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jplaceparser

A python parser for jplace (evolutionary placement) files

https://github.com/robaina/jplaceparser

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, plos.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords

bioinformatics computational-biology evolutionary-algorithms phylogenetic-trees phylogenetics python
Last synced: 4 months ago · JSON representation ·

Repository

A python parser for jplace (evolutionary placement) files

Basic Info
  • Host: GitHub
  • Owner: Robaina
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 85 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
bioinformatics computational-biology evolutionary-algorithms phylogenetic-trees phylogenetics python
Created about 4 years ago · Last pushed about 3 years ago
Metadata Files
Readme Code of conduct Citation

README.md

logo

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

PyPI GitHub release (latest by date) GitHub license Contributor Covenant DOI


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 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

  1. 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.

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.

Owner

  • Name: Semidán Robaina
  • Login: Robaina
  • Kind: user
  • Location: Atlantic Ocean
  • Company: Hapdera

Computational Biology | Data Science | Python Dev. | Ph.D. Systems Biology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Robaina-Estévez"
    given-names: "Semidán"
    orcid: "https://orcid.org/0000-0003-0781-1677"
title: "JPLACEparser: a Python tool to parse and manipulate JPlace files"
version: 0.0.1
doi: 10.5281/zenodo.7031582
date-released: 2022-08-29
url: "https://github.com/Robaina/JPLACEparser"

GitHub Events

Total
Last Year

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 15
  • Total Committers: 1
  • Avg Commits per committer: 15.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Semidán Robaina Estévez s****a@g****m 15

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 9 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Robaina (2)
Pull Request Authors
Top Labels
Issue Labels
documentation (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 3 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
pypi.org: jplaceparser

Tools to parse the JPLACE files

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 3 Last month
Rankings
Dependent packages count: 6.6%
Average: 24.0%
Stargazers count: 28.2%
Forks count: 30.5%
Dependent repos count: 30.6%
Maintainers (1)
semidan.robaina
Last synced: 4 months ago

Dependencies

setup.py pypi
  • biopython *
  • importlib-metadata *