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implement complexsearch and sanitizing expandcomplex
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| #!/bin/sh -e | ||
| fail() { | ||
| echo "Error: $1" | ||
| exit 1 | ||
| } | ||
|
|
||
| notExists() { | ||
| [ ! -f "$1" ] | ||
| } | ||
|
|
||
| if notExists "${TMP_PATH}/result.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" search "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result" "${TMP_PATH}/search_tmp" ${SEARCH_PAR} \ | ||
| || fail "Search died" | ||
| fi | ||
|
|
||
| RESULT="${TMP_PATH}/result" | ||
| if [ "$PREFMODE" != "EXHAUSTIVE" ]; then | ||
| if notExists "${TMP_PATH}/result_expand_pref.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" expandcomplex "${QUERYDB}" "${TARGETDB}" "${RESULT}" "${TMP_PATH}/result_expand_pref" ${THREADS_PAR} \ | ||
| || fail "Expandcomplex died" | ||
| fi | ||
| if notExists "${TMP_PATH}/result_expand_aligned.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" $COMPLEX_ALIGNMENT_ALGO "${QUERYDB}" "${TARGETDB}" "${TMP_PATH}/result_expand_pref" "${TMP_PATH}/result_expand_aligned" ${COMPLEX_ALIGN_PAR} \ | ||
| || fail $COMPLEX_ALIGNMENT_ALGO "died" | ||
| fi | ||
| RESULT="${TMP_PATH}/result_expand_aligned" | ||
| fi | ||
| if notExists "${TMP_PATH}/complex_result.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| $MMSEQS scorecomplex "${QUERYDB}" "${TARGETDB}" "${RESULT}" "${OUTPUT}" ${SCORECOMPLEX_PAR} \ | ||
| || fail "ScoreComplex died" | ||
| fi | ||
|
|
||
| if [ -n "${REMOVE_TMP}" ]; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/result" ${VERBOSITY} | ||
| if [ "$PREFMODE" != "EXHAUSTIVE" ]; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/result_expand_aligned" ${VERBOSITY} | ||
| fi | ||
| rm -rf "${TMP_PATH}/search_tmp" | ||
| rm -f "${TMP_PATH}/complexsearch.sh" | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -263,7 +263,26 @@ std::vector<Command> foldseekCommands = { | |
| {"complexDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::alignmentDb} | ||
| } | ||
| }, | ||
| {"easy-complexsearch", easycomplexsearch, &localPar.easyscorecomplexworkflow, COMMAND_EASY, | ||
| {"complexsearch", complexsearch, &localPar.complexsearchworkflow, COMMAND_MAIN, | ||
| "Complex level search", | ||
| "# Search a single/multiple PDB file against a set of PDB files and get complex level alignments\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp\n" | ||
| "# Format output differently\n" | ||
| "foldseek easy-complexsearch queryDB targetDB result tmp --format-output query,target,qstart,tstart,cigar\n" | ||
| "# Align with TMalign (global)\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp --alignment-type 1\n" | ||
| "# Skip prefilter and perform an exhaustive alignment (slower but more sensitive)\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp --exhaustive-search 1\n\n", | ||
| "Woosub Kim <[email protected]>", | ||
| "<i:queryDB> <i:targetDB> <o:outputFileName> <tmpDir>", | ||
| CITATION_FOLDSEEK, { | ||
| {"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::NEED_HEADER, &DbValidator::sequenceDb}, | ||
| {"targetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::NEED_HEADER, &DbValidator::sequenceDb}, | ||
| {"complexDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::alignmentDb}, | ||
| {"tempDir", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory} | ||
| } | ||
| }, | ||
| {"easy-complexsearch", easycomplexsearch, &localPar.easyscomplexsearchworkflow, COMMAND_EASY, | ||
| "Complex level search", | ||
| "# Search a single/multiple PDB file against a set of PDB files and get complex level alignments\n" | ||
| "foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp\n" | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| #include <cassert> | ||
|
|
||
| #include "LocalParameters.h" | ||
| #include "FileUtil.h" | ||
| #include "CommandCaller.h" | ||
| #include "Util.h" | ||
| #include "Debug.h" | ||
|
|
||
| #include "complexsearch.sh.h" | ||
|
|
||
| int complexsearch(int argc, const char **argv, const Command &command) { | ||
| LocalParameters &par = LocalParameters::getLocalInstance(); | ||
| par.PARAM_ADD_BACKTRACE.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_MAX_REJECTED.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_ZDROP.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_DB_OUTPUT.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_OVERLAP.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_RESCORE_MODE.addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| for (size_t i = 0; i < par.createdb.size(); i++){ | ||
