mutpath_compact_trees.py

Script compacting BEAST .trees files produced using the Markov Jumps mutation mapping feature.

Run this script by typing the script name followed by the name of the .trees file that you want to compact, for example:

mutpath_compact_trees.py largefile.trees

Or if the script is not executable on your platform:

python mutpath_compact_trees.py largefile.trees

These commands will create a more compact version of the file called largefile_compact.trees.

Motivation and details

Running BEAST while mapping mutations to the branches tends to create very large output .trees files due to the large amount of information written. Most of the information is not actually necessary for reconstructing the mutational path. This script makes compact versions by removing information that is not needed to build mutational paths using the mutpath package. You can then store these compact .trees files more easily.

This script takes as input a .trees file created by running BEAST with Markov Jumps mutation mapping. You provide it with a single argument giving the name of the non-compacted .trees file. It creates a new compact version of the file in which the suffix .trees has been replaced by _compact.trees. If a file with the name of this compacted file already exists, the script exits printing an error message. If the specified input file does not exist, the script exists with an error.

Once you have created the _compact.trees file, you should be able to delete the original .trees file and still do all of the mutational mapping using the more compact version. However, the script does not delete the non-compacted file itself – you must do this manually.

The .trees file is compacted by doing the following to all of the lines containing trees:

1. All of the entries of the form c_allTransitions=4.5 are removed.
2. All of the entries of the form &states=”MATGA” (giving sequence states) are removed.
3. All of the history_all notations are replaced with the more compact h in the lines giving the mutations, sites, and times.
4. All of the decimal numbers specifying the branch lengths are rounded to just four decimal places (so 3.872141428850743 becomes 3.8721, for example). Although this slightly decreases the numerical accuracy, for reasonable branch lengths the difference should be unimportant.

Example

Here is example usage of this script to shrink a file called prots.trees into the more compact prots_compact.trees, and then delete the larger prots.trees file:

% du -h prots.trees
939M    prots.trees
% mutpath_compact_trees.py prots.trees
% du -h prots_compact.trees
40M prots_compact.trees
% rm prots.trees