Name:                clustertools
Version:             0.1.5
License:             GPL
License-file:        LICENSE
Author:              Ketil Malde
Maintainer:          Ketil Malde <ketil@malde.org>

Category:            Bioinformatics
Synopsis:            Tools for manipulating sequence clusters
Description:         This is a bunch of stuff I needed at some for manipulating sequence
                     clusters. See the README for details. The tools included are:
                     .
                     * filter - remove unwanted sequences from a clustering
                     .
                     * hist   - produce a histogram of cluster sizes from a "label"-formatted clustering.
                     .
                     * clusc  - compare clusterings, calculating numerous pair-based and entropy based indices.
                     .
                     * add_single - add singletons to a clustering.
                     .
                     * ace2contigs - parse an ACE assembly file, and output the contigs in a FASTA file.
                     .
                     * ace2fasta - parse an ACE assembly, and output each assembly in a separate FASTA file
                     .
                     * ace2clusters - parse an ACE assembly, and output clusters in TGICL format
                     .
                     * clusterlibs - given a table of regular expressions and library names, along with a
                     clustering (TGICL-format), output a table of cluster sizes per library.
                     .
                     * xcerpt - extract sequences from a list of sequence labels.
                     .
                     The Darcs repository is at: <http://malde.org/~ketil/biohaskell/cluster_tools>.
Homepage:            http://malde.org/~ketil/

Tested-With:         GHC==6.10.4
Build-Type:          Simple
Cabal-Version:       >= 1.2

Data-Files:          README

Executable filter
           Hs-source-dirs: src
           Main-Is:     Filter.hs
           Build-Depends:       base >= 4 && < 5, containers, simpleargs>=0.1
           ghc-options:         -Wall -funbox-strict-fields

Executable clusc
           Hs-source-dirs: src
           Main-Is:     Cluscomp.lhs
           Build-Depends: bytestring
           Ghc-Options: -Wall

Executable add_single
           Hs-source-dirs: src
           Main-Is:     AddSingletons.hs
           Ghc-Options: -Wall

Executable ace2contigs
           Hs-source-dirs: src
           Main-Is:     Ace2Contigs.hs
           Build-depends: bio>=0.3.3.4
           Ghc-Options: -Wall

Executable ace2fasta
           Hs-source-dirs: src
           Main-Is:     Ace2Fasta.hs
           Build-depends: bio>=0.4
           Ghc-Options: -Wall

Executable ace2clusters
           Hs-source-dirs: src
           Main-Is:     Ace2Clusters.hs
           Build-depends: bio>=0.3.3.4
           Ghc-Options: -Wall

Executable clusterlibs
           Hs-source-dirs: src
           Main-Is:     ClusterLibs.hs
           Other-modules: Statistics, Formats
           Build-depends: regex-compat, QuickCheck
           Ghc-Options: -Wall

Executable xcerpt
           Hs-source-dirs: src
           Main-Is:     Xcerpt.lhs
           Ghc-Options: -Wall