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liftover

liftover for python, made fast with cython

https://github.com/jeremymcrae/liftover

Science Score: 13.0%

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.3%) to scientific vocabulary

Keywords

cython liftover python
Last synced: 6 months ago · JSON representation

Repository

liftover for python, made fast with cython

Basic Info
  • Host: GitHub
  • Owner: jeremymcrae
  • License: mit
  • Language: C++
  • Default Branch: main
  • Homepage:
  • Size: 1.35 MB
Statistics
  • Stars: 89
  • Watchers: 1
  • Forks: 6
  • Open Issues: 0
  • Releases: 17
Topics
cython liftover python
Created about 7 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

liftover

python liftover utility

Converts point coordinates between genome assemblies. Inspired by pyliftover, this offers a few advantages: - ~5X faster, and lower memory requirements, as loading the chain file and converting coordinates is implemented in c++. - dictionary style conversion, as in access converted coordinates via converter[chrom][pos]

Installation

Install via pip: pip install liftover

Usage

```python from liftover import get_lifter

converter = getlifter('hg19', 'hg38', onebased=True) chrom = '1' pos = 103786442 converter[chrom][pos]

other synonyms for the lift call

converter.convert_coordinate(chrom, pos) converter.query(chrom, pos)

alternatively create a converter directly from a chainfile

from liftover import ChainFile converter = ChainFile('/home/user/hg18ToHg38.over.chain.gz', one_based=True) converter[chrom][pos]

you can also specify an alternative website to load chain files from

converter = getlifter('hg19', 'hg38', chainserver='https://www.example.com') ```

Owner

  • Name: Jeremy McRae
  • Login: jeremymcrae
  • Kind: user
  • Location: San Francisco Bay Area
  • Company: Illumina

GitHub Events

Total
  • Issues event: 2
  • Watch event: 11
  • Push event: 3
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 11
  • Push event: 3
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 80
  • Total Committers: 4
  • Avg Commits per committer: 20.0
  • Development Distribution Score (DDS): 0.188
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jeremy McRae j****e@i****m 65
Jeremy McRae j****e@g****m 13
Nicholas Knoblauch k****h@h****m 1
marius-mather 6****r 1
Committer Domains (Top 20 + Academic)
hey.com: 1 illumina.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 18
  • Total pull requests: 4
  • Average time to close issues: 25 days
  • Average time to close pull requests: about 11 hours
  • Total issue authors: 18
  • Total pull request authors: 4
  • Average comments per issue: 1.61
  • Average comments per pull request: 0.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 20 days
  • Average time to close pull requests: about 21 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • xiucz (1)
  • Shicheng-Guo (1)
  • TheKursta (1)
  • spsc83 (1)
  • Dearwunan (1)
  • ahstram (1)
  • Yiming-Shen (1)
  • akotlar (1)
  • mbaudis (1)
  • dprat (1)
  • lidd77 (1)
  • rkimoakbioinformatics (1)
  • ichauchcc (1)
  • leipzig (1)
  • Mr-Milk (1)
Pull Request Authors
  • akotlar (2)
  • dependabot[bot] (2)
  • CreRecombinase (1)
  • marius-mather (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4,806 last-month
  • Total dependent packages: 6
  • Total dependent repositories: 5
  • Total versions: 24
  • Total maintainers: 1
pypi.org: liftover

Package for converting between genome build coordinates

  • Versions: 24
  • Dependent Packages: 6
  • Dependent Repositories: 5
  • Downloads: 4,806 Last month
Rankings
Dependent packages count: 1.6%
Downloads: 5.6%
Dependent repos count: 6.6%
Average: 7.7%
Stargazers count: 9.3%
Forks count: 15.3%
Maintainers (1)
jeremy.mcrae
Last synced: 7 months ago

Dependencies

.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • pypa/cibuildwheel v2.9.0 composite
  • pypa/gh-action-pypi-publish release/v1 composite
setup.py pypi
  • urllib3 *
pyproject.toml pypi