Introduce experimental a3m filtering module (hidden by default)

soedinglab · Apr 11, 2023 · 167bbd1 · 167bbd1
1 parent 10e0f1b
commit 167bbd1
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diff --git a/src/CommandDeclarations.h b/src/CommandDeclarations.h
@@ -54,6 +54,7 @@ extern int extractalignedregion(int argc, const char **argv, const Command& comm
 extern int extractdomains(int argc, const char **argv, const Command& command);
 extern int extractorfs(int argc, const char **argv, const Command& command);
 extern int extractframes(int argc, const char **argv, const Command& command);
+extern int filtera3m(int argc, const char **argv, const Command& command);
 extern int filterdb(int argc, const char **argv, const Command& command);
 extern int filterresult(int argc, const char **argv, const Command& command);
 extern int gff2db(int argc, const char **argv, const Command& command);

diff --git a/src/MMseqsBase.cpp b/src/MMseqsBase.cpp
@@ -979,6 +979,13 @@ std::vector<Command> baseCommands = {
                                           {"targetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
                                           {"resultDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::allDb },
                                           {"statsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb }}},
+        {"filtera3m",            filtera3m,            &par.filtera3m,            COMMAND_HIDDEN,
+                "DB filtering by given conditions",
+                "",
+                "Milot Mirdita <[email protected]>",
+                "<i:a3mFile> <o:a3mFile>",
+                CITATION_MMSEQS2, {{"a3mFile", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfileAndStdin },
+                                          {"a3mFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile }}},
         {"filterresult",         filterresult,         &par.filterresult,         COMMAND_RESULT,
                 "Pairwise alignment result filter",
                 NULL,

diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
@@ -584,6 +584,19 @@ Parameters::Parameters():
     //result2msa.push_back(&PARAM_FIRST_SEQ_REP_SEQ);
     result2dnamsa.push_back(&PARAM_V);
 
+
+    // filtera3m
+    filtera3m.push_back(&PARAM_SUB_MAT);
+    filtera3m.push_back(&PARAM_GAP_OPEN);
+    filtera3m.push_back(&PARAM_GAP_EXTEND);
+    filtera3m.push_back(&PARAM_FILTER_MIN_ENABLE);
+    filtera3m.push_back(&PARAM_FILTER_MAX_SEQ_ID);
+    filtera3m.push_back(&PARAM_FILTER_QID);
+    filtera3m.push_back(&PARAM_FILTER_QSC);
+    filtera3m.push_back(&PARAM_FILTER_COV);
+    filtera3m.push_back(&PARAM_FILTER_NDIFF);
+    filtera3m.push_back(&PARAM_V);
+
     // filterresult
     filterresult.push_back(&PARAM_SUB_MAT);
     filterresult.push_back(&PARAM_GAP_OPEN);

diff --git a/src/commons/Parameters.h b/src/commons/Parameters.h
@@ -1039,6 +1039,7 @@ class Parameters {
     std::vector<MMseqsParameter*> result2profile;
     std::vector<MMseqsParameter*> result2msa;
     std::vector<MMseqsParameter*> result2dnamsa;
+    std::vector<MMseqsParameter*> filtera3m;
     std::vector<MMseqsParameter*> filterresult;
     std::vector<MMseqsParameter*> convertmsa;
     std::vector<MMseqsParameter*> msa2profile;

diff --git a/src/util/CMakeLists.txt b/src/util/CMakeLists.txt
@@ -27,6 +27,7 @@ set(util_source_files
         util/extractorfs.cpp
         util/orftocontig.cpp
         util/touchdb.cpp
+        util/filtera3m.cpp
         util/filterdb.cpp
         util/gff2db.cpp
         util/renamedbkeys.cpp

