Command line interface

Tszip is intended to be used primarily as a command line interface. The interface for tszip is modelled directly on gzip, and so it should hopefully be immediately familiar and useful to many people. Tszip automatically installs the tszip and tsunzip programs, but depending on your setup, these may not be on your PATH. A slightly less convenient (but reliable) method of running tszip is the following:

python3 -m tszip

Online help is available using the --help option.

The tsunzip program is an alias for tszip -d.

tszip

The following is a placeholder for the argparse directive which is used to auto-generate documentation for a command-line interface defined in a Python module. This requires the sphinx-argparse extension or similar functionality in Jupyter Book.

Compress/decompress tskit trees files.

usage: tszip [-h] [-V] [-v] [--variants-only] [-S SUFFIX] [-k] [-f] [-c]
             [-d | -l]
             files [files ...]

Positional Arguments

files

The files to compress/decompress.

Named Arguments

-V, --version

show program’s version number and exit

-v, --verbosity

Increase the verbosity

Default: 0

--variants-only

Lossy compression; throws out information not needed to represent variants

Default: False

-S, --suffix

Use suffix SUFFIX on compressed files

Default: “.tsz”

-k, --keep

Keep (don’t delete) input files

Default: False

-f, --force

Force overwrite of output file

Default: False

-c, --stdout

Write to stdout

Default: False

-d, --decompress

Decompress

Default: False

-l, --list

List contents of the file

Default: False