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
pip install jplaceparser
or
-
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_jplaceFiltering 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 |
