWriter(synchronizedOutputReportFile);
OutputWriter* threadAccnosWriter = new OutputWriter(synchronizedOutputAccnosFile);
alignStruct* dataBundle = new alignStruct(lines[0], threadAlignWriter, threadReportWriter, threadAccnosWriter, filename, templateDB, align, match, misMatch, gapOpen, gapExtend, threshold, flip, kmerSize, search);
alignDriver(dataBundle);
numFlipped[0] = dataBundle->flippedResults[0];
numFlipped[1] = dataBundle->flippedResults[1];
num = dataBundle->numSeqs;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
num += data[i]->numSeqs;
numFlipped[0] += data[i]->flippedResults[0];
numFlipped[1] += data[i]->flippedResults[1];
delete data[i]->alignWriter;
delete data[i]->reportWriter;
delete data[i]->accnosWriter;
delete data[i];
delete workerThreads[i];
}
synchronizedOutputAlignFile->close(); synchronizedOutputReportFile->close(); synchronizedOutputAccnosFile->close();
delete threadAlignWriter; delete threadAccnosWriter; delete threadReportWriter;
delete dataBundle;
time(&end);
m->mothurOut("It took " + toString(difftime(end, start)) + " secs to align " + toString(num) + " sequences.\n\n");
return num;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "createProcesses");
exit(1);
}
}
//**********************************************************************************************************************
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