standardise

taxpasta standardise --help

Usage: taxpasta standardise [OPTIONS] PROFILE

  Standardise a taxonomic profile (alias: 'standardize').

Arguments:
  PROFILE  A file containing a taxonomic profile.  [required]

Options:
  -p, --profiler [bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus]
                                  The taxonomic profiler used.  [required]
  -o, --output PATH               The desired output file. By default, the
                                  file extension will be used to determine the
                                  output format, but when setting the format
                                  explicitly using the --output-format option,
                                  automatic detection is disabled.  [required]
  --output-format [TSV|CSV|ODS|XLSX|arrow|parquet]
                                  The desired output format. Depending on the
                                  choice, additional package dependencies may
                                  apply. By default it will be parsed from the
                                  output file name but it can be set
                                  explicitly and will then disable the
                                  automatic detection.
  --summarise-at, --summarize-at TEXT
                                  Summarise abundance profiles at higher
                                  taxonomic rank. The provided option must
                                  match a rank in the taxonomy exactly. This
                                  is akin to the clade assigned reads provided
                                  by, for example, kraken2, where the
                                  abundances of a whole taxonomic branch are
                                  assigned to a taxon at the desired rank.
                                  Please note that abundances above the
                                  selected rank are simply ignored. No attempt
                                  is made to redistribute those down to the
                                  desired rank. Some tools, like Bracken, were
                                  designed for this purpose but it doesn't
                                  seem like a problem we can generally solve
                                  here.
  --taxonomy PATH                 The path to a directory containing taxdump
                                  files. At least nodes.dmp and names.dmp are
                                  required. A merged.dmp file is optional.
  --add-name                      Add the taxon name to the output.
  --add-rank                      Add the taxon rank to the output.
  --add-lineage                   Add the taxon's entire lineage to the
                                  output. These are taxon names separated by
                                  semi-colons.
  --add-id-lineage                Add the taxon's entire lineage to the
                                  output. These are taxon identifiers
                                  separated by semi-colons.
  --add-rank-lineage              Add the taxon's entire rank lineage to the
                                  output. These are taxon ranks separated by
                                  semi-colons.
  -h, --help                      Show this message and exit.