void DistanceDB::addSequence(Sequence seq) {
try {
//are the template sequences aligned
if (!isAligned(seq.getAligned())) {
templateAligned = false;
m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method.");
m->mothurOutEndLine();
}
if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
data.push_back(seq);
}
catch(exception& e) {
m->errorOut(e, "DistanceDB", "addSequence");
exit(1);
}
}
int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
try {
MPI_Status status;
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
for(int i=0;i<num;i++){
if (m->control_pressed) { return 1; }
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
delete buf4;
Sequence* candidateSeq = new Sequence(iss); m->gobble(iss);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
if (candidateSeq->getAligned().length() != templateSeqsLength) { //chimeracheck does not require seqs to be aligned
m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
}else{
//find chimeras
chimera->getChimeras(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 1; }
//print results
chimera->print(outMPI, outAccMPI);
}
}
delete candidateSeq;
//report progress
if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; }
}
//report progress
if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "driverMPI");
exit(1);
}
}
map<int, int> DeCalculator::trimSeqs(Sequence& query, vector<Sequence>& topMatches) {
try {
int frontPos = 0; //should contain first position in all seqs that is not a gap character
int rearPos = query.getAligned().length();
//********find first position in topMatches that is a non gap character***********//
//find first position all query seqs that is a non gap character
for (int i = 0; i < topMatches.size(); i++) {
string aligned = topMatches[i].getAligned();
int pos = 0;
//find first spot in this seq
for (int j = 0; j < aligned.length(); j++) {
if (isalpha(aligned[j])) {
pos = j;
break;
}
}
//save this spot if it is the farthest
if (pos > frontPos) { frontPos = pos; }
}
string aligned = query.getAligned();
int pos = 0;
//find first position in query that is a non gap character
for (int j = 0; j < aligned.length(); j++) {
if (isalpha(aligned[j])) {
pos = j;
break;
}
}
//save this spot if it is the farthest
if (pos > frontPos) { frontPos = pos; }
//********find last position in topMatches that is a non gap character***********//
for (int i = 0; i < topMatches.size(); i++) {
string aligned = topMatches[i].getAligned();
int pos = aligned.length();
//find first spot in this seq
for (int j = aligned.length()-1; j >= 0; j--) {
if (isalpha(aligned[j])) {
pos = j;
break;
}
}
//save this spot if it is the farthest
if (pos < rearPos) { rearPos = pos; }
}
aligned = query.getAligned();
pos = aligned.length();
//find last position in query that is a non gap character
for (int j = aligned.length()-1; j >= 0; j--) {
if (isalpha(aligned[j])) {
pos = j;
break;
}
}
//save this spot if it is the farthest
if (pos < rearPos) { rearPos = pos; }
map<int, int> trimmedPos;
//check to make sure that is not whole seq
if ((rearPos - frontPos - 1) <= 0) {
query.setAligned("");
//trim topMatches
for (int i = 0; i < topMatches.size(); i++) {
topMatches[i].setAligned("");
}
}else {
//trim query
string newAligned = query.getAligned();
newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
query.setAligned(newAligned);
//trim topMatches
for (int i = 0; i < topMatches.size(); i++) {
newAligned = topMatches[i].getAligned();
newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
topMatches[i].setAligned(newAligned);
}
for (int i = 0; i < newAligned.length(); i++) {
trimmedPos[i] = i+frontPos;
}
}
return trimmedPos;
}
catch(exception& e) {
m->errorOut(e, "DeCalculator", "trimSequences");
exit(1);
}
}
//***************************************************************************************************************
//gets closest matches to each end, since chimeras will most likely have different parents on each end
vector<Sequence> DeCalculator::findClosest(Sequence querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int numWanted, int minSim) {
try {
//indexes.clear();
vector<Sequence> seqsMatches;
vector<SeqDist> distsLeft;
vector<SeqDist> distsRight;
Dist* distcalculator = new eachGapDist();
string queryUnAligned = querySeq.getUnaligned();
int numBases = int(queryUnAligned.length() * 0.33);
string leftQuery = ""; //first 1/3 of the sequence
string rightQuery = ""; //last 1/3 of the sequence
string queryAligned = querySeq.getAligned();
//left side
bool foundFirstBase = false;
int baseCount = 0;
int leftSpot = 0;
int firstBaseSpot = 0;
for (int i = 0; i < queryAligned.length(); i++) {
//if you are a base
if (isalpha(queryAligned[i])) {
baseCount++;
if (!foundFirstBase) { foundFirstBase = true; firstBaseSpot = i; }
}
//eliminate opening .'s
if (foundFirstBase) { leftQuery += queryAligned[i]; }
//if you have 1/3
if (baseCount >= numBases) { leftSpot = i; break; } //first 1/3
}
//right side - count through another 1/3, so you are at last third
baseCount = 0;
int rightSpot = 0;
for (int i = leftSpot; i < queryAligned.length(); i++) {
//if you are a base
