BiobaseFasta: streaming FASTA parser

[ bioinformatics, bsd3, 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.

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), 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]
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
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Reverse Dependencies 4 direct, 0 indirect [details]
Executables fastaextract
Downloads 7381 total (12 in the last 30 days)
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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/