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Bedparse

Bedparse: feature extraction from BED files - Published in JOSS (2019)

https://github.com/tleonardi/bedparse

Science Score: 95.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 7 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

bed-files bioinformatics cli
Last synced: 4 months ago · JSON representation

Repository

Python module and CLI tool to perform operations on BED files

Basic Info
  • Host: GitHub
  • Owner: tleonardi
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage: http://bedparse.rtfd.io
  • Size: 67.4 MB
Statistics
  • Stars: 13
  • Watchers: 3
  • Forks: 4
  • Open Issues: 4
  • Releases: 2
Topics
bed-files bioinformatics cli
Created over 8 years ago · Last pushed almost 6 years ago
Metadata Files
Readme Changelog Contributing License

README.md

Build Status Docs Status JOSS Status DOI License: MIT

Bedparse

Bedparse is a simple python module and CLI tool to perform common operations on BED files.

It offers 11 sub-commands that implement the following functionality: * filter: Filtering of transcripts based on annotations * join: Joining of annotation files based on transcript names * gtf2bed: Conversion from GTF to BED format * convertChr: Conversion from UCSC to Ensembl chromosome names (and viceversa) * bed12tobed6: Conversion from bed12 to bed6 * promoter: Promoter reporting * introns: Intron reporting * cds: CDS reporting * 3pUTR and 5pUTR: UTR reporting * validateFormat: Check that the file conforms with the BED format

Installation

Installing is as simple as:

pip install bedparse

Basic usage

The basic syntax in the form: bedparse subcommand [parameters].

For a list of all subcommands and a brief explanation of what they do, use: bedparse --help.

For a detailed explanation of each subcommand and a list of its parameters, use the --help option after the subcommand's name, e.g.: bedparse promoter --help

Documentation

Our documentation is hosted on Read the Docs.

We also have a short tutorial to guide you through the basic functions.

Publications

If you use bedparse please cite the following paper:

Leonardi, (2019). Bedparse: feature extraction from BED files. Journal of Open Source Software, 4(34), 1228, https://doi.org/10.21105/joss.01228

Owner

  • Name: Tommaso Leonardi
  • Login: tleonardi
  • Kind: user

JOSS Publication

Bedparse: feature extraction from BED files
Published
February 28, 2019
DOI
Volume 4, Issue 34, Page 1228
Authors
Tommaso Leonardi ORCID
The Gurdon Institute, University of Cambridge, Cambridge, UK, Center for Genomic Science IIT\@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
Editor
Roman Valls Guimera ORCID
Tags
Bioinformatics Genomics BED format
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GitHub Events

Total
Last Year

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 111
  • Total Committers: 3
  • Avg Commits per committer: 37.0
  • Development Distribution Score (DDS): 0.441
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Tommaso Leonardi t****m@i****z 62
Tommaso Leonardi t****m@t****o 45
Tommaso Leonardi t****4@e****k 4
Committer Domains (Top 20 + Academic)
ebi.ac.uk: 1 tleo.io: 1 itm6.xyz: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 15
  • Total pull requests: 9
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 0.67
  • Average comments per pull request: 1.0
  • Merged pull requests: 9
  • 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
  • tleonardi (9)
  • Benjamin-Lee (4)
  • samir-watson (1)
  • lucapandolfini (1)
Pull Request Authors
  • Benjamin-Lee (5)
  • camillaugolini-iit (2)
  • arfon (1)
  • tleonardi (1)
Top Labels
Issue Labels
Feature request (2) TODO (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 327 last-month
  • Total docker downloads: 51
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: bedparse

A simple library and CLI tool to manipulate BED files

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 327 Last month
  • Docker Downloads: 51
Rankings
Docker downloads count: 2.9%
Dependent packages count: 10.1%
Forks count: 15.4%
Stargazers count: 16.1%
Average: 16.3%
Dependent repos count: 21.6%
Downloads: 31.6%
Maintainers (1)
tleonardi
Last synced: 4 months ago

Dependencies

setup.py pypi
  • argparse *
  • setuptools *