obitaxonomy

obitaxonomy: manage and request a taxonomy database #

Description #

Synopsis # 

obitaxonomy [--alternative-names|-a] [--batch-size <int>] [--debug]
            [--download-ncbi] [--dump|-D <TAXID>] [--extract-taxonomy]
            [--fixed|-F] [--force-one-cpu] [--help|-h|-?] [--max-cpu <int>]
            [--no-progressbar] [--out|-o <FILENAME>] [--parents|-p <TAXID>]
            [--pprof] [--pprof-goroutine <int>] [--pprof-mutex <int>]
            [--rank <RANK>] [--rank-list|-l] [--raw-taxid]
            [--restrict-to-taxon|-r <string>]... [--solexa]
            [--sons|-s <TAXID>] [--taxonomy|-t <string>] [--version]
            [--with-path] [--with-query|-P] [--without-parent]
            [--without-rank|-R] [--without-scientific-name|-S] [<args>]

Options #

obitaxonomy specific options #

  • --alternative-names | -a : Enable the search on all alternative names and not only scientific names. (default: false)
  • --download-ncbi: Download the current NCBI taxonomy taxdump (default: false)
  • --dump | -D <TAXID>: Dump a sub-taxonomy corresponding to the precised clade (default: “”)
  • --extract-taxonomy: Extract taxonomy from a sequence file (default: false)
  • --fixed: Match taxon names using a fixed pattern, not a regular expression (default: false)
  • --parents | -p <TAXID>: Displays every parental tree’s information for the provided taxid. (default: “NA”)
  • --rank <RANK>: Restrict to the given taxonomic rank. (default: “”)
  • --rank-list | -l : List every taxonomic rank available in the taxonomy. (default: false)
  • --restrict-to-taxon | -r <string>: Restrict output to some subclades. (default: [])
  • --sons | -s <TAXID>: Displays every sons’ tree’s information for the provided taxid. (default: “NA”)
  • --with-path: Adds a column containing the full path for each displayed taxon. (default: false)
  • --with-query | -P : Adds a column containing query used to filter taxon name for each displayed taxon. (default: false)
  • --without-parent: Supress the column containing the parent’s taxonid from the output. (default: false)
  • --without-rank | -R : Supress the column containing the taxonomic rank from the output. (default: false)
  • --without-scientific-name | -S : Supress the column containing the scientific name from the output. (default: false)

Taxonomic options #

  • --taxonomy | -t <string>: Path to the taxonomic database.

General options #

  • --help | -h|-? : shows this help.
  • --version: prints the version and exits.
  • --silent-warning: This option tells obitools to stop displaying warnings. This behaviour can be controlled by setting the OBIWARNINGS environment variable.
  • --max-cpu <INTEGER>: OBITools can take advantage of your computer’s multi-core architecture by parallelizing the computation across all available CPUs. Computing on more CPUs usually requires more memory to perform the computation. Reducing the number of CPUs used to perform a calculation is also a way to indirectly control the amount of memory used by the process. The number of CPUs used by OBITools can also be controlled by setting the OBIMAXCPU environment variable.
  • --force-one-cpu: forces the use of a single CPU core for parallel processing (default: false).
  • --batch-size <INTEGER>: number of sequence per batch for parallel processing (default: 1000, env: OBIBATCHSIZE)
  • --debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG)
  • --pprof: enables pprof server. Look at the log for details. (default: false).
  • --pprof-mutex <INTEGER>: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX)
  • --pprof-goroutine <INTEGER>: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE)

Examples # 

obitaxonomy --help