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Add nucleotide database support to result2msa #1084

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3df5eab
Advance util/regression submodule commit
antonvnv Mar 6, 2026
e23cfb4
Add nucleotide database support to result2msa
antonvnv Mar 6, 2026
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64 changes: 44 additions & 20 deletions src/util/result2msa.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
#include "DBConcat.h"
#include "HeaderSummarizer.h"
#include "CompressedA3M.h"
#include "NucleotideMatrix.h"

#ifdef OPENMP
#include <omp.h>
Expand Down Expand Up @@ -128,8 +129,19 @@ int result2msa(int argc, const char **argv, const Command &command) {
size_t maxSetSize = resultReader.maxCount('\n') + 1;

// adjust score of each match state by -0.2 to trim alignment
SubstitutionMatrix subMat(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0f, -0.2f);
EvalueComputation evalueComputation(tDbr->getAminoAcidDBSize(), &subMat, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid());
bool isNucl = Parameters::isEqualDbtype(tDbr->getDbtype(), Parameters::DBTYPE_NUCLEOTIDES);
SubstitutionMatrix *subMat;
int gapOpen, gapExtend;
if (isNucl) {
subMat = new NucleotideMatrix(par.scoringMatrixFile.values.nucleotide().c_str(), 1.0f, -0.2f);
gapOpen = par.gapOpen.values.nucleotide();
gapExtend = par.gapExtend.values.nucleotide();
} else {
subMat = new SubstitutionMatrix(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0f, -0.2f);
gapOpen = par.gapOpen.values.aminoacid();
gapExtend = par.gapExtend.values.aminoacid();
}
EvalueComputation evalueComputation(tDbr->getAminoAcidDBSize(), subMat, gapOpen, gapExtend);
if (qDbr->getDbtype() == -1 || tDbr->getDbtype() == -1) {
Debug(Debug::ERROR) << "Please recreate your database or add a .dbtype file to your sequence/profile database\n";
return EXIT_FAILURE;
Expand All @@ -150,20 +162,20 @@ int result2msa(int argc, const char **argv, const Command &command) {
thread_idx = (unsigned int) omp_get_thread_num();
#endif

Matcher matcher(qDbr->getDbtype(), maxSequenceLength, &subMat, &evalueComputation, par.compBiasCorrection,
par.compBiasCorrectionScale, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid(), 0.0, par.zdrop);
MultipleAlignment aligner(maxSequenceLength, &subMat);
Matcher matcher(qDbr->getDbtype(), maxSequenceLength, subMat, &evalueComputation, par.compBiasCorrection,
par.compBiasCorrectionScale, gapOpen, gapExtend, 0.0, par.zdrop);
MultipleAlignment aligner(maxSequenceLength, subMat);
PSSMCalculator calculator(
&subMat, maxSequenceLength, maxSetSize, par.pcmode, par.pca, par.pcb
subMat, maxSequenceLength, maxSetSize, par.pcmode, par.pca, par.pcb
#ifdef GAP_POS_SCORING
, par.gapOpen.values.aminoacid()
, gapOpen
, par.gapPseudoCount
#endif
);
MsaFilter filter(maxSequenceLength, maxSetSize, &subMat, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid());
MsaFilter filter(maxSequenceLength, maxSetSize, subMat, gapOpen, gapExtend);
UniprotHeaderSummarizer summarizer;
Sequence centerSequence(maxSequenceLength, qDbr->getDbtype(), &subMat, 0, false, par.compBiasCorrection);
Sequence edgeSequence(maxSequenceLength, tDbr->getDbtype(), &subMat, 0, false, false);
Sequence centerSequence(maxSequenceLength, qDbr->getDbtype(), subMat, 0, false, par.compBiasCorrection);
Sequence edgeSequence(maxSequenceLength, tDbr->getDbtype(), subMat, 0, false, false);

