General usage

qax is composed by five subprogram, and the general syntax is:

qax [program] parameters

The programs are:

  • list (it's the default action and can be omitteed)
  • extract or x
  • citations or c
  • provenance or p
  • view or v

list

This is the default module, and can be used to list the properties of one or more artifacts.

Some features:

  • Supports multiple files at once
  • 100X times faster than Qiime2
  • Can be used to find an artifact given the ID

Example:

qax_mac -b -u input/*.*
┌───────────────────────────┬────────────────┬─────────────────────────┬─────────────────────────────┐
│ ID                        │ Basename       │ Type                    │ Format                      │
├───────────────────────────┼────────────────┼─────────────────────────┼─────────────────────────────┤
│ bb1b2e93-...-2afa2110b5fb │ rep-seqs.qza   │ FeatureData[Sequence]   │ DNASequencesDirectoryFormat │
│ 313a0cf3-...-befad4ebf2f3 │ table.qza      │ FeatureTable[Frequency] │ BIOMV210DirFmt              │
│ 35c32fe7-...-85ef27545f00 │ taxonomy.qzv   │ Visualization           │ HTML                        │
└───────────────────────────┴────────────────┴─────────────────────────┴─────────────────────────────┘

extract

This program extract the content of an artifact. By default, if a single file is present it will be extracted in the specified path. If multiple files are present, a directory containing them will be created instead.

Example:

# Extract representative sequences (will be called rep-seqs.fasta)
qax x -o ./ rep-seqs.qza

# Extract a visualization (a folder called "taxonomy" will be created)
qax x -o ./ taxonomy.qzv

citations

Each Qiime module provides the citations for the software and resources that it uses, storing the citations in BibTeX format inside the artifacts. The cite module allows to extract all the citations from a list of artifacts, removing the duplicates, thus effectively allowing to prepare the bibliography for a complete Qiime2 analysis.

Example:

qax c files/*.qza > bibliography.bib

provenance

This program allows to print the provenance of an artifact, or to produce a publication grade graph of the provenance.

Example:

# To view a summary
qax p taxonomy.qzv

# To save the plot
qax p -o graph.dot taxonomy.qza

view

This program allows to print the content of an artifact data file to the terminal. If the artifact contains a single file, it will be printed. Otherwise the user can specify one or multiple files to be printed, and if none is specified, a list of files will be printed.

# Example: count the number of representative sequences
qax view rep-seqs.qza | grep -c '>'

make

This program converts a directory containing a website (index.html) into a visualization artifact.

qax make -o report.qzv /path/to/webpage/

New in 0.9.6 Specifying a --type different than Visualization (which is the default), any directory can be included in data, even without an index.html file.