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ssw

🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD

https://github.com/nanxstats/ssw-r

Science Score: 13.0%

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Keywords

bioinformatics reticulate sequence-alignment simd smith-waterman
Last synced: 6 months ago · JSON representation

Repository

🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD

Basic Info
  • Host: GitHub
  • Owner: nanxstats
  • License: other
  • Language: R
  • Default Branch: main
  • Homepage: https://nanx.me/ssw-r/
  • Size: 1.36 MB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Topics
bioinformatics reticulate sequence-alignment simd smith-waterman
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Code of conduct

README.md

ssw-r

R-CMD-check CRAN status <!-- badges: end -->

ssw-r offers an R interface for SSW, a fast implementation of the Smith-Waterman algorithm for sequence alignment using SIMD. ssw-r is currently built on the Python package ssw-py.

Installation

You can install ssw-r from CRAN once available:

r install.packages("ssw")

Or try the development version on GitHub:

r remotes::install_github("nanxstats/ssw-r")

Install ssw-py

A simple way to install the Python package ssw-py that ssw-r can discover easily, is to run the helper function ssw::install_ssw_py(). By default, it installs ssw-py into an virtual environment named r-ssw-py.

r ssw::install_ssw_py()

This follows the best practices suggested by the reticulate vignette Managing an R Package's Python Dependencies. There are also recommendations in the vignette on how to manage multiple R packages with different Python dependencies.

Usage

r library("ssw")

r "ACGT" |> align("TTTTACGTCCCCC")

```text CIGAR start index 4: 4M optimalscore: 8 sub-optimalscore: 0 targetbegin: 4 targetend: 7 querybegin: 0 queryend: 3

Target: 4 ACGT 7 |||| Query: 0 ACGT 3 ```

r "ACGT" |> align("TTTTACTCCCCC", gap_open = 3)

```text CIGAR start index 4: 2M optimalscore: 4 sub-optimalscore: 0 targetbegin: 4 targetend: 5 querybegin: 0 queryend: 1

Target: 4 AC 5 || Query: 0 AC 1 ```

r "ACTG" |> force_align("TTTTCTGCCCCCACG") |> formatter(print = TRUE)

text TTTTCTGCCCCCACG ACTG

For detailed usage, see the vignette.

Acknowledgements

ssw-r is built upon the work of two outstanding projects:

  1. SSW - Original C implementation. Author: Mengyao Zhao
  2. ssw-py - Python binding for SSW. Author: Nick Conway

We extend our sincere gratitude to Mengyao Zhao for developing the original SSW library and to Nick Conway for maintaining the ssw-py package. Their work forms the foundation of ssw-r. While ssw-r does not directly incorporate code from these projects, it serves as an R interface to their functionality. We encourage users to visit the original repositories for more information about the underlying implementation and to consider citing these works in publications that use ssw-r.

Code of Conduct

Please note that the ssw-r project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

  • Name: Nan Xiao
  • Login: nanxstats
  • Kind: user
  • Location: Upper Gwynedd, PA
  • Company: Merck & Co.

Statistician

GitHub Events

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

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 8
  • Total pull requests: 16
  • Average time to close issues: 7 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.88
  • Average comments per pull request: 0.0
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 16
  • Average time to close issues: 8 days
  • Average time to close pull requests: 1 minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • nanxstats (6)
  • mantzaris (2)
Pull Request Authors
  • nanxstats (30)
Top Labels
Issue Labels
cran (3) enhancement (2) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 410 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: ssw

Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 410 Last month
Rankings
Dependent packages count: 28.3%
Dependent repos count: 34.9%
Average: 49.9%
Downloads: 86.7%
Maintainers (1)
me@nanx.me
Last synced: 6 months ago