diff --git a/src/util/filtera3m.cpp b/src/util/filtera3m.cpp
@@ -0,0 +1,104 @@
+#include "Debug.h"
+#include "Util.h"
+#include "FileUtil.h"
+#include "KSeqWrapper.h"
+#include "MsaFilter.h"
+#include "MultipleAlignment.h"
+
+MultipleAlignment::MSAResult readMSA(const std::string &a3mPath) {
+    KSeqWrapper* kseq = KSeqFactory(a3mPath.c_str());
+    MultipleAlignment::MSAResult msa(0, 0, 0, NULL);
+    msa.msaSequenceLength = 0;
+    msa.centerLength = 0;
+    msa.setSize = 0;
+    std::vector<std::string> sequences;
+    std::string seq;
+    Debug::Progress progress;
+    while (kseq->ReadEntry()) {
+        progress.updateProgress();
+        const KSeqWrapper::KSeqEntry &e = kseq->entry;
+        seq.reserve(e.sequence.l);
+        if (msa.setSize == 0) {
+            msa.msaSequenceLength = e.sequence.l;
+            msa.centerLength = e.sequence.l;
+        }
+
+        for (size_t i = 0; i < e.sequence.l; i++) {
+            char c = e.sequence.s[i];
+            if (!(c >= 'a' && c <= 'z')) {
+                seq.push_back(c);
+            }
+        }
+        sequences.push_back(seq);
+        seq.clear();
+        msa.setSize++;
+    }
+    msa.msaSequence = new char*[msa.setSize];
+    for (size_t i = 0; i < msa.setSize; i++) {
+        msa.msaSequence[i] = &(sequences[i])[0];
+    }
+    delete kseq;
+    return msa;
+}
+
+int filtera3m(int argc, const char **argv, const Command& command) {
+    Parameters &par = Parameters::getInstance();
+    par.parseParameters(argc, argv, command, true, 0, 0);
+
+    std::vector<std::string> qid_str_vec = Util::split(par.qid, ",");
+    std::vector<int> qid_vec;
+    for (size_t qid_idx = 0; qid_idx < qid_str_vec.size(); qid_idx++) {
+        float qid_float = strtod(qid_str_vec[qid_idx].c_str(), NULL);
+        qid_vec.push_back(static_cast<int>(qid_float*100));
+    }
+    std::sort(qid_vec.begin(), qid_vec.end());
+
+    MultipleAlignment::MSAResult msa = readMSA(par.db1.c_str());
+    FILE* handle = FileUtil::openFileOrDie(par.db2.c_str(), "w", false);
+
+    SubstitutionMatrix subMat(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0f, -0.2f);
+    MsaFilter filter(msa.centerLength + 1, msa.setSize, &subMat, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid());
+    filter.filter(
+        msa.setSize,
+        msa.centerLength,
+        static_cast<int>(par.covMSAThr * 100),
+        qid_vec,
+        par.qsc,
+        static_cast<int>(par.filterMaxSeqId * 100),
+        par.Ndiff,
+        par.filterMinEnable,
+        (const char **) msa.msaSequence,
+        false
+    );
+    bool* kept = new bool[msa.setSize];
+    filter.getKept(kept, msa.setSize);
+
+    KSeqWrapper* kseq2 = KSeqFactory(par.db1.c_str());
+    size_t i = 0;
+    while (kseq2->ReadEntry()) {
+        if (kept[i] == false) {
+            i++;
+            continue;
+        }
+        fwrite(">", sizeof(char), 1, handle);
+        fwrite(kseq2->entry.name.s, sizeof(char), kseq2->entry.name.l, handle);
+        if (kseq2->entry.comment.l > 0) {
+            fwrite(" ", sizeof(char), 1, handle);
+            fwrite(kseq2->entry.comment.s, sizeof(char), kseq2->entry.comment.l, handle);
+        }
+        fwrite("\n", sizeof(char), 1, handle);
+        fwrite(kseq2->entry.sequence.s, sizeof(char), kseq2->entry.sequence.l, handle);
+        fwrite("\n", sizeof(char), 1, handle);
+        i++;
+    }
+    if (fclose(handle) != 0) {
+        Debug(Debug::ERROR) << "Cannot close file " << par.db2 << "\n";
+        return EXIT_FAILURE;
+    }
+
+    delete kseq2;
+    delete[] kept;
+    delete[] msa.msaSequence;
+
+    return EXIT_SUCCESS;
+}