| par.createdb[i]->addCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| } | ||
|
|
||
| par.PARAM_COMPRESSED.removeCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_THREADS.removeCategory(MMseqsParameter::COMMAND_EXPERT); | ||
| par.PARAM_V.removeCategory(MMseqsParameter::COMMAND_EXPERT); | ||
|
|
||
| par.parseParameters(argc, argv, command, false, Parameters::PARSE_VARIADIC, 0); | ||
| if(par.PARAM_FORMAT_OUTPUT.wasSet == false){ | ||
| par.outfmt = "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,complexassignid"; | ||
| } | ||
| par.addBacktrace = true; | ||
| par.PARAM_ADD_BACKTRACE.wasSet = true; | ||
| par.printParameters(command.cmd, argc, argv, *command.params); | ||
|
|
||
| bool needBacktrace = false; | ||
| bool needTaxonomy = false; | ||
| bool needTaxonomyMapping = false; | ||
| bool needLookup = false; | ||
| { | ||
| bool needSequenceDB = false; | ||
| bool needFullHeaders = false; | ||
| bool needSource = false; | ||
| bool needQCA = false; | ||
| bool needTCA = false; | ||
| bool needTMalign = false; | ||
| bool needLDDT = false; | ||
| LocalParameters::getOutputFormat(par.formatAlignmentMode, par.outfmt, needSequenceDB, needBacktrace, needFullHeaders, | ||
| needLookup, needSource, needTaxonomyMapping, needTaxonomy, needQCA, needTCA, needTMalign, needLDDT); | ||
| } | ||
|
|
||
| if (par.formatAlignmentMode == Parameters::FORMAT_ALIGNMENT_SAM || | ||
| par.formatAlignmentMode == LocalParameters::FORMAT_ALIGNMENT_PDB_SUPERPOSED || | ||
| par.greedyBestHits) { | ||
| needBacktrace = true; | ||
| } | ||
| if (needBacktrace) { | ||
| Debug(Debug::INFO) << "Alignment backtraces will be computed, since they were requested by output format.\n"; | ||
| par.addBacktrace = true; | ||
| par.PARAM_ADD_BACKTRACE.wasSet = true; | ||
| } | ||
| if (needLookup) { | ||
| par.writeLookup = true; | ||
| } | ||
|
|
||
| std::string tmpDir = par.filenames.back(); | ||
| std::string hash = SSTR(par.hashParameter(command.databases, par.filenames, *command.params)); | ||
| if (par.reuseLatest) { | ||
| hash = FileUtil::getHashFromSymLink(tmpDir + "/latest"); | ||
| } | ||
| tmpDir = FileUtil::createTemporaryDirectory(tmpDir, hash); | ||
| par.filenames.pop_back(); | ||
| CommandCaller cmd; | ||
| if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN){ | ||
| cmd.addVariable("COMPLEX_ALIGNMENT_ALGO", "tmalign"); | ||
| cmd.addVariable("COMPLEX_ALIGN_PAR", par.createParameterString(par.tmalign).c_str()); | ||
| }else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA || par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI){ | ||
| cmd.addVariable("COMPLEX_ALIGNMENT_ALGO", "structurealign"); | ||
| cmd.addVariable("COMPLEX_ALIGN_PAR", par.createParameterString(par.structurealign).c_str()); | ||
| } | ||
|
|
||
| switch(par.prefMode){ | ||
| case LocalParameters::PREF_MODE_KMER: | ||
| cmd.addVariable("PREFMODE", "KMER"); | ||
| break; | ||
| case LocalParameters::PREF_MODE_UNGAPPED: | ||
| cmd.addVariable("PREFMODE", "UNGAPPED"); | ||
| break; | ||
| case LocalParameters::PREF_MODE_EXHAUSTIVE: | ||
| cmd.addVariable("PREFMODE", "EXHAUSTIVE"); | ||
| break; | ||
| } | ||
| if(par.exhaustiveSearch){ | ||
| cmd.addVariable("PREFMODE", "EXHAUSTIVE"); | ||
| } | ||
| 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(); | ||
| cmd.addVariable("TARGETDB", par.filenames.back().c_str()); | ||
| par.filenames.pop_back(); | ||
| cmd.addVariable("QUERYDB", par.filenames.back().c_str()); | ||
| cmd.addVariable("LEAVE_INPUT", par.dbOut ? "TRUE" : NULL); | ||
| par.filenames.pop_back(); | ||
| cmd.addVariable("SEARCH_PAR", par.createParameterString(par.structuresearchworkflow, true).c_str()); | ||
| cmd.addVariable("SCORECOMPLEX_PAR", par.createParameterString(par.scorecomplex).c_str()); | ||
| cmd.addVariable("THREADS_PAR", par.createParameterString(par.onlythreads).c_str()); | ||
| cmd.addVariable("REMOVE_TMP", par.removeTmpFiles ? "TRUE" : NULL); | ||
| cmd.addVariable("VERBOSITY", par.createParameterString(par.onlyverbosity).c_str()); | ||
| std::string program = tmpDir + "/complexsearch.sh"; | ||
| FileUtil::writeFile(program, complexsearch_sh, complexsearch_sh_len); | ||
| cmd.execProgram(program.c_str(), par.filenames); | ||
| // Should never get here | ||
| assert(false); | ||
| return EXIT_FAILURE; | ||
| } |