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IDSEQ-BENCH-SCORE(1) User Commands IDSEQ-BENCH-SCORE(1)

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:

ID of the project
ID of the sample
Pipeline version to retrieve: <major>.<minor>

optional arguments:

show this help message and exit
Path of output file to write the results to (if not set results are written to stdout)
Space separated list of truth files. Truth files are TSV files with the fields <tax_id, absolute abundance, relative abundance, rank, tax_name>
String name of environment in which sample exists; options are: prod (default), staging
Root of local path where IDseq files are stored. Must follow the same structure to store files as IDseq
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.

July 2020 idseq-bench-score 0.0~git20200627.4040457