The bio package

[Tags:lgpl, library]

This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities.

Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading Gene Ontology (GO) annotations (GOA) and definitions/hierarchy.

The Darcs repository is at: http://malde.org/~ketil/biohaskell/biolib.


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Versions 0.3.3, 0.3.3.1, 0.3.3.2, 0.3.3.4, 0.3.5, 0.4, 0.4.4, 0.4.5, 0.4.6, 0.4.7, 0.4.8, 0.5, 0.5.0.1, 0.5.1, 0.5.2, 0.5.3
Dependencies array, base (==4.*), binary (==0.4.*), bytestring (>=0.9.1), containers, mtl, old-time, parallel, parsec, QuickCheck (>=2), random, tagsoup (>=0.4 && <0.8) [details]
License LGPL
Author Ketil Malde
Maintainer ketil@ii.uib.no
Stability Unknown
Category Bioinformatics
Home page http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
Uploaded Tue Jul 20 14:21:41 UTC 2010 by KetilMalde
Distributions FreeBSD:0.5.3, NixOS:0.5.3
Downloads 4154 total (39 in the last 30 days)
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Status Docs uploaded by user
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Readme for bio

Readme for bio-0.4.6

biolib - a Haskell library for bioinformatics

This is a collection of data structures and algorithms
I've found useful when building various bioinformatics-related tools
and utilities.

Current list of features includes: a Sequence data type supporting
protein and nucleotide sequences and conversion between them, quality
data, reading and writing FASTA formatted files, reading TwoBit and
phd formats, and also FastQ.  Rudimentary support for doing alignments
- including dynamic adjustment of scores based on sequence quality -
and Blast output parsing.  Partly implemented single linkage
clustering, and multiple alignment.  Reading and writing 454-style SFF
sequences, with a bunch of useful (and not-so-useful) operations on
them.

To install, you need to acquire a working GHC (possibly other Haskell
system).  You also need the following external libraries:

  QuickCheck   - for unit tests ('make test' to run them)
  binary       - mainly for dealing with the TwoBit sequence format
  tagsoup      - for parsing XML output from Blast
  parsec       - for parsing ACE, Bowtie and Soap output

You should be able to get what you need from <http://hackage.haskell.org/>.

The easiest way these days, is to use 'cabal'.  You can get away with

  cabal install bio

As an alternative, you can build with 'make', doing either 'make
install' if you can sudo, or 'make user_install' if you can not.  Of
course, the Makefile just proxies for the regular Cabal routine, which
will work just as well:

  runhaskell Setup configure
  runhaskell Setup build
  sudo runhaskell Setup install

(Use --prefix=$HOME and remove the sudo, if you don't want to install as root.)

If that didn't work, mail me at <ketil@malde.org>, and we'll try to
work things out.