The clustertools package
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 clusters with the library name prepended to the sequences.
xcerpt - extract sequences from a list of sequence labels.
The Darcs repository is at: http://malde.org/~ketil/biohaskell/cluster_tools.
Properties
| Versions | 0.1, 0.1.1, 0.1.2, 0.1.5 |
|---|---|
| Dependencies | base (>3), bio (≥0.3.3.4), bytestring, containers, haskell98, QuickCheck, regex-compat, simpleargs (≥0.1) |
| License | GPL |
| Author | Ketil Malde |
| Maintainer | Ketil Malde <ketil@malde.org> |
| Category | Bioinformatics |
| Home page | http://malde.org/~ketil/ |
| Executables | xcerpt, clusterlibs, ace2clusters, ace2fasta, ace2contigs, add_single, clusc, filter |
| Upload date | Fri Jan 30 19:39:20 UTC 2009 |
| Uploaded by | KetilMalde |
| Build failure | ghc-6.10 (log) |
Downloads
- clustertools-0.1.2.tar.gz (Cabal source package)
- package description (included in the package)