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.