clustertools: Tools for manipulating sequence clusters
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.
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- clustertools-0.1.5.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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Versions [RSS] | 0.1, 0.1.1, 0.1.2, 0.1.5 |
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Dependencies | base (>=4 && <5), bio (>=0.4), bytestring, containers, QuickCheck, regex-compat, simpleargs (>=0.1) [details] |
Tested with | ghc ==6.10.4 |
License | LicenseRef-GPL |
Author | Ketil Malde |
Maintainer | Ketil Malde <ketil@malde.org> |
Category | Bioinformatics |
Home page | http://malde.org/~ketil/ |
Uploaded | by KetilMalde at 2011-06-06T13:02:03Z |
Distributions | |
Reverse Dependencies | 1 direct, 0 indirect [details] |
Executables | xcerpt, clusterlibs, ace2clusters, ace2fasta, ace2contigs, add_single, clusc, filter |
Downloads | 3704 total (8 in the last 30 days) |
Rating | (no votes yet) [estimated by Bayesian average] |
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Status | Docs not available [build log] All reported builds failed as of 2016-11-10 [all 10 reports] |