obiconvert

obiconvert: convert a sequence file #

Description #

Convert a sequence file to fasta , fastq , or JSON format.

Synopsis #

obiconvert [--batch-size <int>] [--compress|-Z] [--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>] [--pprof] [--pprof-goroutine <int>]
           [--pprof-mutex <int>] [--skip-empty] [--solexa]
           [--taxonomy|-t <string>] [--version] [<args>]

Options #

obiconvert specific options #

  • --paired-with <FILENAME>: filename containing the paired reads.

Check taxids against a taxonomy #

OBITools4 allow loading a taxonomy database when they are processing sequence data. If done, the command checks the validity of taxids during the processing of the command. Three cases can occur:
  • The taxon is valid
  • The taxon is no more valid, but a new one replaces it
  • The taxon is no more valid, and no new taxid exists to replace it.
In the first case, the obitools normalize the writing of the taxid in the form:
    TAXCOD:TAXID [SCIENTIFIC NAME]@RANK
As example with the NCBI taxonomy the human taxid looks like :
    taxon:9606 [Homo sapiens]@species
That rewriting doesn't happen if the --raw-taxid option is set. In that case only the raw taxid is conserved.
    9606
In the second case, a warning message is logged on the standard error. If the --update-taxid is set, the command will update the expired taxid to the new equivalent one, and the valid taxon rules apply. Otherwise, the old taxid is maintained in the result. In the last case, a warning message is also issued to the standard error, and non-valid taxid is conserved as is. If the --fail-on-taxonomy option is set, the command stop and exit with an error at the first non-valid taxid encountred in input data.
  • --taxonomy | -t <string>: Path to the taxonomic database.
  • --raw-taxid: Displays the raw taxid for each displayed taxon. (default: false)
  • --update-taxid: Make obitools automatically updating the taxids that are declared merged to a newest one (default: false).
  • --fail-on-taxonomy: Make obitools failing on error if a used taxid is not a currently valid one (default: false).

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 #

obiconvert --help