NAME

       idseq-bench-score - Score benchmark samples based on answer key

SYNOPSIS

       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

DESCRIPTION

       Score benchmark samples based on answer key (against key encode in fastq read IDs for IDseq Bench samples
       or against a provided answer key).

OPTIONS

   positional arguments:
       project_id
              ID of the project

       sample_id
              ID of the sample

       pipeline_version
              Pipeline version to retrieve: <major>.<minor>

   optional arguments:
       -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

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

idseq-bench-score 0.0~git20200627.4040457           July 2020                               IDSEQ-BENCH-SCORE(1)