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Add SKIP_ORF option in translated_search #885

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merged 11 commits into from
Nov 22, 2024
Merged

Add SKIP_ORF option in translated_search #885

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0284092
recover longest orf after fragment elimination
LunaJang Apr 4, 2024
4c6f74f
delete unused variable
LunaJang Apr 4, 2024
3263e9d
Merge branch 'soedinglab:master' into master
LunaJang Sep 2, 2024
a035b87
add ORF_SKIP option in translated_search
LunaJang Sep 2, 2024
9dce49a
change extractframes function to consider multiple frames in forward/…
LunaJang Sep 3, 2024
b1e5139
fix error with DB key
LunaJang Sep 5, 2024
2c1f500
make sure translated_search with skip_orf option (extractorfs->extrac…
LunaJang Sep 5, 2024
88b3670
add translation in extract frames
LunaJang Sep 6, 2024
94eae3a
add PARAM_TRANSLATE into extractframes
LunaJang Sep 6, 2024
964bfaa
change extracframes to have same output with extractframes+tranlatenucs
LunaJang Sep 9, 2024
a804518
make full frame mode available through --translation-mode
milot-mirdita Sep 30, 2024
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48 changes: 38 additions & 10 deletions data/workflow/translated_search.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,24 @@ TMP_PATH="$4"
QUERY="$1"
QUERY_ORF="$1"
if [ -n "$QUERY_NUCL" ]; then
if notExists "${TMP_PATH}/q_orfs_aa.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" extractorfs "$1" "${TMP_PATH}/q_orfs_aa" ${ORF_PAR} \
|| fail "extract orfs step died"
# introduce EXTRACT_FRAMES_PAR, TRANSLATE_PAR, ORF_SKIP to Search.cpp and to Parameters::Parameters
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if [ "$ORF_SKIP" ]; then
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if notExists "${TMP_PATH}/q_orfs_aa.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" extractframes "$1" "${TMP_PATH}/q_orfs_nucl" ${EXTRACT_FRAMES_PAR} \
|| fail "extractframes died"
# we want to avoid this \/
# shellcheck disable=SC2086
"$MMSEQS" translatenucs "${TMP_PATH}/q_orfs_nucl" "${TMP_PATH}/q_orfs_aa" ${TRANSLATE_PAR} \
|| fail "translatenucs died"
"$MMSEQS" rmdb "${TMP_PATH}/q_orfs_nucl"
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see below

fi
else
if notExists "${TMP_PATH}/q_orfs_aa.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" extractorfs "$1" "${TMP_PATH}/q_orfs_aa" ${ORF_PAR} \
|| fail "extract orfs step died"
fi
fi
QUERY="${TMP_PATH}/q_orfs_aa"
QUERY_ORF="${TMP_PATH}/q_orfs_aa"
Expand All @@ -34,13 +48,27 @@ TARGET="$2"
TARGET_ORF="$2"
if [ -n "$TARGET_NUCL" ]; then
if [ -n "$NO_TARGET_INDEX" ]; then
if notExists "${TMP_PATH}/t_orfs_aa.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" extractorfs "$2" "${TMP_PATH}/t_orfs_aa" ${ORF_PAR} \
|| fail "extract target orfs step died"
if [ "$ORF_SKIP" ]; then
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same as above

if notExists "${TMP_PATH}/t_orfs_aa.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" extractframes "$1" "${TMP_PATH}/t_orfs_nucl" ${EXTRACT_FRAMES_PAR} \
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This should be "$2".

|| fail "extractframes died"
# we want to avoid this \/
# shellcheck disable=SC2086
"$MMSEQS" translatenucs "${TMP_PATH}/t_orfs_nucl" "${TMP_PATH}/t_orfs_aa" ${TRANSLATE_PAR} \
|| fail "translatenucs died"
"$MMSEQS" rmdb "${TMP_PATH}/t_orfs_nucl"
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The rmdb calls need ${VERBOSITY}:

# shellcheck disable=SC2086
"$MMSEQS" rmdb "${TMP_PATH}/t_orfs_nucl" ${VERBOSITY}

fi
else
if notExists "${TMP_PATH}/t_orfs_aa.dbtype"; then
# same here
# shellcheck disable=SC2086
"$MMSEQS" extractorfs "$2" "${TMP_PATH}/t_orfs_aa" ${ORF_PAR} \
|| fail "extract target orfs step died"
fi
fi
TARGET="${TMP_PATH}/t_orfs_aa"
TARGET_ORF="${TMP_PATH}/t_orfs_aa"
TARGET="${TMP_PATH}/t_orfs_aa"
TARGET_ORF="${TMP_PATH}/t_orfs_aa"
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Please check if this whitespace should be here. From the diff, this looks wrong.

fi
fi

Expand Down
4 changes: 4 additions & 0 deletions src/commons/Parameters.cpp
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Expand Up @@ -172,6 +172,7 @@ Parameters::Parameters():
PARAM_ORF_FILTER_S(PARAM_ORF_FILTER_S_ID, "--orf-filter-s", "ORF filter sensitivity", "Sensitivity used for query ORF prefiltering", typeid(float), (void *) &orfFilterSens, "^[0-9]*(\\.[0-9]+)?$"),
PARAM_ORF_FILTER_E(PARAM_ORF_FILTER_E_ID, "--orf-filter-e", "ORF filter e-value", "E-value threshold used for query ORF prefiltering", typeid(double), (void *) &orfFilterEval, "^([-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)|[0-9]*(\\.[0-9]+)?$"),
PARAM_LCA_SEARCH(PARAM_LCA_SEARCH_ID, "--lca-search", "LCA search mode", "Efficient search for LCA candidates", typeid(bool), (void *) &lcaSearch, "", MMseqsParameter::COMMAND_PROFILE | MMseqsParameter::COMMAND_EXPERT),
PARAM_ORF_SKIP(PARAM_ORF_SKIP_ID, "--orf-skip", "ORF skip mode", "???", typeid(bool), (void *) &orfSkip, ""),
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Still TODO

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PARAM_ORF_SKIP(PARAM_ORF_SKIP_ID, "--orf-skip", "Extract frames instead of ORFs", "Extract frames instead of ORFs during translated search", typeid(bool), (void *) &orfSkip, ""),

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@martin-steinegger any better ideas for a parameter name?

// easysearch
PARAM_GREEDY_BEST_HITS(PARAM_GREEDY_BEST_HITS_ID, "--greedy-best-hits", "Greedy best hits", "Choose the best hits greedily to cover the query", typeid(bool), (void *) &greedyBestHits, ""),
// extractorfs
Expand Down Expand Up @@ -1251,6 +1252,7 @@ Parameters::Parameters():
searchworkflow = combineList(searchworkflow, rescorediagonal);
searchworkflow = combineList(searchworkflow, result2profile);
searchworkflow = combineList(searchworkflow, extractorfs);
searchworkflow = combineList(searchworkflow, extractframes);
searchworkflow = combineList(searchworkflow, translatenucs);
searchworkflow = combineList(searchworkflow, splitsequence);
searchworkflow = combineList(searchworkflow, offsetalignment);
Expand All @@ -1268,6 +1270,7 @@ Parameters::Parameters():
searchworkflow.push_back(&PARAM_RUNNER);
searchworkflow.push_back(&PARAM_REUSELATEST);
searchworkflow.push_back(&PARAM_REMOVE_TMP_FILES);
searchworkflow.push_back(&PARAM_ORF_SKIP);

linsearchworkflow = combineList(align, kmersearch);
linsearchworkflow = combineList(linsearchworkflow, swapresult);
Expand Down Expand Up @@ -2277,6 +2280,7 @@ void Parameters::setDefaults() {
orfFilterSens = 2.0;
orfFilterEval = 100;
lcaSearch = false;
orfSkip = false;

greedyBestHits = false;

Expand Down
2 changes: 2 additions & 0 deletions src/commons/Parameters.h
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Expand Up @@ -467,6 +467,7 @@ class Parameters {
float orfFilterSens;
double orfFilterEval;
bool lcaSearch;
bool orfSkip;

// easysearch
bool greedyBestHits;
Expand Down Expand Up @@ -886,6 +887,7 @@ class Parameters {
PARAMETER(PARAM_ORF_FILTER_S)
PARAMETER(PARAM_ORF_FILTER_E)
PARAMETER(PARAM_LCA_SEARCH)
PARAMETER(PARAM_ORF_SKIP)

// easysearch
PARAMETER(PARAM_GREEDY_BEST_HITS)
Expand Down
12 changes: 11 additions & 1 deletion src/workflow/Search.cpp
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Expand Up @@ -208,6 +208,9 @@ int search(int argc, const char **argv, const Command& command) {
for (size_t i = 0; i < par.extractorfs.size(); i++) {
par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
}
for (size_t i = 0; i < par.extractframes.size(); i++) {
par.extractframes[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
}
for (size_t i = 0; i < par.translatenucs.size(); i++) {
par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
}
Expand Down Expand Up @@ -541,9 +544,16 @@ int search(int argc, const char **argv, const Command& command) {
par.subDbMode = 1;
cmd.addVariable("CREATESUBDB_PAR", par.createParameterString(par.createsubdb).c_str());
par.translate = 1;
cmd.addVariable("ORF_PAR", par.createParameterString(par.extractorfs).c_str());
cmd.addVariable("OFFSETALIGNMENT_PAR", par.createParameterString(par.offsetalignment).c_str());
cmd.addVariable("SEARCH", program.c_str());
if (par.orfSkip) {
cmd.addVariable("ORF_SKIP", "TRUE");
cmd.addVariable("TRANSLATE_PAR", par.createParameterString(par.translatenucs).c_str());
cmd.addVariable("EXTRACT_FRAMES_PAR", par.createParameterString(par.extractframes).c_str());
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}
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code/whitespace style: please do } else {

else{
cmd.addVariable("ORF_PAR", par.createParameterString(par.extractorfs).c_str());
}
program = std::string(tmpDir + "/translated_search.sh");
}else if(searchMode & Parameters::SEARCH_MODE_FLAG_QUERY_NUCLEOTIDE &&
searchMode & Parameters::SEARCH_MODE_FLAG_TARGET_NUCLEOTIDE){
Expand Down