if (isalpha(queryAligned[i])) { baseCount++; }
//if you have 1/3
if (baseCount > numBases + 1) { rightSpot = i; break; } //last 1/3
}
//trim end
//find last position in query that is a non gap character
int lastBaseSpot = queryAligned.length()-1;
for (int j = queryAligned.length()-1; j >= 0; j--) {
if (isalpha(queryAligned[j])) {
lastBaseSpot = j;
break;
}
}
rightQuery = queryAligned.substr(rightSpot, (lastBaseSpot-rightSpot+1)); //sequence from pos spot to end
Sequence queryLeft(querySeq.getName(), leftQuery);
Sequence queryRight(querySeq.getName(), rightQuery);
//cout << querySeq->getName() << '\t' << leftSpot << '\t' << rightSpot << '\t' << firstBaseSpot << '\t' << lastBaseSpot << endl;
//cout << queryUnAligned.length() << '\t' << queryLeft.getUnaligned().length() << '\t' << queryRight.getUnaligned().length() << endl;
for(int j = 0; j < thisFilteredTemplate.size(); j++){
string dbAligned = thisFilteredTemplate[j]->getAligned();
string leftDB = dbAligned.substr(firstBaseSpot, (leftSpot-firstBaseSpot+1)); //first 1/3 of the sequence
string rightDB = dbAligned.substr(rightSpot, (lastBaseSpot-rightSpot+1)); //last 1/3 of the sequence
Sequence dbLeft(thisFilteredTemplate[j]->getName(), leftDB);
Sequence dbRight(thisFilteredTemplate[j]->getName(), rightDB);
distcalculator->calcDist(queryLeft, dbLeft);
float distLeft = distcalculator->getDist();
distcalculator->calcDist(queryRight, dbRight);
float distRight = distcalculator->getDist();
SeqDist subjectLeft;
subjectLeft.seq = NULL;
subjectLeft.dist = distLeft;
subjectLeft.index = j;
distsLeft.push_back(subjectLeft);
SeqDist subjectRight;
subjectRight.seq = NULL;
subjectRight.dist = distRight;
subjectRight.index = j;
distsRight.push_back(subjectRight);
}
delete distcalculator;
//sort by smallest distance
sort(distsRight.begin(), distsRight.end(), compareSeqDist);
sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
//merge results
map<string, string> seen;
map<string, string>::iterator it;
vector<SeqDist> dists;
float lastRight = distsRight[0].dist;
float lastLeft = distsLeft[0].dist;
float maxDist = 1.0 - (minSim / 100.0);
for (int i = 0; i < numWanted+1; i++) {
if (m->control_pressed) { return seqsMatches; }
//add left if you havent already
it = seen.find(thisTemplate[distsLeft[i].index]->getName());
if (it == seen.end() && distsLeft[i].dist <= maxDist) {
dists.push_back(distsLeft[i]);
seen[thisTemplate[distsLeft[i].index]->getName()] = thisTemplate[distsLeft[i].index]->getName();
lastLeft = distsLeft[i].dist;
// cout << "loop-left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
}
//add right if you havent already
it = seen.find(thisTemplate[distsRight[i].index]->getName());
if (it == seen.end() && distsRight[i].dist <= maxDist) {
dists.push_back(distsRight[i]);
seen[thisTemplate[distsRight[i].index]->getName()] = thisTemplate[distsRight[i].index]->getName();
lastRight = distsRight[i].dist;
// cout << "loop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
}
if (i == numWanted) { break; }
}
//are we still above the minimum similarity cutoff
if ((lastLeft >= minSim) || (lastRight >= minSim)) {
//add in ties from left
int i = numWanted;
while (i < distsLeft.size()) {
if (distsLeft[i].dist == lastLeft) { dists.push_back(distsLeft[i]); }
else { break; }
i++;
}
//add in ties from right
i = numWanted;
while (i < distsRight.size()) {
if (distsRight[i].dist == lastRight) { dists.push_back(distsRight[i]); }
else { break; }
i++;
}
}
//cout << numWanted << endl;
for (int i = 0; i < dists.size(); i++) {
// cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
if ((thisTemplate[dists[i].index]->getName() != querySeq.getName()) && (((1.0-dists[i].dist)*100) >= minSim)) {
Sequence temp(thisTemplate[dists[i].index]->getName(), thisTemplate[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
//cout << querySeq->getName() << '\t' << thisTemplate[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
seqsMatches.push_back(temp);
}
}
return seqsMatches;
}
catch(exception& e) {
m->errorOut(e, "DeCalculator", "findClosest");
exit(1);
}
}
//***************************************************************************************************************
vector<Sequence*> MothurChimera::readSeqs(string file) {
try {
vector<Sequence*> container;
int count = 0;
length = 0;
unaligned = false;
ReferenceDB* rdb = ReferenceDB::getInstance();
if (file == "saved") {
m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
Sequence* temp = new Sequence(rdb->referenceSeqs[i].getName(), rdb->referenceSeqs[i].getAligned());
if (count == 0) { length = temp->getAligned().length(); count++; } //gets first seqs length
else if (length != temp->getAligned().length()) { unaligned = true; }
if (temp->getName() != "") { container.push_back(temp); }
}
templateFileName = rdb->getSavedReference();
}else {
m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
ifstream in;
m->openInputFile(file, in);
//read in seqs and store in vector
while(!in.eof()){
if (m->control_pressed) { return container; }
Sequence* current = new Sequence(in); m->gobble(in);
if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
