//**********************************************************************************************************************
-AlignCommand::AlignCommand(string option){
+AlignCommand::AlignCommand(string option) {
try {
- // globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false;
+
//allow user to run help
if(option == "help") { help(); abort = true; }
templateFileName = validParameter.validFile(parameters, "template", true);
if (templateFileName == "not found") {
- mothurOut("template is a required parameter for the align.seqs command.");
- mothurOutEndLine();
+ m->mothurOut("template is a required parameter for the align.seqs command.");
+ m->mothurOutEndLine();
abort = true;
}else if (templateFileName == "not open") { abort = true; }
candidateFileName = validParameter.validFile(parameters, "candidate", false);
- if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true; }
+ if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }
else {
splitAtDash(candidateFileName, candidateFileNames);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
}
-
+
int ableToOpen;
ifstream in;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
+
ableToOpen = openInputFile(candidateFileNames[i], in);
+ in.close();
+
+ #ifdef USE_MPI
+ for (int j = 1; j < processors; j++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Status status;
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ #endif
+
if (ableToOpen == 1) {
- mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
+ m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
}
- in.close();
+
}
//make sure there is at least one valid file left
- if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
+ if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "AlignCommand");
+ m->errorOut(e, "AlignCommand", "AlignCommand");
exit(1);
}
}
void AlignCommand::help(){
try {
- mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
- mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
- 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");
- 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");
- 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");
- mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- 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");
- 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");
- mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
- 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");
- mothurOut("The align.seqs command should be in the following format: \n");
- mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
- 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");
- mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
+ m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
+ m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
+ m->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");
+ m->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");
+ m->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");
+ m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
+ m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
+ m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
+ m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
+ m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
+ m->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");
+ m->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");
+ m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
+ m->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");
+ m->mothurOut("The align.seqs command should be in the following format: \n");
+ m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
+ m->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");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "help");
+ m->errorOut(e, "AlignCommand", "help");
exit(1);
}
}
int AlignCommand::execute(){
try {
if (abort == true) { return 0; }
-
+
templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
int longestBase = templateDB->getLongestBase();
-
+
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
- mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- mothurOutEndLine();
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
+ vector<string> outputNames;
for (int s = 0; s < candidateFileNames.size(); s++) {
- mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
int numFastaSeqs = 0;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
int start = time(NULL);
+
+#ifdef USE_MPI
+ int pid, end, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<long> MPIPos;
+ MPIWroteAccnos = false;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ MPI_File inMPI;
+ MPI_File outMPIAlign;
+ MPI_File outMPIReport;
+ MPI_File outMPIAccnos;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ //char* outAlignFilename = new char[alignFileName.length()];
+ //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
+
+ char outAlignFilename[1024];
+ strcpy(outAlignFilename, alignFileName.c_str());
+
+ //char* outReportFilename = new char[reportFileName.length()];
+ //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
+
+ char outReportFilename[1024];
+ strcpy(outReportFilename, reportFileName.c_str());
+
+ //char* outAccnosFilename = new char[accnosFileName.length()];
+ //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+
+ char outAccnosFilename[1024];
+ strcpy(outAccnosFilename, accnosFileName.c_str());
+
+ //char* inFileName = new char[candidateFileNames[s].length()];
+ //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
+
+ char inFileName[1024];
+ strcpy(inFileName, candidateFileNames[s].c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
+ MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
+ MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; }
+
+ if (pid == 0) { //you are the root process
+
+ MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; }
+
+ for (int i = 1; i < processors; i++) {
+ bool tempResult;
+ MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+ if (tempResult != 0) { MPIWroteAccnos = true; }
+ }
+ }else{ //you are a child process
+ MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numFastaSeqs+1);
+ MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numFastaSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; }
+
+ MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ }
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPIAlign);
+ MPI_File_close(&outMPIReport);
+ MPI_File_close(&outMPIAccnos);
+
+ //delete accnos file if blank
+ if (pid == 0) {
+ //delete accnos file if its blank else report to user
+ if (MPIWroteAccnos) {
+ m->mothurOut("Some of you 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.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
+ }else {
+ //MPI_Info info;
+ //MPI_File_delete(outAccnosFilename, info);
+ hasAccnos = false;
+ remove(accnosFileName.c_str());
+ }
+ }
+
+#else
