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qax list

This is the default subprogram.

Synopsis:

Usage: list [options] [<inputfile> ...]

Options:
  -a, --all              Show all fields [default: false]
  --abs                  Show absolute paths [default: false]
  -b, --basename         Use basename instead of path [default: false]
  -s, --sortby SORT      Column to sort (uuid, type, format, date) [default: type]
  -f, --force            Accept non standard extensions
  --verbose              Verbose output
  --help                 Show this help

Nice output (default):
  -d, --datetime         Show artifact's date time [default: false]
  -u, --uuid             Show uuid [default: false]

Raw table output:
  -r, --rawtable         Print a CSV table (-s) with all fields [default: false]   
  -h, --header           Print header [default: false]
  -z, --separator SEP    Separator when using --rawtable [default: tab]

This is the default module, so its name can be omitted. This means that the following two commands are equivalent:

qxa list directory/*.qza
qxa directory/*.qza

File path

By default the file path will be printed as received by the program. Witht -b (--basename) the basename will be printed instead, and wiht --abs the absolute path.

Output

The program will prepare a table with the artifacts metadata, supporting a nice Unicode table (default) or a raw computer-friendly tabular output (enabled with -r).

Nice (Unicode) table

By default, only path, type and format of the artifact are printed:

┌────────────────────┬───────────────────────┬─────────────────────────────┐
│ Path               │ Type                  │ Format                      │
├────────────────────┼───────────────────────┼─────────────────────────────┤
│ input/rep-seqs.qza │ FeatureData[Sequence] │ DNASequencesDirectoryFormat │
│ input/taxonomy.qzv │ Visualization         │ HTML                        │
└────────────────────┴───────────────────────┴─────────────────────────────┘

With -u the UUID is added, with -d the generation timestamp is added. With -a all fields are printed:

┌──────────────────────────────────────┬──────────────┬───────────────────────┬─────────────────────────────┬───────────┬──────────────────┬───────┐
│ ID                                   │ Basename     │ Type                  │ Format                      │ Version   │ Date             │ Files │
├──────────────────────────────────────┼──────────────┼───────────────────────┼─────────────────────────────┼───────────┼──────────────────┼───────┤
│ bb1b2e93-0c45-4c8e-a140-2afa2110b5fb │ rep-seqs.qza │ FeatureData[Sequence] │ DNASequencesDirectoryFormat │ 2019.10.0 │ 2020-11-12;17:23 │ 1     │
│ 35c32fe7-3eb5-4b31-aa34-85ef27545f00 │ taxonomy.qzv │ Visualization         │ HTML                        │ 2019.10.0 │ 2020-11-12;17:23 │ 18    │
└──────────────────────────────────────┴──────────────┴───────────────────────┴─────────────────────────────┴───────────┴──────────────────┴───────┘

Raw tabular output

With the raw tabular output all the fields are printed, to allow easier parsing. By default the fields are separated by tabs, but a different separator can be specified (-s SEP).

The fields are:

  1. UUID (e.g. b1b2e93-0c45-4c8e-a140-2afa2110b5fb)
  2. File path (e.g. rep-seqs.qza)
  3. Artifact Type (e.g. FeatureData[Sequence])
  4. Artifact Format (e.g. DNASequencesDirectoryFormat)
  5. Qiime2 Version (e.g. 2019.10.0)
  6. Timestamp (e.g. 2020-11-12;17:23 )
  7. Data files contained (e.g. 1)

Usage examples

To find an artifact given the ID:

find ${PATH_TO_SCAN} -name "*.qz?" | xargs qxa | grep ${UUID}

Performance

Using hyperfine to compare the performance with Qiime2:

hyperfine --export-markdown docs/list_speed.md "qiime tools peek input/taxonomy.qzv" "./bin/qax input/taxonomy.qzv"
Command Mean [s] Min [s] Max [s] Relative
qiime tools peek input/taxonomy.qzv 1.981 ± 0.056 1.925 2.087 109.58 ± 34.30
./bin/qax input/taxonomy.qzv 0.018 ± 0.006 0.011 0.031 1.00