Add --complex-report-mode to allow disabling report in easy-scorecomplex

steineggerlab · Nov 23, 2023 · 79f865d · 79f865d
1 parent 38290cf
commit 79f865d
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Showing 4 changed files with 12 additions and 4 deletions.
diff --git a/data/easycomplexsearch.sh b/data/easycomplexsearch.sh
@@ -42,9 +42,11 @@ fi
 "$MMSEQS" convertalis "${QUERY}" "${TARGET}" "${TMP_PATH}/result2" "${OUTPUT}" ${CONVERT_PAR} \
     || fail "Convert Alignments died"
 
-# shellcheck disable=SC2086
-"$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${TMP_PATH}/result2" "${OUTPUT}_report" ${REPORT_PAR} \
-    || fail "createcomplexreport died"
+if [ -z "${NO_REPORT}" ]; then
+    # shellcheck disable=SC2086
+    "$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${TMP_PATH}/result2" "${OUTPUT}_report" ${REPORT_PAR} \
+        || fail "createcomplexreport died"
+fi
 
 if [ -n "${REMOVE_TMP}" ]; then
     # shellcheck disable=SC2086

diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -25,7 +25,8 @@ LocalParameters::LocalParameters() :
         PARAM_CLUSTER_SEARCH(PARAM_CLUSTER_SEARCH_ID, "--cluster-search", "Cluster search", "first find representative then align all cluster members", typeid(int), (void *) &clusterSearch, "^[0-1]{1}$",MMseqsParameter::COMMAND_MISC),
         PARAM_FILE_INCLUDE(PARAM_FILE_INCLUDE_ID, "--file-include", "File Inclusion Regex", "Include file names based on this regex", typeid(std::string), (void *) &fileInclude, "^.*$"),
         PARAM_FILE_EXCLUDE(PARAM_FILE_EXCLUDE_ID, "--file-exclude", "File Exclusion Regex", "Exclude file names based on this regex", typeid(std::string), (void *) &fileExclude, "^.*$"),
-        PARAM_INDEX_EXCLUDE(PARAM_INDEX_EXCLUDE_ID, "--index-exclude", "Index Exclusion", "Exclude parts of the index:\n0: Full index\n1: Exclude k-mer index (for use with --prefilter-mode 1)\n2: Exclude C-alpha coordinates (for use with --sort-by-structure-bits 0)\nFlags can be combined bit wise", typeid(int), (void *) &indexExclude, "^[0-3]{1}$", MMseqsParameter::COMMAND_EXPERT)
+        PARAM_INDEX_EXCLUDE(PARAM_INDEX_EXCLUDE_ID, "--index-exclude", "Index Exclusion", "Exclude parts of the index:\n0: Full index\n1: Exclude k-mer index (for use with --prefilter-mode 1)\n2: Exclude C-alpha coordinates (for use with --sort-by-structure-bits 0)\nFlags can be combined bit wise", typeid(int), (void *) &indexExclude, "^[0-3]{1}$", MMseqsParameter::COMMAND_EXPERT),
+        PARAM_COMPLEX_REPORT_MODE(PARAM_COMPLEX_REPORT_MODE_ID, "--complex-report-mode", "Complex report mode", "Complex report mode:\n0: No report\n1: Write complex report", typeid(int), (void *) &complexReportMode, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT)
 {
     PARAM_ALIGNMENT_MODE.description = "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id";
     PARAM_ALIGNMENT_MODE.regex = "^[0-3]{1}$";
@@ -180,6 +181,7 @@ LocalParameters::LocalParameters() :
     easyscorecomplexworkflow = combineList(easyscorecomplexworkflow, scorecomplex);
     easyscorecomplexworkflow = combineList(easyscorecomplexworkflow, convertalignments);
     easyscorecomplexworkflow = combineList(easyscorecomplexworkflow, createcomplexreport);
+    easyscorecomplexworkflow.push_back(&PARAM_COMPLEX_REPORT_MODE);
 
     prefMode = PREF_MODE_KMER;
     alignmentType = ALIGNMENT_TYPE_3DI_AA;
@@ -203,6 +205,7 @@ LocalParameters::LocalParameters() :
     fileExclude = "^$";
     dbSuffixList = "_h,_ss,_ca";
     indexExclude = 0;
+    complexReportMode = 1;
     citations.emplace(CITATION_FOLDSEEK, "van Kempen, M., Kim, S.S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C.L.M., Söding, J., and Steinegger, M. Fast and accurate protein structure search with Foldseek. Nature Biotechnology, doi:10.1038/s41587-023-01773-0 (2023)");
 
     //rewrite param vals.

diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
@@ -109,6 +109,7 @@ class LocalParameters : public Parameters {
     PARAMETER(PARAM_FILE_INCLUDE)
     PARAMETER(PARAM_FILE_EXCLUDE)
     PARAMETER(PARAM_INDEX_EXCLUDE)
+    PARAMETER(PARAM_COMPLEX_REPORT_MODE)
 
     int prefMode;
     float tmScoreThr;
@@ -127,6 +128,7 @@ class LocalParameters : public Parameters {
     std::string fileInclude;
     std::string fileExclude;
     int indexExclude;
+    int complexReportMode;
 
     static std::vector<int> getOutputFormat(int formatMode, const std::string &outformat, bool &needSequences, bool &needBacktrace, bool &needFullHeaders,
                                             bool &needLookup, bool &needSource, bool &needTaxonomyMapping, bool &needTaxonomy, bool &needQCa, bool &needTCa, bool &needTMaligner,

diff --git a/src/workflow/EasyComplexSearch.cpp b/src/workflow/EasyComplexSearch.cpp
@@ -70,6 +70,7 @@ int easycomplexsearch(int argc, const char **argv, const Command &command) {
     tmpDir = FileUtil::createTemporaryDirectory(tmpDir, hash);
     par.filenames.pop_back();
     CommandCaller cmd;
+    cmd.addVariable("NO_REPORT", par.complexReportMode == 0 ? "TRUE" : NULL);
     cmd.addVariable("TMP_PATH", tmpDir.c_str());
     cmd.addVariable("OUTPUT", par.filenames.back().c_str());
     par.filenames.pop_back();