https://github.com/robaina/jplaceparser

A python parser for jplace (evolutionary placement) files
https://github.com/robaina/jplaceparser

bioinformatics computational-biology evolutionary-algorithms phylogenetic-trees phylogenetics python

Last synced: 2 months ago
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A python parser for jplace (evolutionary placement) files

• Host: GitHub
• URL: https://github.com/robaina/jplaceparser
• Owner: Robaina
• License: apache-2.0
• Created: 2021-11-15T15:57:39.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-12-18T14:19:11.000Z (over 2 years ago)
• Last Synced: 2025-04-06T10:38:00.902Z (2 months ago)
• Topics: bioinformatics, computational-biology, evolutionary-algorithms, phylogenetic-trees, phylogenetics, python
• Language: Python
• Homepage:
• Size: 85 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATION.cff

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README

        
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a Python tool to parse and manipulate [JPlace files](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009), the format of [Evolutionary Placement](https://arxiv.org/abs/0911.2852) results.

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## What is JPLACEparser?

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](https://github.com/lczech/gappa/wiki/Subcommand:-assign#automatic-ratio-example) 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

* Filter my minimum LWR

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```

## Usage

You can find a jupyter notebook with usage examples [here](examples/examples.ipynb).

## Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2022). JPLACEparser: a Python tool to parse and manipulate JPlace files (Version 0.0.1)[Computer software]. https://doi.org/10.5281/zenodo.7031582.