jonchang / beastcommentparser

Extracts and does other stuff with comments from BEAST trees

Purpose

beastcommentparser extracts and formats data from BEAST summary trees for use in downstream analyses.

Dependencies

• Python 2.7
• DendroPy

Installation

OS X

The simplest way is to use Homebrew. With Homebrew:

brew install python
pip install dendropy
pip install https://github.com/jonchang/beastcommentparser/archive/master.zip

Usage

An example BEAST summary tree, arctoid.tree, is included in the examples/ directory.

bcp.py examples/arctoid.tree
#=> Output written to arctoid.txt

Running the program with only a tree as the argument will create a text file of the same name in the current directory. You can then view this file in a spreadsheet program or analzyze it further in R, Python, etc.

Only report on leaf nodes:

bcp.py --report=leaf examples/arctoid.tree

For more options, consult the help:

python bcp.py --help

There is also preliminary support for summary trees from phylogeographic analyses.

beastcommentparser's Issues

Better node labels

bcp should use node labels if present in the source tree. The root node should be labeled as "root", if present. Longest common prefix could also be used to automatically label certain clades.