https://github.com/relrod/bioparse

A set of parsing combinators for various bioinformatics sequencing formats using the `parsers` library.
https://github.com/relrod/bioparse

bioinformatics haskell parse

Last synced: 12 days ago
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A set of parsing combinators for various bioinformatics sequencing formats using the `parsers` library.

• Host: GitHub
• URL: https://github.com/relrod/bioparse
• Owner: relrod
• License: bsd-2-clause
• Created: 2014-11-28T10:32:29.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2017-11-15T19:25:33.000Z (almost 7 years ago)
• Last Synced: 2024-10-04T21:21:57.372Z (about 1 month ago)
• Topics: bioinformatics, haskell, parse
• Language: Haskell
• Homepage: https://relrod.github.io/bioparse/
• Size: 1 MB
• Stars: 4
• Watchers: 5
• Forks: 0
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# bioparse

[![Build Status](https://travis-ci.org/relrod/bioparse.svg?branch=master)](https://travis-ci.org/relrod/bioparse)

**NOTE: Don't rely on this for anything critical!**

This is a collection of parsers built on modern tooling (`parsers`, `lens`) for

dealing with biological sequencing formats such as FASTA, FastQ, and phd.

Silly benchmarks here: https://relrod.github.io/bioparse/benchmarks.html

Because we use `parsers`, bioparse will work with a variety of parser combinator

libraries without any code changes. The choice of parser combinator library is

left up to the user/call-site. `attoparsec` should be somewhat fast, but have

less useful errors than, say, something like `trifecta`.

## License

`biocore` is released under the BSD-2 license. See `LICENSE` for details.

Note that we provide instances for `biocore` classes in

[bioparse-biocore-instances](https://github.com/relrod/bioparse-biocore-instances).

`biocore` is released under the LGPL, as is `bioparse-biocore-instances`.