`obisplit`: #

Description #

Synopsis #

obisplit [--allows-indels] [--batch-size <int>] [--compress|-Z]
         [--config|-C <string>] [--debug] [--ecopcr] [--embl] [--fasta]
         [--fasta-output] [--fastq] [--fastq-output] [--force-one-cpu]
         [--genbank] [--help|-h|-?] [--input-OBI-header]
         [--input-json-header] [--json-output] [--max-cpu <int>] [--no-order]
         [--no-progressbar] [--out|-o <FILENAME>] [--output-OBI-header|-O]
         [--output-json-header] [--paired-with <FILENAME>]
         [--pattern-error <int>] [--pprof] [--pprof-goroutine <int>]
         [--pprof-mutex <int>] [--skip-empty] [--solexa]
         [--taxonomy|-t <string>] [--template] [--version] [<args>]

Options #

`obisplit` specific options #

--allows-indels: Allows for indels during pattern DNA pattern matching.
--config | -C <string>: The configuration file.
--pattern-error <INTEGER>: Maximum number of allowed error during pattern matching (default: 4).
--template: Print on the standard output a script template. (default: false)

Taxonomic options #

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

Controlling the input data #

OBITools4 generally recognizes the input file format. It also recognizes whether the input file is compressed using GZIP. But some rare files can be misidentified, so the following options allow the user to force the format, thus bypassing the format identification step.

The file format options #

--fasta: indicates that sequence data is in fasta format.
--fastq: indicates that sequence data is in fastq format.
--embl: indicates that sequence data is in EMBL-ENA flatfile format.
--csv: indicates that sequence data is in CSV format.
--genbank: indicates that sequence data is in GenBank flatfile format.
--ecopcr: indicates that sequence data is in the old ecoPCR tabulated format.

Controlling the way OBITools4 are formatting annotations #

These options only apply to the FASTA and FASTQ formats

--input-OBI-header: FASTA/FASTQ title line annotations follow the old OBI format.
--input-json-header: FASTA/FASTQ title line annotations follow the JSON format.

Controlling quality score decoding #

This option only applies to the FASTQ formats

--solexa: decodes quality string according to the Solexa specification. (default: the standard Sanger encoding is used, env: OBISSOLEXA)

Controlling the output data #

--compress | -Z : output is compressed using gzip. (default: false)
--no-order: the OBITools ensure that the order between the input file and the output file does not change. When multiple files are processed, they are processed one at a time. If the –no-order option is added to a command, multiple input files can be opened at the same time and their contents processed in parallel. This usually increases processing speed, but does not guarantee the order of the sequences in the output file. Also, processing multiple files in parallel may require more memory to perform the computation.
--fasta-output: writes sequence data in fasta format (default if quality data is not available).
--fastq-output: writes sequence data in fastq format (default if quality data is available).
--json-output: writes sequence data in JSON format.
--out | -o <FILENAME>: filename used for saving the output (default: “-”, the standard output)
--output-OBI-header | -O : writes output FASTA/FASTQ title line annotations in OBI format (default: JSON).
--output-json-header: writew output FASTA/FASTQ title line annotations in JSON format (the default format).
--skip-empty: sequences of length equal to zero are removed from the output (default: false).
--no-progressbar: deactivates progress bar display (default: false).

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 #

obisplit --help

obisplit: #