else if (length != current->getAligned().length()) { unaligned = true; }
if (current->getName() != "") {
container.push_back(current);
if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
}
}
in.close();
m->mothurOut("Done."); m->mothurOutEndLine();
filterString = (string(container[0]->getAligned().length(), '1'));
}
return container;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "readSeqs");
exit(1);
}
}
//**********************************************************************************************************************
int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
try {
ofstream alignmentFile;
m->openOutputFile(alignFName, alignmentFile);
ofstream accnosFile;
m->openOutputFile(accnosFName, accnosFile);
NastReport report(reportFName);
ifstream inFASTA;
m->openInputFile(filename, inFASTA);
inFASTA.seekg(filePos->start);
bool done = false;
int count = 0;
//moved this into driver to avoid deep copies in windows paralellized version
Alignment* alignment;
int longestBase = templateDB->getLongestBase();
if (m->debug) { m->mothurOut("[DEBUG]: template longest base = " + toString(templateDB->getLongestBase()) + " \n"); }
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 {
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);
}
while (!done) {
if (m->control_pressed) { break; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
report.setCandidate(candidateSeq);
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()+1 > alignment->getnRows()) {
if (m->debug) { m->mothurOut("[DEBUG]: " + candidateSeq->getName() + " " + toString(candidateSeq->getUnaligned().length()) + " " + toString(alignment->getnRows()) + " \n"); }
alignment->resize(candidateSeq->getUnaligned().length()+2);
}
Sequence temp = templateDB->findClosestSequence(candidateSeq);
Sequence* templateSeq = new Sequence(temp.getName(), temp.getAligned());
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();
if (m->debug) { m->mothurOut("[DEBUG]: flipping " + candidateSeq->getName() + " \n"); }
//rerun alignment
Sequence temp2 = templateDB->findClosestSequence(copy);
Sequence* templateSeq2 = new Sequence(temp2.getName(), temp2.getAligned());
if (m->debug) { m->mothurOut("[DEBUG]: closest template " + temp2.getName() + " \n"); }
searchScore = templateDB->getSearchScore();
nast2 = new Nast(alignment, copy, templateSeq2);
if (m->debug) { 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;
wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
}else{
wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
delete nast2;
delete templateSeq2;
delete copy;
}
if (m->debug) { m->mothurOut("[DEBUG]: done.\n"); }
}
//create accnos file with names
accnosFile << candidateSeq->getName() << wasBetter << endl;
}
report.setTemplate(templateSeq);
report.setSearchParameters(search, searchScore);
report.setAlignmentParameters(align, alignment);
report.setNastParameters(*nast);
alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
report.print();
delete nast;
delete templateSeq;
if (needToDeleteCopy) { delete copy; }
count++;
}
delete candidateSeq;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (inFASTA.eof()) { break; }
#endif
//report progress
if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count) + "\n"); }
}
//report progress
if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count) + "\n"); }
delete alignment;
alignmentFile.close();
inFASTA.close();
accnosFile.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "driver");
exit(1);
}
}
int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){
try {
ofstream out;
m->openOutputFile(outputFName, out);
ofstream out2;
m->openOutputFile(accnos, out2);
ifstream inFASTA;
m->openInputFile(filename, inFASTA);
inFASTA.seekg(filePos->start);
bool done = false;
int count = 0;
while (!done) {
if (m->control_pressed) { return 1; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
if (candidateSeq->getAligned().length() != templateSeqsLength) { //chimeracheck does not require seqs to be aligned
m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
}else{
//find chimeras
chimera->getChimeras(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 1; }
//print results
chimera->print(out, out2);
}
count++;
}
delete candidateSeq;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (inFASTA.eof()) { break; }
#endif
//report progress
if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
}
//report progress
if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
out.close();
out2.close();
inFASTA.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "driver");
exit(1);
}
}
int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long 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;
}
Alignment* alignment;
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 {
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);
}
for(int i=0;i<num;i++){
if (m->control_pressed) { delete alignment; 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);
report.setCandidate(candidateSeq);
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;
wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
