BiobaseFasta: streaming FASTA parser

[ bioinformatics, gpl, library, program ] [ Propose Tags ]

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 0.0.0.1, 0.0.0.2, 0.0.0.3, 0.0.0.4, 0.0.1.0, 0.2.0.0
Change log changelog.md
Dependencies base (>=4.7 && <5.0), BiobaseTypes (==0.1.4.*), bytestring, deepseq, lens, resourcet (>=1.0), streaming (>=0.1), streaming-bytestring (>=0.1) [details]
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
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 Wed Dec 12 23:43:51 UTC 2018
Distributions NixOS:0.2.0.0
Downloads 2793 total (82 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2018-12-12 [all 1 reports]
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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/