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Merge pull request #48 from jaebeom-kim/master
make modules under development invisible
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@@ -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 <[email protected]>", | ||
"<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, | ||
|
@@ -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 <[email protected]>", | ||
"<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 <[email protected]>", | ||
// "<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, | ||
|
@@ -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 <[email protected]>", | ||
"<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 <[email protected]>", | ||
// "<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, | ||
|
@@ -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 <[email protected]>", | ||
"<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 <[email protected]>", | ||
// "<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, | ||
|
@@ -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 <[email protected]>", | ||
"<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 <[email protected]>", | ||
// "<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, | ||
|