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.
FastaTool is a simple tool providing information on FASTA files, and allowing to extract sequences and subsequences.
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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| 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), BiobaseTypes (>=0.1.4 && <0.1.5), bytestring, deepseq, lens, resourcet (>=1.0), streaming (>=0.1), streaming-bytestring (>=0.1) [details] |
| Tested with | ghc ==8.4.3 |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2011-2018 |
| Author | Christian Hoener zu Siederdissen, Florian Eggenhofer |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Uploaded | by ChristianHoener at 2018-12-12T23:43:51Z |
| 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 |
| Distributions | |
| Reverse Dependencies | 4 direct, 0 indirect [details] |
| Downloads | 7723 total (20 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2018-12-12 [all 1 reports] |
Readme for BiobaseFasta-0.2.0.0
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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/