Add ppos format-output to convertalis for count of positive substitution scores (#723)

Dohyun-s · web-flow · commit 5edc79bc35f0 · 2023-10-31T15:26:08.000+09:00
Co-authored-by: dohyun-s &lt;ts25&gt;
diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
@@ -102,7 +102,7 @@ Parameters::Parameters():
         PARAM_V(PARAM_V_ID, "-v", "Verbosity", "Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info", typeid(int), (void *) &verbosity, "^[0-3]{1}$", MMseqsParameter::COMMAND_COMMON),
         // convertalignments
         PARAM_FORMAT_MODE(PARAM_FORMAT_MODE_ID, "--format-mode", "Alignment format", "Output format:\n0: BLAST-TAB\n1: SAM\n2: BLAST-TAB + query/db length\n3: Pretty HTML\n4: BLAST-TAB + column headers\nBLAST-TAB (0) and BLAST-TAB + column headers (4) support custom output formats (--format-output)", typeid(int), (void *) &formatAlignmentMode, "^[0-4]{1}$"),
-        PARAM_FORMAT_OUTPUT(PARAM_FORMAT_OUTPUT_ID, "--format-output", "Format alignment output", "Choose comma separated list of output columns from: query,target,evalue,gapopen,pident,fident,nident,qstart,qend,qlen\ntstart,tend,tlen,alnlen,raw,bits,cigar,qseq,tseq,qheader,theader,qaln,taln,qframe,tframe,mismatch,qcov,tcov\nqset,qsetid,tset,tsetid,taxid,taxname,taxlineage,qorfstart,qorfend,torfstart,torfend", typeid(std::string), (void *) &outfmt, ""),
+        PARAM_FORMAT_OUTPUT(PARAM_FORMAT_OUTPUT_ID, "--format-output", "Format alignment output", "Choose comma separated list of output columns from: query,target,evalue,gapopen,pident,fident,nident,qstart,qend,qlen\ntstart,tend,tlen,alnlen,raw,bits,cigar,qseq,tseq,qheader,theader,qaln,taln,qframe,tframe,mismatch,qcov,tcov\nqset,qsetid,tset,tsetid,taxid,taxname,taxlineage,qorfstart,qorfend,torfstart,torfend,ppos", typeid(std::string), (void *) &outfmt, ""),
         PARAM_DB_OUTPUT(PARAM_DB_OUTPUT_ID, "--db-output", "Database output", "Return a result DB instead of a text file", typeid(bool), (void *) &dbOut, "", MMseqsParameter::COMMAND_EXPERT),
         // --include-only-extendablediagonal
         PARAM_RESCORE_MODE(PARAM_RESCORE_MODE_ID, "--rescore-mode", "Rescore mode", "Rescore diagonals with:\n0: Hamming distance\n1: local alignment (score only)\n2: local alignment\n3: global alignment\n4: longest alignment fulfilling window quality criterion", typeid(int), (void *) &rescoreMode, "^[0-4]{1}$"),
@@ -2828,6 +2828,7 @@ std::vector<int> Parameters::getOutputFormat(int formatMode, const std::string &
         else if (outformatSplit[i].compare("qorfend") == 0){ code = Parameters::OUTFMT_QORFEND;}
         else if (outformatSplit[i].compare("torfstart") == 0){ code = Parameters::OUTFMT_TORFSTART;}
         else if (outformatSplit[i].compare("torfend") == 0){ code = Parameters::OUTFMT_TORFEND;}
+        else if (outformatSplit[i].compare("ppos") == 0){ needSequences = true; needBacktrace = true; code = Parameters::OUTFMT_PPOS;}
         else if (outformatSplit[i].compare("empty") == 0){ code = Parameters::OUTFMT_EMPTY;}
         else {
             Debug(Debug::ERROR) << "Format code " << outformatSplit[i] << " does not exist.";
diff --git a/src/commons/Parameters.h b/src/commons/Parameters.h
@@ -182,6 +182,7 @@ class Parameters {
     static const int OUTFMT_TORFSTART = 37;
     static const int OUTFMT_TORFEND = 38;
     static const int OUTFMT_FIDENT = 39;
+    static const int OUTFMT_PPOS = 40;
 
     static const int INDEX_SUBSET_NORMAL = 0;
     static const int INDEX_SUBSET_NO_HEADERS = 1;
diff --git a/src/util/convertalignments.cpp b/src/util/convertalignments.cpp
@@ -636,6 +636,36 @@ int convertalignments(int argc, const char **argv, const Command &command) {
                                     case Parameters::OUTFMT_TORFEND:
                                         result.append(SSTR(res.dbOrfEndPos));
                                         break;
+                                    case Parameters::OUTFMT_PPOS: {
+                                        float pPositive = 0;
+                                        int matchCount = 0;
+                                        if (res.backtrace.empty() == false) {
+                                            int qPos = 0;
+                                            int tPos = 0;
+                                            for (size_t pos = 0; pos < res.backtrace.size(); pos++) {
+                                                switch (res.backtrace[pos]) {
+                                                    case 'M': {
+                                                        char qRes = queryProfile ? queryProfData[qPos] : querySeqData[qPos];
+                                                        char tRes = targetProfile ? targetProfData[tPos] : targetSeqData[tPos];
+                                                        pPositive += (subMat->subMatrix[subMat->aa2num[(int)qRes]][subMat->aa2num[(int)tRes]] > 0);
+                                                        matchCount += 1;
+                                                        qPos++;
+                                                        tPos++;
+                                                        break;
+                                                    }
+                                                    case 'D':
+                                                        qPos++;
+                                                        break;
+                                                    case 'I':
+                                                        tPos++;
+                                                        break;
+                                                }
+                                            }
+                                            pPositive /= matchCount;
+                                        }
+                                        result.append(SSTR(pPositive));
+                                        break;
+                                    }
                                 }
                                 if (i < outcodes.size() - 1) {
                                     result.push_back('\t');