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
ifstream inFASTA;
openInputFile(candidateFileNames[s], inFASTA);
driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+ if (m->control_pressed) {
+ remove(accnosFileName.c_str());
+ remove(alignFileName.c_str());
+ remove(reportFileName.c_str());
+ return 0;
+ }
+
//delete accnos file if its blank else report to user
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}
}
else{
appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
remove(nonBlankAccnosFiles[h].c_str());
}
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}else{ hasAccnos = false; }
+
+ if (m->control_pressed) {
+ remove(accnosFileName.c_str());
+ remove(alignFileName.c_str());
+ remove(reportFileName.c_str());
+ return 0;
+ }
}
-#else
+ #else
ifstream inFASTA;
openInputFile(candidateFileNames[s], inFASTA);
numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+ if (m->control_pressed) {
+ remove(accnosFileName.c_str());
+ remove(alignFileName.c_str());
+ remove(reportFileName.c_str());
+ return 0;
+ }
+
//delete accnos file if its blank else report to user
if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}
-#endif
-
- mothurOut("Output File Names: " + alignFileName + ", " + reportFileName);
- if (hasAccnos) { mothurOut(", " + accnosFileName + "."); }
- else { mothurOut("."); }
- mothurOutEndLine();
+ #endif
+
+#endif
+
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ outputNames.push_back(alignFileName);
+ outputNames.push_back(reportFileName);
+ if (hasAccnos) { outputNames.push_back(accnosFileName); }
- mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
+ #ifdef USE_MPI
+ }
+ #endif
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
+ m->mothurOutEndLine();
+ m->mothurOutEndLine();
}
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "execute");
+ m->errorOut(e, "AlignCommand", "execute");
exit(1);
}
}
openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
-
+
for(int i=0;i<line->numSeqs;i++){
-
+
+ if (m->control_pressed) { return 0; }
+
Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * threshold;
delete candidateSeq;
//report progress
- if((i+1) % 100 == 0){ mothurOut(toString(i+1)); mothurOutEndLine(); }
+ if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
}
//report progress
- if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine(); }
+ if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine(); }
alignmentFile.close();
inFASTA.close();
return 1;
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "driver");
+ m->errorOut(e, "AlignCommand", "driver");
exit(1);
}
}
+//**********************************************************************************************************************
+#ifdef USE_MPI
+int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
+ try {
+ string outputString = "";
+ MPI_Status statusReport;
+ MPI_Status statusAlign;
+ MPI_Status statusAccnos;
+ MPI_Status status;
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ NastReport report;
+
+ if (pid == 0) {
+ outputString = report.getHeaders();
+ int length = outputString.length();
+
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
+
+ delete buf;
+ }
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+
+ char* buf4 = new char[length];
+ memcpy(buf4, outputString.c_str(), length);
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+
+ delete buf4;
+
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence* candidateSeq = new Sequence(iss);
+ int origNumBases = candidateSeq->getNumBases();
+ string originalUnaligned = candidateSeq->getUnaligned();
+ int numBasesNeeded = origNumBases * threshold;
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+ if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(candidateSeq->getUnaligned().length()+1);
+ }
+
+ Sequence temp = templateDB->findClosestSequence(candidateSeq);
+ Sequence* templateSeq = &temp;
+
+ float searchScore = templateDB->getSearchScore();
+
+ Nast* nast = new Nast(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) {
+
+ string wasBetter = "";
+ //if the user wants you to try the reverse
+ if (flip) {
+ //get reverse compliment
+ copy = new Sequence(candidateSeq->getName(), originalUnaligned);
+ copy->reverseComplement();
+
+ //rerun alignment
+ Sequence temp2 = templateDB->findClosestSequence(copy);
+ Sequence* templateSeq2 = &temp2;
+
+ searchScore = templateDB->getSearchScore();
+
+ nast2 = new Nast(alignment, copy, templateSeq2);
+
+ //check if any better
+ if (copy->getNumBases() > candidateSeq->getNumBases()) {
+ candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
+ templateSeq = templateSeq2;
+ delete nast;
+ nast = nast2;
+ needToDeleteCopy = true;
+ }else{
+ wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
+ delete nast2;
+ delete copy;
+ }
+ }
+
+ //create accnos file with names
+ outputString = candidateSeq->getName() + wasBetter + "\n";
+
+ //send results to parent
+ int length = outputString.length();
+
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
+ delete buf;
+ MPIWroteAccnos = true;
+ }
+
+ report.setCandidate(candidateSeq);
+ report.setTemplate(templateSeq);
+ report.setSearchParameters(search, searchScore);
+ report.setAlignmentParameters(align, alignment);
+ report.setNastParameters(*nast);
+
+ outputString = ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
+
+ delete buf2;
+
+ outputString = report.getReport();
+
+ //send results to parent
+ length = outputString.length();
+ char* buf3 = new char[length];
+ memcpy(buf3, outputString.c_str(), length);
+
+ MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
+
+ delete buf3;
+ delete nast;
+ if (needToDeleteCopy) { delete copy; }
+ }
+ delete candidateSeq;
+
+ //report progress
+ if((i+1) % 100 == 0){ cout << (toString(i+1)) << endl; }
+ }
+ //report progress
+ if((num) % 100 != 0){ cout << (toString(num)) << endl; }
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
/**************************************************************************************************/
-void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
+int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
+ int exitCommand = 1;
// processIDS.resize(0);
//loop through and create all the processes you want
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
+ exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
//force parent to wait until all the processes are done
int temp = processIDS[i];
wait(&temp);
}
+
+ return exitCommand;
#endif
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "createProcesses");
+ m->errorOut(e, "AlignCommand", "createProcesses");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "appendAlignFiles");
+ m->errorOut(e, "AlignCommand", "appendAlignFiles");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "appendReportFiles");
+ m->errorOut(e, "AlignCommand", "appendReportFiles");
exit(1);
}
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff