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).

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
[email protected]
http://www.bioinf.uni-leipzig.de/~choener/