Add SKIP_ORF option in translated_search #885
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data/workflow/translated_search.sh
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| if [ "$ORF_SKIP" ]; then | ||
| if notExists "${TMP_PATH}/t_orfs_aa.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" extractframes "$1" "${TMP_PATH}/t_orfs_nucl" ${EXTRACT_FRAMES_PAR} \ |
data/workflow/translated_search.sh
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| TARGET="${TMP_PATH}/t_orfs_aa" | ||
| TARGET_ORF="${TMP_PATH}/t_orfs_aa" | ||
| TARGET="${TMP_PATH}/t_orfs_aa" | ||
| TARGET_ORF="${TMP_PATH}/t_orfs_aa" |
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Please check if this whitespace should be here. From the diff, this looks wrong.
src/commons/Parameters.cpp
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| @@ -172,6 +172,7 @@ Parameters::Parameters(): | |||
| PARAM_ORF_FILTER_S(PARAM_ORF_FILTER_S_ID, "--orf-filter-s", "ORF filter sensitivity", "Sensitivity used for query ORF prefiltering", typeid(float), (void *) &orfFilterSens, "^[0-9]*(\\.[0-9]+)?$"), | |||
| 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]+)?$"), | |||
| PARAM_LCA_SEARCH(PARAM_LCA_SEARCH_ID, "--lca-search", "LCA search mode", "Efficient search for LCA candidates", typeid(bool), (void *) &lcaSearch, "", MMseqsParameter::COMMAND_PROFILE | MMseqsParameter::COMMAND_EXPERT), | |||
| PARAM_ORF_SKIP(PARAM_ORF_SKIP_ID, "--orf-skip", "ORF skip mode", "???", typeid(bool), (void *) &orfSkip, ""), | |||
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PARAM_ORF_SKIP(PARAM_ORF_SKIP_ID, "--orf-skip", "Extract frames instead of ORFs", "Extract frames instead of ORFs during translated search", typeid(bool), (void *) &orfSkip, ""),
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@martin-steinegger any better ideas for a parameter name?
src/workflow/Search.cpp
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| cmd.addVariable("ORF_SKIP", "TRUE"); | ||
| cmd.addVariable("TRANSLATE_PAR", par.createParameterString(par.translatenucs).c_str()); | ||
| cmd.addVariable("EXTRACT_FRAMES_PAR", par.createParameterString(par.extractframes).c_str()); | ||
| } |
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code/whitespace style: please do } else {
data/workflow/translated_search.sh
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| # shellcheck disable=SC2086 | ||
| "$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" ${VERBOSITY}
data/workflow/translated_search.sh
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| # shellcheck disable=SC2086 | ||
| "$MMSEQS" translatenucs "${TMP_PATH}/q_orfs_nucl" "${TMP_PATH}/q_orfs_aa" ${TRANSLATE_PAR} \ | ||
| || fail "translatenucs died" | ||
| "$MMSEQS" rmdb "${TMP_PATH}/q_orfs_nucl" |
…tframes & translatenucs) works
data/workflow/translated_search.sh
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| # shellcheck disable=SC2086 | ||
| "$MMSEQS" extractorfs "$2" "${TMP_PATH}/t_orfs_aa" ${ORF_PAR} \ | ||
| || fail "extract target orfs step died" | ||
| if [ "$ORF_SKIP" ]; then |
|
I agree the PR can be merged under the MIT license |
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added a new parameter, and changed translated_search.sh to run extractframes and translatenucs instead of extractorf according to the user's choice