// which sequences where kept after filtering
bool *kept = new bool[maxSetSize];
Expand Down Expand Up @@ -244,15 +256,26 @@ int result2msa(int argc, const char **argv, const Command &command) {
seqKeys.emplace_back(key);

const size_t columns = Util::getWordsOfLine(data, entry, 255);
bool hasBt = (columns == Matcher::ALN_RES_WITH_BT_COL_CNT || columns == Matcher::ALN_RES_WITH_ORF_AND_BT_COL_CNT);
if (columns > Matcher::ALN_RES_WITHOUT_BT_COL_CNT) {
alnResults.emplace_back(Matcher::parseAlignmentRecord(data));
} else {
// Recompute if not all the backtraces are present
}
if (!hasBt) {
if (isQueryInit == false) {
matcher.initQuery(&centerSequence);
isQueryInit = true;
}
alnResults.emplace_back(matcher.getSWResult(&edgeSequence, INT_MAX, false, 0, 0.0, FLT_MAX, Matcher::SCORE_COV_SEQID, 0, false));
if (columns <= Matcher::ALN_RES_WITHOUT_BT_COL_CNT) {
// No parsed result — recompute from scratch
alnResults.emplace_back(matcher.getSWResult(&edgeSequence, INT_MAX, false, 0, 0.0, FLT_MAX, Matcher::SCORE_COV_SEQID, 0, false));
} else {
// Parsed result exists but backtrace is missing — recompute using diagonal from parsed result
Matcher::result_t &parsed = alnResults.back();
bool isReverse = (parsed.qStartPos > parsed.qEndPos);
int diagonal = parsed.dbStartPos - parsed.qStartPos;
Matcher::result_t recomputed = matcher.getSWResult(&edgeSequence, diagonal, isReverse, 0, 0.0, FLT_MAX, Matcher::SCORE_COV_SEQID, 0, false);
parsed.backtrace = recomputed.backtrace;
}
}
data = Util::skipLine(data);
}
Expand Down Expand Up @@ -326,7 +349,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
// need to allow insertion in the centerSequence
for (size_t pos = 0; pos < res.centerLength; pos++) {
char aa = res.msaSequence[i][pos];
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat.num2aa[(int) aa] : '-'));
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat->num2aa[(int) aa] : '-'));
}
result.append(1, '\n');
}
Expand Down Expand Up @@ -382,7 +405,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
// need to allow insertion in the centerSequence
for (size_t pos = 0; pos < res.centerLength; pos++) {
char aa = res.msaSequence[i][pos];
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat.num2aa[(int) aa] : '-'));
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat->num2aa[(int) aa] : '-'));
}
result.append(1, '\n');
}
Expand Down Expand Up @@ -437,7 +460,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
if(i == 0){
for (size_t pos = 0; pos < res.centerLength; pos++) {
char aa = res.msaSequence[i][pos];
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat.num2aa[(int) aa] : '-'));
result.append(1, ((aa < MultipleAlignment::GAP) ? subMat->num2aa[(int) aa] : '-'));
}
result.append(1, '\n');
}else{
Expand All @@ -453,7 +476,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
if(aa>=MultipleAlignment::GAP){
result.push_back('-');
}else if(aa<MultipleAlignment::GAP){
result.push_back( subMat.num2aa[(int) aa]);
result.push_back( subMat->num2aa[(int) aa]);
btPos++;
seqPos++;
}
Expand All @@ -462,7 +485,7 @@ int result2msa(int argc, const char **argv, const Command &command) {

// add lower case deletions
while(btPos < bt.size() && bt[btPos] == 'D') {
result.push_back(tolower(subMat.num2aa[seq[seqStartPos+seqPos]]));
result.push_back(tolower(subMat->num2aa[seq[seqStartPos+seqPos]]));
btPos++;
seqPos++;
}
Expand Down Expand Up @@ -492,15 +515,15 @@ int result2msa(int argc, const char **argv, const Command &command) {
result.append(">consensus_");
result.append(centerSequenceHeader, centerHeaderLength);
for (int pos = 0; pos < centerSequence.L; pos++) {
result.push_back(subMat.num2aa[pssmRes.consensus[pos]]);
result.push_back(subMat->num2aa[pssmRes.consensus[pos]]);
}
result.append("\n;");
} else {
result.append(1, '>');
result.append(centerSequenceHeader, centerHeaderLength);
// Retrieve the master sequence
for (int pos = 0; pos < centerSequence.L; pos++) {
result.push_back(subMat.num2aa[centerSequence.numSequence[pos]]);
result.push_back(subMat->num2aa[centerSequence.numSequence[pos]]);
}
result.append("\n;");
}
Expand Down Expand Up @@ -559,6 +582,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
if (seqConcat != NULL) {
delete seqConcat;
}
delete subMat;

#ifdef HAVE_MPI
MPI_Barrier(MPI_COMM_WORLD);
Expand Down
2 changes: 1 addition & 1 deletion util/regression
Open in desktop
Submodule regression updated 2 files
+94 −0 regression/run_nuclnucl_result2msa.sh
+1 −0 run_regression.sh
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