idseq-bench-score - Score benchmark samples based on answer
key
idseq-bench-score [-h] [-o OUTPUT_FILE] [-t [TRUTH_FILES
[TRUTH_FILES ...]]] [-e ENV] [-p LOCAL_PATH] [--mono-aupr] project_id
sample_id pipeline_version
Score benchmark samples based on answer key (against key encode in
fastq read IDs for IDseq Bench samples or against a provided answer
key).
- -h, --help
- show this help message and exit
- -o OUTPUT_FILE,
--output-file OUTPUT_FILE
- Path of output file to write the results to (if not set results are
written to stdout)
- -t [TRUTH_FILES [TRUTH_FILES
...]], --truth_files [TRUTH_FILES [TRUTH_FILES ...]]
- Space separated list of truth files. Truth files are TSV files with the
fields <tax_id, absolute abundance, relative abundance, rank,
tax_name>
- -e ENV, --env
ENV
- String name of environment in which sample exists; options are: prod
(default), staging
- -p LOCAL_PATH,
--local-path LOCAL_PATH
- Root of local path where IDseq files are stored. Must follow the same
structure to store files as IDseq
- --mono-aupr
- Computed adjusted AUPR by forcing the precision/recall curve to be
monotonic decreasing
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.