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Open Source Science

https://github.com/databio/bedshift

Bedfile perturbation tool

https://github.com/databio/bedshift

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.4%) to scientific vocabulary

Keywords

genomic-intervals genomic-regions region-of-interest
Last synced: 11 months ago · JSON representation

Repository

Bedfile perturbation tool

Basic Info
  • Host: GitHub
  • Owner: databio
  • License: bsd-2-clause
  • Language: Python
  • Default Branch: master
  • Homepage: http://bedshift.databio.org
  • Size: 728 KB
Statistics
  • Stars: 17
  • Watchers: 15
  • Forks: 3
  • Open Issues: 4
  • Releases: 2
Topics
genomic-intervals genomic-regions region-of-interest
Created almost 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

Bedshift

Docs: bedshift.databio.org

Install from PyPi: pip install bedshift

Install from local repository: pip install .

Command line

Run with:

bedshift -l tests/hg38.chrom.sizes -b tests/test.bed

See bedshift -h for parameters.

Python

```py import bedshift

bedshifter = bedshift.Bedshift('tests/test.bed', 'hg38.chrom.sizes') bedshifter.all_perturbations(addrate=0.3, addmean=320.0, addstdev=20.0, shiftrate=0.3, shiftmean=-10.0, shiftstdev=120.0, cutrate=0.1, mergerate=0.11, droprate=0.03)

can also run single operations: shift, add, cut, merge, drop

bedshifter.tobed('testoutput.bed') ```

Development

Run tests (from this directory):

python -m unittest

Double check the output files to see if the regions make sense.

build docs:

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 146
  • Total Committers: 3
  • Avg Commits per committer: 48.667
  • Development Distribution Score (DDS): 0.459
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
aaron-gu a****m@v****u 79
nsheff n****f 48
Hyun Jae Cho h****c@v****u 19
Committer Domains (Top 20 + Academic)
virginia.edu: 2

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 39
  • Total pull requests: 51
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 14 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 1.69
  • Average comments per pull request: 0.88
  • Merged pull requests: 40
  • 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
  • nsheff (11)
  • aaron-gu (9)
  • nleroy917 (2)
Pull Request Authors
  • aaron-gu (13)
  • berkuva (10)
  • nsheff (5)
Top Labels
Issue Labels
bug (8) enhancement (6) documentation (1) help wanted (1)
Pull Request Labels

Dependencies

requirements/requirements-all.txt pypi
  • logmuse *
  • numpy *
  • pandas *
  • pyranges *
requirements/requirements-doc.txt pypi
  • sorted_nearest *
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
pyproject.toml pypi
setup.py pypi