Data

Tools

Indexes

Applications

Experiments

Open Source Science

bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

https://github.com/bxlab/bx-python

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    17 of 34 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords from Contributors

bioinformatics genomics usegalaxy dna ngs sequencing workflow-engine closember pypi cloudman
Last synced: 10 months ago · JSON representation

Repository

Tools for manipulating biological data, particularly multiple sequence alignments

Basic Info
  • Host: GitHub
  • Owner: bxlab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 8.96 MB
Statistics
  • Stars: 158
  • Watchers: 11
  • Forks: 53
  • Open Issues: 19
  • Releases: 20
Created about 10 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

Build Status

Read the Docs

bx-python

The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:

  • Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
  • Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
  • Data structures for working with intervals on sequences
    • "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
    • "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation

Requirements

Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu).

Installing

The package can be installed with pip:

pip install bx-python

It is available in bioconda (recommended):

conda install -c conda-forge -c bioconda bx-python

It is available in Debian and Ubuntu:

sudo apt install python3-bx

Or can be built from a checkout of the repository:

python setup.py install

Owner

  • Name: Taylor Lab at Johns Hopkins University
  • Login: bxlab
  • Kind: organization
  • Email: james@taylorlab.org
  • Location: Atlanta, GA

GitHub Events

Total
  • Watch event: 11
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 2
Last Year
  • Watch event: 11
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 774
  • Total Committers: 34
  • Avg Commits per committer: 22.765
  • Development Distribution Score (DDS): 0.651
Past Year
  • Commits: 17
  • Committers: 3
  • Avg Commits per committer: 5.667
  • Development Distribution Score (DDS): 0.588
Top Committers
Name Email Commits
James Taylor j****s@j****g 270
Bob Harris r****s@b****u 137
Nicola Soranzo n****o@e****k 79
Ian Schenk i****n@b****u 58
David King d****g@b****u 46
Kanwei Li k****i@g****m 27
Adam Labadorf a****f@g****m 23
Lucille Delisle l****e@e****h 20
Dan Blankenberg d****n@b****u 14
Marcel Bargull m****l@u****u 14
mvdbeek m****k@g****m 13
guru d****l@l****t 11
Matthew Ruffalo m****o@c****u 9
olgert denas g****s@g****m 9
Nate Coraor n****e@b****u 7
brentp b****e@g****m 7
Guruprasad Ananda g****0@b****u 4
Greg Von Kuster g****g@b****u 3
Radmila Kompova r****o@i****o 3
adadiehl a****l@u****u 3
James Taylor j****r@e****u 2
Nicola Soranzo n****o@t****k 2
Brad Chapman c****b@5****m 2
Steffen Möller m****r@d****g 1
odidev o****v@p****m 1
Jacob Silterra j****r@g****m 1
Nicola Soranzo n****o@g****m 1
sontek s****k@g****m 1
Nicola Soranzo n****o@t****t 1
Hayato anzawa a****a@s****p 1
and 4 more...
Committer Domains (Top 20 + Academic)
bx.psu.edu: 7 jamestaylor.org: 1 earlham.ac.uk: 1 epfl.ch: 1 udo.edu: 1 case.edu: 1 ifi.uio.no: 1 umich.edu: 1 emory.edu: 1 tgac.ac.uk: 1 50mail.com: 1 debian.org: 1 puresoftware.com: 1 tiscali.it: 1 sb.ecei.tohoku.ac.jp: 1 princeton.edu: 1 me.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 57
  • Total pull requests: 45
  • Average time to close issues: 10 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 50
  • Total pull request authors: 16
  • Average comments per issue: 2.14
  • Average comments per pull request: 1.67
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 3
  • Average time to close issues: about 24 hours
  • Average time to close pull requests: about 20 hours
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 1.8
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • yurivict (4)
  • songtaogui (3)
  • tirkarthi (2)
  • Carldeboer (2)
  • scottgigante (1)
  • peterch405 (1)
  • mikpom (1)
  • EricDeveaud (1)
  • alexlenail (1)
  • zxl124 (1)
  • mufernando (1)
  • hmontenegro (1)
  • lzamparo (1)
  • brobr (1)
  • endrebak (1)
Pull Request Authors
  • nsoranzo (17)
  • mr-c (13)
  • mvdbeek (4)
  • lldelisle (3)
  • jxtx (2)
  • mbargull (1)
  • cclauss (1)
  • smoe (1)
  • adamlabadorf (1)
  • ronin-gw (1)
  • adadiehl (1)
  • cool-RR (1)
  • juliangehring (1)
  • santosh653 (1)
  • odidev (1)
Top Labels
Issue Labels
Pull Request Labels
bug (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 30,128 last-month
  • Total docker downloads: 381,090
  • Total dependent packages: 20
    (may contain duplicates)
  • Total dependent repositories: 133
    (may contain duplicates)
  • Total versions: 26
  • Total maintainers: 2
pypi.org: bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

  • Versions: 23
  • Dependent Packages: 15
  • Dependent Repositories: 133
  • Downloads: 30,128 Last month
  • Docker Downloads: 381,090
Rankings
Dependent packages count: 0.8%
Docker downloads count: 0.9%
Dependent repos count: 1.3%
Downloads: 1.5%
Average: 2.7%
Forks count: 5.7%
Stargazers count: 6.0%
Maintainers (1)
nsoranzo
Last synced: 10 months ago
spack.io: py-bx-python

The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

  • Versions: 3
  • Dependent Packages: 5
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 9.7%
Average: 10.2%
Forks count: 14.4%
Stargazers count: 16.8%
Maintainers (1)
adamjstewart
Last synced: 10 months ago

Dependencies

.github/workflows/deploy.yaml actions
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • docker/setup-qemu-action v1 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/test.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
doc/requirements.txt pypi
  • numpy *