Rebuild foldseek createclusearch workflow in clusterdb

soedinglab · Feb 7, 2025 · 56a7f5f · 56a7f5f
1 parent 886bc67
commit 56a7f5f
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Showing 2 changed files with 84 additions and 2 deletions.
diff --git a/data/clusterdb.sh b/data/clusterdb.sh
@@ -3,6 +3,11 @@
 [ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
 [ "$#" -ne 2 ] && echo "Please provide <inputDB> <tmpDir>" && exit 1
 
+fail() {
+    echo "Error: $1"
+    exit 1
+}
+
 notExists() {
 	[ ! -f "$1" ]
 }
@@ -24,10 +29,69 @@ if [ -n "${USE_FOLDSEEK}" ]; then
             || fail "foldseek cluster failed"
     fi
 
+    if notExists "${IN}_clu_seq.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" cpdb "${IN}" "${IN}_clu_seq" ${VERBOSITY}
+    fi
+
+    if notExists "${IN}_clu_seq_h.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" cpdb "${IN}_h" "${IN}_clu_seq_h" ${VERBOSITY}
+    fi
+
+    if notExists "${IN}_clu_seq_ss.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" cpdb "${IN}_ss" "${IN}_clu_seq_ss" ${VERBOSITY}
+    fi
+
+    if [ -f "${IN}_ca.dbtype" ] && notExists "${IN}_clu_seq_ca.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" cpdb "${IN}_ca" "${IN}_clu_seq_ca" ${VERBOSITY}
+    fi
+
+    if notExists "${IN}_clu_clu.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" cpdb ${TMP_PATH}/cluster_foldseek "${IN}_clu_clu" ${VERBOSITY}
+    fi
+
+    if [ -f "${IN}_clu_seq_ca.dbtype" ] && notExists "${IN}_clu_ca.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" createsubdb ${TMP_PATH}/cluster_foldseek "${IN}_clu_seq_ca" "${IN}_clu_ca" ${VERBOSITY}
+    fi
+
+    if notExists "${IN}_clu_aln.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" structurealign  "${IN}_clu_seq" "${IN}_clu_seq" "${TMP_PATH}/cluster_foldseek" "${IN}_clu_aln" -a -e 0.1 --sort-by-structure-bits 0 ${MERGECLU_PAR}
+    fi
+
+    if notExists "${IN}_clu_profile.dbtype"; then
+        # shellcheck disable=SC2086
+        "${MMSEQS}" result2profile  "${IN}_clu_seq" "${IN}_clu_seq" "${IN}_clu_aln" "${IN}_clu_profile" ${PROFILE_PAR}
+    fi
+
     if notExists "${IN}_clu.dbtype"; then
         # shellcheck disable=SC2086
-        "${FOLDSEEK}" createclusearchdb "${IN}" "${TMP_PATH}/cluster_foldseek" "${IN}_clu" ${THREADS_PAR} \
-            || fail "foldseek createclusearchdb failed"
+        "${FOLDSEEK}" profile2consensus "${IN}_clu_profile" "${IN}_clu" ${MERGECLU_PAR}
+        if [ -n "$REMOVE_TMP" ]; then
+            # shellcheck disable=SC2086
+            "${FOLDSEEK}" rmdb "${IN}_clu_profile" ${VERBOSITY}
+        fi
+    fi
+
+    if notExists "${IN}_clu_profile_ss.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" result2profile  "${IN}_clu_seq_ss" "${IN}_clu_seq_ss" "${IN}_clu_aln" "${IN}_clu_profile_ss" ${PROFILE_SS_PAR}
+    fi
+
+    if notExists "${IN}_clu_ss.dbtype"; then
+        # shellcheck disable=SC2086
+        "${FOLDSEEK}" profile2consensus "${IN}_clu_profile_ss" "${IN}_clu_ss" ${MERGECLU_PAR}
+        if [ -n "$REMOVE_TMP" ]; then
+            # shellcheck disable=SC2086
+            "${FOLDSEEK}" rmdb "${IN}_clu_profile_ss" ${VERBOSITY}
+            # shellcheck disable=SC2086
+            "${FOLDSEEK}" rmdb "${IN}_clu_aln" ${VERBOSITY}
+        fi
     fi
 else
     if notExists "${TMP_PATH}/cluster_mmseqs.dbtype"; then

diff --git a/src/workflow/clusterdb.cpp b/src/workflow/clusterdb.cpp
@@ -62,9 +62,27 @@ int clusterdb(int argc, const char **argv, const Command &command) {
     cmd.addVariable("USE_FOLDSEEK", useFoldseek ? "TRUE" : NULL);
     cmd.addVariable("CLUSTER_PAR", par.createParameterString(par.clusterworkflow).c_str());
     cmd.addVariable("CONSENSUS_PAR", par.createParameterString(par.profile2seq).c_str());
+    cmd.addVariable("PROFILE_PAR", par.createParameterString(par.result2profile).c_str());
     cmd.addVariable("THREADS_PAR", par.createParameterString(par.onlythreads).c_str());
     cmd.addVariable("VERBOSITY", par.createParameterString(par.onlyverbosity).c_str());
     cmd.addVariable("MERGECLU_PAR", par.createParameterString(par.threadsandcompression).c_str());
+    par.pca = 1.4;
+    par.pcb = 1.5;
+    par.scoringMatrixFile = "3di.out";
+    par.seedScoringMatrixFile = "3di.out";
+    par.maskProfile = 0;
+    par.compBiasCorrection = 0;
+    if(par.PARAM_E_PROFILE.wasSet == false){
+        par.evalProfile = 0.1;
+        par.evalThr = 0.1;
+    }
+    std::vector<MMseqsParameter*> result2profile_ss;
+    for (size_t i = 0; i < par.result2profile.size(); i++) {
+        if (par.result2profile[i]->uniqid != par.PARAM_GAP_PSEUDOCOUNT.uniqid) {
+            result2profile_ss.push_back(par.result2profile[i]);
+        }
+    }
+    cmd.addVariable("PROFILE_SS_PAR", par.createParameterString(result2profile_ss).c_str());
 
     FileUtil::writeFile(tmpDir + "/clusterdb.sh", clusterdb_sh, clusterdb_sh_len);
     std::string program(tmpDir + "/clusterdb.sh");