BiobaseInfernal: Infernal data structures and tools
Provides import and export facilities for Infernal/Rfam data formats. We include Stockholm, CM, verbose Infernal results, and tabulated Infernal results. Some small tools are included.
The VerboseHit format is slightly extended to allow simple annotations. This extension should be backward-compatible with standard-compliant parsers.
This package uses Int's to store sequence position information. Don't compile for 32bit. (And yes, this is a TODO, to change to Int64).
Changes in 0.6.0.0
multiple changes to data representation (mostly newtypes) and documentation
load the Rfam.fasta.gz file (and prepare lookup structures)
partial biocore integration
Changes in 0.5.4.1
fix-up for VH export
half-baked CM type (not useful yet)
Modules
- Biobase
- Biobase.Infernal
- Biobase.Infernal.CM
- Biobase.Infernal.CM.Export
- Biobase.Infernal.CM.Import
- Biobase.Infernal.Clan
- Biobase.Infernal.Clan.Import
- Biobase.Infernal.Hit
- Biobase.Infernal.RfamFasta
- Biobase.Infernal.RfamFasta.Import
- Biobase.Infernal.TabularHit
- Biobase.Infernal.TabularHit.Import
- Biobase.Infernal.Taxonomy
- Biobase.Infernal.Taxonomy.Import
- Biobase.Infernal.Types
- Biobase.Infernal.VerboseHit
- Biobase.Infernal.VerboseHit.Export
- Biobase.Infernal.VerboseHit.Import
- Biobase.Infernal.VerboseHit.Internal
- Biobase.Infernal.CM
- Biobase.Infernal
Downloads
- BiobaseInfernal-0.6.0.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
Versions [RSS] | 0.0.2.0, 0.0.2.1, 0.5.0.0, 0.5.1.0, 0.5.2.0, 0.5.3.0, 0.5.3.1, 0.5.4.0, 0.5.4.1, 0.6.0.0, 0.6.0.1, 0.6.2.0, 0.7.0.0, 0.7.0.1, 0.7.1.0, 0.8.1.0 |
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Dependencies | attoparsec, attoparsec-iteratee, base (>3 && <5), biocore, bytestring, containers, either-unwrap, iteratee, iteratee-compress, PrimitiveArray, transformers, tuple, vector [details] |
License | GPL-3.0-only |
Copyright | Christian Hoener zu Siederdissen, 2011 |
Author | Christian Hoener zu Siederdissen |
Maintainer | choener@tbi.univie.ac.at |
Category | Bioinformatics |
Home page | http://www.tbi.univie.ac.at/~choener/ |
Uploaded | by ChristianHoener at 2011-11-30T14:03:07Z |
Distributions | |
Reverse Dependencies | 3 direct, 0 indirect [details] |
Downloads | 15817 total (30 in the last 30 days) |
Rating | (no votes yet) [estimated by Bayesian average] |
Your Rating | |
Status | Docs not available [build log] All reported builds failed as of 2016-12-26 [all 8 reports] |