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clustertools: Tools for manipulating sequence clusters

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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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Versions [RSS] 0.1, 0.1.1, 0.1.2, 0.1.5
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 (13 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2016-11-10 [all 10 reports]

Readme for clustertools-0.1.5

[back to package description] 
This contains the following tools:

To build these, you will need a Haskell compiler (the most likely
candidate begin GHC), and my bioinformatics library and the SimpleArgs
module installed (Downloadable from: <http://malde.org/~ketil/biohaskell/>).

filter - remove unwanted sequences from a clustering
         usage: filter seq.list < cluster.L > cluster2.L
         cluster2.L will only contain sequence labels found in seq.list

hist   - produce a histogram of cluster sizes from a "label"-formatted
         clustering.

clusc  - compare clusterings, calculating numerous pair-based and
         entropy based indices.

xcerpt - given a file containing a list of sequence labels (e.g. a
         "label" formatted clustering), extract matching sequences
         from a FASTA file.  Like "agrep -d '^>'" without the bugs.

         Usage: xcerpt list.txt fasta.seq
         creates "fasta.seq.match" and "fasta.seq.rest"

add_single - add singletons to a clustering.
        Usage: add_single all.L clustering.L
        creates clustering.L_s listing all sequences in all.L but not in
        clustering.L, one per line.

ace2contigs - parse an ACE assembly file, and output the contigs in a
        FASTA file (named by tacking on .fasta to the ACE file name),
        and the corresponding quality information (.qual).

ace2fasta - parse an ACE assembly, and output each assembly in a separate
        FASTA formatted file, with the necessary gaps inserted to align the
        sequences (suitable for import into e.g. Seaview)

ace2clusters - parse an ACE assembly, and output clusters composed of the
 	sequences used for each contig.  The format is similar to TGICL's, 
	with cluster output as one line consisting of a '>' and the contig name,
	and the next line containing the names of the sequences that comprise
	the cluster.

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.