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' 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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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
Category Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2021-06-04T13:59:41Z
Reverse Dependencies 4 direct, 0 indirect [details]
Executables fastaextract
Downloads 7308 total (15 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-

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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:


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany