BiobaseFasta: conduit-based FASTA parser

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

Conduit-based handling of FASTA files. This library provides a streaming interface. The user selects a window size, 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.

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 streamFasta function, however, should already be useable enough.

Versions 0.0.0.1, 0.0.0.2, 0.0.0.3, 0.0.0.4, 0.0.1.0
Change log changelog
Dependencies base (>3 && <5), biocore (>=0.2), bytestring, cmdargs (==0.10.*), conduit (==0.5.*), containers, transformers [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2011-2013
Author Christian Hoener zu Siederdissen
Maintainer choener@tbi.univie.ac.at
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Source repo head: git clone git://github.com/choener/BiobaseFasta
Uploaded by ChristianHoener at Fri Dec 6 21:54:37 UTC 2013
Distributions NixOS:0.0.1.0
Executables FastaTool
Downloads 2550 total (8 in the last 30 days)
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Status Docs available [build log]
Successful builds reported [all 1 reports]
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