BiobaseFasta: streaming FASTA parser
Stream-based handling of FASTA files. The user selects a window size, the library then handles the window. For each window, the previous (past) window is available, in case some data sits on the boundary between windows.
Greg Schwartz' http://hackage.haskell.org/package/fasta package is a lot more complete. This one is mostly tailored to my usage requirements (and may at some point use his library).
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- BiobaseFasta-0.4.0.1.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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| Versions [RSS] | 0.0.0.1, 0.0.0.2, 0.0.0.3, 0.0.0.4, 0.0.1.0, 0.2.0.0, 0.3.0.0, 0.3.0.1, 0.4.0.0, 0.4.0.1 |
|---|---|
| Change log | changelog.md |
| Dependencies | base (>=4.7 && <5.0), BiobaseFasta, BiobaseTypes (>=0.2.1 && <0.2.2), bytestring, DPutils (>=0.1.1 && <0.1.2), lens (>=4.0), optparse-applicative (>=0.14), resourcet (>=1.0), streaming (>=0.1), streaming-bytestring (>=0.2), string-conversions (>=0.4) [details] |
| Tested with | ghc ==8.8.4, ghc ==8.10.4, ghc ==9.0 |
| License | BSD-3-Clause |
| Copyright | Christian Hoener zu Siederdissen, 2011-2021 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Category | Bioinformatics |
| Home page | https://github.com/choener/BiobaseFasta |
| Bug tracker | https://github.com/choener/BiobaseFasta/issues |
| Source repo | head: git clone git://github.com/choener/BiobaseFasta |
| Uploaded | by ChristianHoener at 2021-06-04T13:59:41Z |
| Distributions | |
| Reverse Dependencies | 4 direct, 0 indirect [details] |
| Executables | fastaextract |
| Downloads | 7445 total (26 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
| Your Rating | |
| Status | Docs available [build log] Last success reported on 2021-06-04 [all 1 reports] |
Readme for BiobaseFasta-0.4.0.1
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BiobaseFasta
A Haskell library for FASTA-file handling.
The version does streaming using the 'streaming' library.
The library is, in general, in a "preview" state. In cases where you need to scan large FASTA files fast and with low memory overhead, the functions within should already be useable enough.
The wikipedia has information on the format:
http://en.wikipedia.org/wiki/FASTA_format
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/