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Merge pull request #48 from jaebeom-kim/master
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make modules under development invisible
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@jaebeom-kim
jaebeom-kim committed Dec 2, 2023
2 parents 8e69e35 + ad1b7f4 commit 160a6ce
Showing 1 changed file with 35 additions and 44 deletions.
79 changes: 35 additions & 44 deletions src/metabuli.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -48,15 +48,6 @@ std::vector<Command> commands = {
"<i: DBDIR> ",
CITATION_SPACEPHARER,
{{"Directory where the DB will be generated", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"updateDB", build, &localPar.build, COMMAND_DB,
"Update database based on the list of FASTA files.",
nullptr,
"Jaebeom Kim <jbeom0731@gmail.com>",
"<DB dir> <FASTA list> <Accesssion2taxid>",
CITATION_SPACEPHARER,
{{"DB directory to be updated", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::empty},
{"A list of FASTA files", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
{"classify", classify, &localPar.classify, COMMAND_MAIN,
"Assigning taxonomy label to query reads",
nullptr,
Expand All @@ -67,14 +58,14 @@ std::vector<Command> commands = {
{"DB dir", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory},
{"out dir", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory},
{"job ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
{"filter", filter, &localPar.filter, COMMAND_MAIN,
"Filtering reads based on the classification result",
nullptr,
"Jaebeom Kim <jbeom0731@gmail.com>",
"<i:READ FILE> <i:FILTER DB>",
CITATION_SPACEPHARER,
{{"READ FILE", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfile},
{"FILTER DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}},
// {"filter", filter, &localPar.filter, COMMAND_MAIN,
// "Filtering reads based on the classification result",
// nullptr,
// "Jaebeom Kim <jbeom0731@gmail.com>",
// "<i:READ FILE> <i:FILTER DB>",
// CITATION_SPACEPHARER,
// {{"READ FILE", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfile},
// {"FILTER DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"grade", grade, &localPar.grade, COMMAND_EXPERT,
"Grade the classification result (only for benchmarking)",
nullptr,
Expand All @@ -94,14 +85,14 @@ std::vector<Command> commands = {
{"List of answer sheets (Query ID 2 tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"List of assembly accessions of reference sequences", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"Taxonomy directory", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::directory}}},
{"seqHeader2TaxId", seqHeader2TaxId, &localPar.seqHeader2TaxId, COMMAND_EXPERT,
"It extracts k-mers from query sequences, and compares them to the target database",
nullptr,
"Jaebeom Kim <jbeom0731@gmail.com>",
"<i:read-classification> <i:mapping>",
CITATION_SPACEPHARER,
{{"read-classification", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
// {"seqHeader2TaxId", seqHeader2TaxId, &localPar.seqHeader2TaxId, COMMAND_EXPERT,
// "It extracts k-mers from query sequences, and compares them to the target database",
// nullptr,
// "Jaebeom Kim <jbeom0731@gmail.com>",
// "<i:read-classification> <i:mapping>",
// CITATION_SPACEPHARER,
// {{"read-classification", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
// {"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
{"add-to-library", addToLibrary, &localPar.addToLibrary, COMMAND_DATABASE_CREATION,
"It bins sequences into files according to their species.",
nullptr,
Expand All @@ -111,16 +102,16 @@ std::vector<Command> commands = {
{{"List of absolute paths of files to be added. One path per line.", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"NCBI style accession2taxid file. It should be consistent to tax dump files.", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"DB directory", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"apply-threshold", applyThreshold, &localPar.applyThreshold, COMMAND_EXPERT,
"Assigning taxonomy label to query reads",
nullptr,
"Jaebeom Kim <jbeom0731@gmail.com>",
"<i:Old readclassification> <o:OUT DIR> <o:JOB ID> <i: TAXONOMY DIR> ",
CITATION_SPACEPHARER,
{{"Old Results", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory},
{"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
// {"apply-threshold", applyThreshold, &localPar.applyThreshold, COMMAND_EXPERT,
// "Assigning taxonomy label to query reads",
// nullptr,
// "Jaebeom Kim <jbeom0731@gmail.com>",
// "<i:Old readclassification> <o:OUT DIR> <o:JOB ID> <i: TAXONOMY DIR> ",
// CITATION_SPACEPHARER,
// {{"Old Results", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
// {"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory},
// {"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile},
// {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"binning2report", binning2report, &localPar.binning2report, COMMAND_FORMAT_CONVERSION,
"It generates Kraken style report file from binning results",
nullptr,
Expand All @@ -131,15 +122,15 @@ std::vector<Command> commands = {
{"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory},
{"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"filter-by-genus", filterByGenus, &localPar.filterByGenus, COMMAND_EXPERT,
"It filters out reads classified as a specific genus",
nullptr,
"Jaebeom Kim <jbeom0731@gmail.com>",
"<i:Binning Result> <i:Genus list> <i: TAXONOMY DIR> ",
CITATION_SPACEPHARER,
{{"Binning Result", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"Genus list", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile},
{"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
// {"filter-by-genus", filterByGenus, &localPar.filterByGenus, COMMAND_EXPERT,
// "It filters out reads classified as a specific genus",
// nullptr,
// "Jaebeom Kim <jbeom0731@gmail.com>",
// "<i:Binning Result> <i:Genus list> <i: TAXONOMY DIR> ",
// CITATION_SPACEPHARER,
// {{"Binning Result", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile},
// {"Genus list", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile},
// {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
{"mapping2taxon", mapping2taxon, &localPar.mapping2taxon, COMMAND_EXPERT,
"It takes a mapping file (multiple targets for each read) and generates a read2taxon file (one target for each read)",
nullptr,
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