}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.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);
}
}
//**********************************************************************************************************************
void alignDriver(alignStruct* params) {
try {
NastReport 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;
//moved this into driver to avoid deep copies in windows paralellized version
Alignment* alignment;
int longestBase = params->templateDB->getLongestBase();
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: template longest base = " + toString(longestBase) + " \n"); }
if(params->alignMethod == "gotoh") { alignment = new GotohOverlap(params->gapOpen, params->gapExtend, params->match, params->misMatch, longestBase); }
else if(params->alignMethod == "needleman") { alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, longestBase); }
else if(params->alignMethod == "blast") { alignment = new BlastAlignment(params->gapOpen, params->gapExtend, params->match, params->misMatch); }
else if(params->alignMethod == "noalign") { alignment = new NoAlign(); }
else {
params->m->mothurOut(params->alignMethod + " is not a valid alignment option. I will run the command using needleman.");
params->m->mothurOutEndLine();
alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, longestBase);
}
while (!done) {
if (params->m->getControl_pressed()) { break; }
Sequence* candidateSeq = new Sequence(inFASTA); params->util.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 > alignment->getnRows()) {
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + candidateSeq->getName() + " " + toString(candidateSeq->getUnaligned().length()) + " " + toString(alignment->getnRows()) + " \n"); }
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(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++;
string wasBetter = "";
//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(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;
wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
numFlipped_0++;
}else{
wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
delete nast2;
delete templateSeq2;
delete copy;
}
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: done.\n"); }
}
//create accnos file with names
params->accnosWriter->write(candidateSeq->getName() + wasBetter + "\n");
}
report.setTemplate(templateSeq);
report.setSearchParameters(params->search, searchScore);
report.setAlignmentParameters(params->alignMethod, alignment);
report.setNastParameters(*nast);
params->alignWriter->write('>' + candidateSeq->getName() + '\n' + candidateSeq->getAligned() + '\n');
params->reportWriter->write(report.getReport());
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;
delete alignment;
inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "AlignCommand", "driver");
exit(1);
}
}
//**********************************************************************************************************************
string ChopSeqsCommand::getChopped(Sequence seq, string& qualValues) {
try {
string temp = seq.getAligned();
string tempUnaligned = seq.getUnaligned();
if (countGaps) {
//if needed trim sequence
if (keep == "front") {//you want to keep the beginning
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (!keepN) { if (toupper(temp[i]) == 'N') { temp[i] = '.'; } }
numBasesCounted++;
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
}
}else { //you are keeping the back
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
if (!keepN) { if (toupper(temp[i]) == 'N') { temp[i] = '.'; } }
numBasesCounted++;
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot+1); }
}else {
if (!Short) { temp = ""; } //sequence too short
}
}
}else{
//if needed trim sequence
if (keep == "front") {//you want to keep the beginning
int tempLength = tempUnaligned.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (!keepN) {
if (toupper(temp[i]) == 'N') {
temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if(isalpha(temp[i])) { numBasesCounted++; }
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot+1); }
qualValues = seq.getName() +'\t' + toString(0) + '\t' + toString(stopSpot+1) + '\n';
}else {
if (!Short) { temp = ""; qualValues = seq.getName() +'\t' + toString(0) + '\t' + toString(0) + '\n'; } //sequence too short
else { qualValues = seq.getName() +'\t' + toString(0) + '\t' + toString(tempLength) + '\n'; }
}
}else { //you are keeping the back
int tempLength = tempUnaligned.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
if (!keepN) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if(isalpha(temp[i])) { numBasesCounted++; }
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot); }
qualValues = seq.getName() +'\t' + toString(stopSpot) + '\t' + toString(temp.length()-1) + '\n';
}else {
if (!Short) { temp = ""; qualValues = seq.getName() +'\t' + toString(0) + '\t' + toString(0) + '\n'; } //sequence too short
else { qualValues = seq.getName() +'\t' + toString(0) + '\t' + toString(tempLength) + '\n'; }
}
}
}
return temp;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "getChopped");
exit(1);
}
}
