smutch / treefrog-meraxes_augmented_stats

Calculate Meraxes augmented stats file for Treefrog trees.

Treefrog augmented stats for Meraxes

author: Simon Mutch

Installation

pip install --user git+https://github.com/smutch/treefrog-meraxes_augmented_stats

This will install 3 command line tools in your current python environment.

treefrog_gen_alist

Use this to generate an expansion factor list from a Treefrog file. It accepts one input argument - the path to the Treefrog file.

treefrog_gen_forestinfo

Use this to generate the forest info files required for Meraxes to do it's domain decomposition.

Usage:

treefrog_gen_forestinfo [OPTIONS] FNAME_IN FNAME_OUT

Note that this script will make use of multiple threads and/or processes.

treefrog_test_forestinfo

Use this to do some simple sanity checks on the produced forest info file from treefrog_gen_forestinfo.

Usage:

treefrog_test_forestinfo FNAME_IN