jplaceparser 0.0.2

Tools to parse the JPLACE files

JplaceParser

Python tools to parse and manipulate JPlace files, the format of Evolutionary Placement results.

JplaceParser allows not only reading Jplace files as python dictionaries but also manipulating field values and exporting back to jplace files. It contains a number of filters to remove placements that do not satisfy quality criteria. Currently, placements can be filtered by three criteria involving the pendant and distal placement length as well as the phylogenetic tree diameter:

• Filter by maximum pendant length
• Filter by maximum pendant to distal length ratio
• Filter by maximum pendant to tree diameter ratio

This is an ongoing project!

Installation

1. pip install jplaceparser

or

2. Git clone project to local directory.

   In terminal navigate to directory and enter: python setup.py install

from jplaceparser import JplaceParser


jplace = JplaceParser.fromJplaceFile("examples/example.jplace")
jplace

Number of Placements	19
Fields	edge_num, likelihood, like_weight_ratio, distal_length, pendant_length
JplaceParser version	0.0.1
Author	Semidán Robaina Estévez, 2022

filtered_jplace = jplace.filterByMaxPendantToTreeDiameterRatio(
    max_pendant_ratio=0.001
)

filtered_jplace.writeToFile("examples/filtered_example.jplace")

filtered_jplace

Filtering placements for tree diameter: 4.519636416

Number of Placements	9
Fields	edge_num, likelihood, like_weight_ratio, distal_length, pendant_length
JplaceParser version	0.0.1
Author	Semidán Robaina Estévez, 2022