Add command to extract Neff scores for MSA (#647)

Add command to extract Neff scores for an MSA
soedinglab · Jan 30, 2023 · 4148e09 · 4148e09
1 parent a5d4965
commit 4148e09
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diff --git a/src/CommandDeclarations.h b/src/CommandDeclarations.h
@@ -86,6 +86,7 @@ extern int prefilter(int argc, const char **argv, const Command& command);
 extern int prefixid(int argc, const char **argv, const Command& command);
 extern int profile2cs(int argc, const char **argv, const Command& command);
 extern int profile2pssm(int argc, const char **argv, const Command& command);
+extern int profile2neff(int argc, const char **argv, const Command& command);
 extern int profile2consensus(int argc, const char **argv, const Command& command);
 extern int profile2repseq(int argc, const char **argv, const Command& command);
 extern int proteinaln2nucl(int argc, const char **argv, const Command& command);

diff --git a/src/MMseqsBase.cpp b/src/MMseqsBase.cpp
@@ -1087,6 +1087,13 @@ std::vector<Command> baseCommands = {
                 "<i:profileDB> <o:pssmFile>",
                 CITATION_MMSEQS2, {{"profileDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::profileDb },
                                                            {"pssmFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb }}},
+        {"profile2neff",         profile2neff,         &par.profile2neff,         COMMAND_PROFILE,
+                "Convert a profile DB to a tab-separated list of Neff scores",
+                NULL,
+                "Johannes Spies <[email protected]>",
+                "<I:profileDB> <o:neffFile>",
+                CITATION_MMSEQS2, {{"profileDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::profileDb },
+                                          {"neffFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb }}},
         {"profile2consensus",    profile2consensus,    &par.profile2seq,          COMMAND_PROFILE,
                 "Extract consensus sequence DB from a profile DB",
                 NULL,

diff --git a/src/commons/Parameters.h b/src/commons/Parameters.h
@@ -1111,6 +1111,7 @@ class Parameters {
     std::vector<MMseqsParameter*> renamedbkeys;
     std::vector<MMseqsParameter*> createtaxdb;
     std::vector<MMseqsParameter*> profile2pssm;
+    std::vector<MMseqsParameter*> profile2neff;
     std::vector<MMseqsParameter*> profile2seq;
     std::vector<MMseqsParameter*> besthitbyset;
     std::vector<MMseqsParameter*> combinepvalbyset;

diff --git a/src/util/CMakeLists.txt b/src/util/CMakeLists.txt
@@ -42,6 +42,7 @@ set(util_source_files
         util/pairaln.cpp
         util/prefixid.cpp
         util/profile2pssm.cpp
+        util/profile2neff.cpp
         util/profile2seq.cpp
         util/result2dnamsa.cpp
         util/result2flat.cpp

diff --git a/src/util/profile2neff.cpp b/src/util/profile2neff.cpp
@@ -0,0 +1,79 @@
+#include "Parameters.h"
+#include "DBReader.h"
+#include "DBWriter.h"
+#include "Util.h"
+#include "Debug.h"
+#include "Sequence.h"
+#include "SubstitutionMatrix.h"
+#include "itoa.h"
+
+#ifdef OPENMP
+#include <omp.h>
+#endif
+
+int profile2neff(int argc, const char **argv, const Command &command) {
+    Parameters &par = Parameters::getInstance();
+    par.parseParameters(argc, argv, command, true, 0, MMseqsParameter::COMMAND_PROFILE);
+
+    DBReader<unsigned int> reader(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA);
+    reader.open(DBReader<unsigned int>::LINEAR_ACCCESS);
+
+    const bool isDbOutput = par.dbOut;
+    const bool shouldCompress = isDbOutput == true && par.compressed == true;
+    const int dbType = isDbOutput == true ? Parameters::DBTYPE_GENERIC_DB : Parameters::DBTYPE_OMIT_FILE;
+    DBWriter writer(par.db2.c_str(), par.db2Index.c_str(), par.threads, shouldCompress, dbType);
+    writer.open();
+
+    SubstitutionMatrix subMat(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0f, 0.0);
+
+    size_t entries = reader.getSize();
+    Debug::Progress progress(entries);
+#pragma omp parallel
+    {
+        unsigned int thread_idx = 0;
+#ifdef OPENMP
+        thread_idx = static_cast<unsigned int>(omp_get_thread_num());
+#endif
+
+        Sequence seq(par.maxSeqLen, Parameters::DBTYPE_HMM_PROFILE, &subMat, 0, false, par.compBiasCorrection, false);
+
+        char buffer[256];
+        std::string result;
+        result.reserve(10 * 1024 * 1024);
+
+#pragma omp for schedule(dynamic, 1000)
+        for (size_t i = 0; i < entries; ++i) {
+            progress.updateProgress();
+
+            unsigned int key = reader.getDbKey(i);
+            seq.mapSequence(i, key, reader.getData(i, thread_idx), reader.getSeqLen(i));
+
+            if (isDbOutput == false) {
+                result.append("Neff_Ms of sequence ");
+                Itoa::u32toa_sse2(key, buffer);
+                result.append(buffer);
+                result.push_back('\n');
+            }
+
+            // add a line containing Neff_M scores of `seq`
+            for(int j = 0; j < seq.L; ++j) {
+                // TODO(johannes): Here, the precision for the floating point conversion is not specified and set to 2
+                // digits. Consider setting the precision using a commandline parameter.
+                snprintf(buffer, sizeof(buffer), "%0.4f", seq.neffM[j]);
+                result.append(buffer);
+                if(j < (seq.L - 1)) result.push_back('\t');
+            }
+            result.push_back('\n');
+
+            writer.writeData(result.c_str(), result.length(), key, thread_idx, isDbOutput);
+            result.clear();
+        }
+    }
+    writer.close(isDbOutput == false);
+    if (isDbOutput == false) {
+        remove(par.db2Index.c_str());
+    }
+    reader.close();
+
+    return EXIT_SUCCESS;
+}